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chenrui333/# kallisto - 2023-11-04_15-39-30.txt

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kallisto on macOS 13.6 - Homebrew build logs
Raw
# kallisto - 2023-11-04_15-39-30.txt
Homebrew build logs for kallisto on macOS 13.6
Build date: 2023-11-04 15:39:30
Raw
00.config.out
HOMEBREW_VERSION: 4.1.16-17-g65da878
ORIGIN: https://github.com/Homebrew/brew
HEAD: 65da8782755c442ee9dd8d83e04c1eaaa45644f0
Last commit: 9 days ago
Core tap origin: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 7475de6b7e560793c108d4d87aa812cf38de99e2
Core tap last commit: 3 minutes ago
Core tap branch: bump-kallisto-0.50.1
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DEVELOPER: set
HOMEBREW_EDITOR: vim
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_MAKE_JOBS: 10
HOMEBREW_NO_ANALYTICS: set
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_INSTALL_FROM_API: set
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 2.6.10 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: 10-core 64-bit arm_firestorm_icestorm
Clang: 15.0.0 build 1500
Git: 2.42.0 => /opt/homebrew/bin/git
Curl: 8.1.2 => /usr/bin/curl
macOS: 13.6.1-arm64
CLT: 15.0.0.0.1.1694021235
Xcode: 15.0.1
Rosetta 2: false
Raw
00.doctor.out
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!
Warning: Suspicious https://github.com/Homebrew/homebrew-core git origin remote found.
The current git origin is:
[email protected]:Homebrew/homebrew-core.git
With a non-standard origin, Homebrew won't update properly.
You can solve this by setting the origin remote:
git -C "/opt/homebrew/Library/Taps/homebrew/homebrew-core" remote set-url origin https://github.com/Homebrew/homebrew-core
Warning: Some installed kegs have no formulae!
This means they were either deleted or installed manually.
You should find replacements for the following formulae:
dtf
blush
rvvm
protobuf241
buildcache
camouflage
[email protected]
timecraft
termtunnel
dbcrossbar
libemf
polyrhythmix
sish
cross
ktop
pa11y
kibi
munit
ketch
tree-sitter-c
kplot
boofuzz
magicbell-cli
featurebase
mrustc
kubecolor
whatstyle
slashbase
lensm
libjuice
layerform
otto
stringsext
dovitool
polyclipping
mox
Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
dotnet
[email protected]
minimal-racket
mono
naturaldocs
[email protected]
spotify-tui
Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause formulae that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
protobuf241
ghostscript
redo
open-mpi
pkgconf
mysql
bash-completion@2
pmix
bash-completion
git-extras
Warning: You have uncommitted modifications to Homebrew/homebrew-core.
If this is a surprise to you, then you should stash these modifications.
Stashing returns Homebrew to a pristine state but can be undone
should you later need to do so for some reason.
cd /opt/homebrew/Library/Taps/homebrew/homebrew-core && git stash -u && git clean -d -f
Uncommitted files:
M Formula/k/kallisto.rb
Warning: Some taps are not on the default git origin branch and may not receive
updates. If this is a surprise to you, check out the default branch with:
git -C $(brew --repo homebrew/core) checkout master
Warning: /usr/bin occurs before /opt/homebrew/bin in your PATH.
This means that system-provided programs will be used instead of those
provided by Homebrew. Consider setting your PATH so that
/opt/homebrew/bin occurs before /usr/bin. Here is a one-liner:
echo 'export PATH="/opt/homebrew/bin:$PATH"' >> /Users/rui/.bash_profile
The following tools exist at both paths:
cpan
rview
vim
cmp
instmodsh
db_upgrade
perlivp
vi
pod2usage
corelist
db_hotbackup
demandoc
git-receive-pack
xmllint
vimdiff
libnetcfg
diff3
python3
xxd
xsltproc
encguess
db_printlog
less
db_archive
pip3
xslt-config
pod2text
bashbug
mail
irb
ptardiff
wish
db_stat
json_pp
bsdtar
perl
ex
perlbug
db_load
piconv
ptargrep
h2ph
rake
rvim
vimtutor
prove
podchecker
shasum
bundle
git-upload-archive
xml2-config
diff
ri
ptar
pl2pm
curl-config
tclsh
curl
db_verify
perlthanks
patch
xsubpp
tidy
streamzip
perldoc
mandoc
view
h2xs
db_checkpoint
pod2man
enc2xs
git-shell
lessecho
sdiff
db_deadlock
git-upload-pack
erb
openssl
splain
xmlcatalog
pod2html
tar
rdoc
db_recover
zipinfo
db_dump
bundler
ruby
git
zipdetails
cpio
gem
Warning: Homebrew's "bin" was not found in your PATH.
Consider setting your PATH for example like so:
echo 'export PATH="/opt/homebrew/bin:$PATH"' >> /Users/rui/.bash_profile
Warning: Homebrew's "sbin" was not found in your PATH but you have installed
formulae that put executables in /opt/homebrew/sbin.
Consider setting your PATH for example like so:
echo 'export PATH="/opt/homebrew/sbin:$PATH"' >> /Users/rui/.bash_profile
Warning: Some installed formulae are missing dependencies.
You should `brew install` the missing dependencies:
brew install cpr libpaper
Run `brew missing` for more details.
Raw
01.cmake
2023-11-04 19:38:53 +0000
cmake
-S
.
-B
build
-DUSE_HDF5=ON
-DCMAKE_INSTALL_PREFIX=/opt/homebrew/Cellar/kallisto/0.50.1
-DCMAKE_INSTALL_LIBDIR=lib
-DCMAKE_BUILD_TYPE=Release
-DCMAKE_FIND_FRAMEWORK=LAST
-DCMAKE_VERBOSE_MAKEFILE=ON
-Wno-dev
-DBUILD_TESTING=OFF
-DCMAKE_OSX_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk
-- The C compiler identification is AppleClang 15.0.0.15000040
-- The CXX compiler identification is AppleClang 15.0.0.15000040
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/homebrew/Library/Homebrew/shims/mac/super/clang - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test COMPILER_SUPPORTS_CXX17
-- Performing Test COMPILER_SUPPORTS_CXX17 - Success
shared build
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found HDF5: /opt/homebrew/lib/libhdf5.dylib;/opt/homebrew/lib/libsz.dylib;/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/lib/libz.tbd;/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/lib/libdl.tbd;/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/lib/libm.tbd (found version "1.14.2")
-- Found ZLIB: /opt/homebrew/lib/libzlibstatic.a (found version "1.2.11")
-- Configuring done (1.6s)
-- Generating done (0.1s)
-- Build files have been written to: /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build
Raw
01.cmake.cc
clang called with: CMakeCCompilerId.c
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang CMakeCCompilerId.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang++ called with: CMakeCXXCompilerId.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ CMakeCXXCompilerId.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang called with: -Wl,--help
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang -Wl,--help -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang called with: -Wl,--help
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang -Wl,--help -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang called with: -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -v -Wl,-v -MD -MT CMakeFiles/cmTC_e3e33.dir/CMakeCCompilerABI.c.o -MF CMakeFiles/cmTC_e3e33.dir/CMakeCCompilerABI.c.o.d -o CMakeFiles/cmTC_e3e33.dir/CMakeCCompilerABI.c.o -c /opt/homebrew/Cellar/cmake/3.27.7/share/cmake/Modules/CMakeCCompilerABI.c
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -v -Wl,-v -MD -MT CMakeFiles/cmTC_e3e33.dir/CMakeCCompilerABI.c.o -MF CMakeFiles/cmTC_e3e33.dir/CMakeCCompilerABI.c.o.d -o CMakeFiles/cmTC_e3e33.dir/CMakeCCompilerABI.c.o -c /opt/homebrew/Cellar/cmake/3.27.7/share/cmake/Modules/CMakeCCompilerABI.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang called with: -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTC_e3e33.dir/CMakeCCompilerABI.c.o -o cmTC_e3e33
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
superenv executed: clang -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTC_e3e33.dir/CMakeCCompilerABI.c.o -o cmTC_e3e33 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang++ called with: -Wl,--help
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ -Wl,--help -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang++ called with: -Wl,--help
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ -Wl,--help -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang++ called with: -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -v -Wl,-v -MD -MT CMakeFiles/cmTC_1e7c8.dir/CMakeCXXCompilerABI.cpp.o -MF CMakeFiles/cmTC_1e7c8.dir/CMakeCXXCompilerABI.cpp.o.d -o CMakeFiles/cmTC_1e7c8.dir/CMakeCXXCompilerABI.cpp.o -c /opt/homebrew/Cellar/cmake/3.27.7/share/cmake/Modules/CMakeCXXCompilerABI.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -v -Wl,-v -MD -MT CMakeFiles/cmTC_1e7c8.dir/CMakeCXXCompilerABI.cpp.o -MF CMakeFiles/cmTC_1e7c8.dir/CMakeCXXCompilerABI.cpp.o.d -o CMakeFiles/cmTC_1e7c8.dir/CMakeCXXCompilerABI.cpp.o -c /opt/homebrew/Cellar/cmake/3.27.7/share/cmake/Modules/CMakeCXXCompilerABI.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTC_1e7c8.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_1e7c8
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
superenv executed: clang++ -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTC_1e7c8.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_1e7c8 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang++ called with: -DCOMPILER_SUPPORTS_CXX17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -std=c++17 -MD -MT CMakeFiles/cmTC_9e98d.dir/src.cxx.o -MF CMakeFiles/cmTC_9e98d.dir/src.cxx.o.d -o CMakeFiles/cmTC_9e98d.dir/src.cxx.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/CMakeFiles/CMakeScratch/TryCompile-s2irvU/src.cxx
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DCOMPILER_SUPPORTS_CXX17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -std=c++17 -MD -MT CMakeFiles/cmTC_9e98d.dir/src.cxx.o -MF CMakeFiles/cmTC_9e98d.dir/src.cxx.o.d -o CMakeFiles/cmTC_9e98d.dir/src.cxx.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/CMakeFiles/CMakeScratch/TryCompile-s2irvU/src.cxx -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_9e98d.dir/src.cxx.o -o cmTC_9e98d
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
superenv executed: clang++ -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_9e98d.dir/src.cxx.o -o cmTC_9e98d -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang called with: -DCMAKE_HAVE_LIBC_PTHREAD -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -MD -MT CMakeFiles/cmTC_86446.dir/src.c.o -MF CMakeFiles/cmTC_86446.dir/src.c.o.d -o CMakeFiles/cmTC_86446.dir/src.c.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/CMakeFiles/CMakeScratch/TryCompile-MKJ9dG/src.c
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang -DCMAKE_HAVE_LIBC_PTHREAD -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -MD -MT CMakeFiles/cmTC_86446.dir/src.c.o -MF CMakeFiles/cmTC_86446.dir/src.c.o.d -o CMakeFiles/cmTC_86446.dir/src.c.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/CMakeFiles/CMakeScratch/TryCompile-MKJ9dG/src.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang called with: -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_86446.dir/src.c.o -o cmTC_86446
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
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clang called with: -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -MD -MT CMakeFiles/cmTC_42d79.dir/cmake_hdf5_test.c.o -MF CMakeFiles/cmTC_42d79.dir/cmake_hdf5_test.c.o.d -o CMakeFiles/cmTC_42d79.dir/cmake_hdf5_test.c.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src/CMakeFiles/hdf5/cmake_hdf5_test.c
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superenv executed: clang -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -MD -MT CMakeFiles/cmTC_42d79.dir/cmake_hdf5_test.c.o -MF CMakeFiles/cmTC_42d79.dir/cmake_hdf5_test.c.o.d -o CMakeFiles/cmTC_42d79.dir/cmake_hdf5_test.c.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src/CMakeFiles/hdf5/cmake_hdf5_test.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang called with: -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_42d79.dir/cmake_hdf5_test.c.o -o cmTC_42d79
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
superenv executed: clang -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_42d79.dir/cmake_hdf5_test.c.o -o cmTC_42d79 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang called with: -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -c cmake_hdf5_test.c
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superenv executed: clang -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -c cmake_hdf5_test.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang called with: -I/opt/homebrew/opt/libaec/include cmake_hdf5_test.o -L/opt/homebrew/Cellar/hdf5/1.14.2/lib /opt/homebrew/Cellar/hdf5/1.14.2/lib/libhdf5_hl.a /opt/homebrew/Cellar/hdf5/1.14.2/lib/libhdf5.a -L/opt/homebrew/opt/libaec/lib -lsz -lz -ldl -lm
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superenv executed: clang -I/opt/homebrew/opt/libaec/include cmake_hdf5_test.o -L/opt/homebrew/Cellar/hdf5/1.14.2/lib /opt/homebrew/Cellar/hdf5/1.14.2/lib/libhdf5_hl.a /opt/homebrew/Cellar/hdf5/1.14.2/lib/libhdf5.a -L/opt/homebrew/opt/libaec/lib -lsz -lz -ldl -lm -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
Raw
02.cmake
2023-11-04 19:38:55 +0000
cmake
--build
build
Change Dir: '/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build'
Run Build Command(s): /opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E env VERBOSE=1 /opt/homebrew/bin/gmake -f Makefile
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -S/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1 -B/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build --check-build-system CMakeFiles/Makefile.cmake 0
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E cmake_progress_start /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/CMakeFiles /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build//CMakeFiles/progress.marks
/opt/homebrew/bin/gmake -f CMakeFiles/Makefile2 all
gmake[1]: Entering directory '/private/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build'
/opt/homebrew/bin/gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/depend
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gmake[2]: Entering directory '/private/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build'
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build && /opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1 /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1 /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/CMakeFiles/bifrost.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/private/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build'
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build && /opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1 /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/private/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build'
gmake[2]: Leaving directory '/private/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build'
/opt/homebrew/bin/gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/build
/opt/homebrew/bin/gmake -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build
gmake[2]: Entering directory '/private/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build'
gmake[2]: Entering directory '/private/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build'
[ 7%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSTools.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp
[ 11%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o
[ 11%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o
[ 15%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o
[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o
[ 23%] Creating directories for 'bifrost'
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -Dcfgdir= -P /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/tmp/bifrost-mkdirs.cmake
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -MF CMakeFiles/kallisto_core.dir/MinCollector.cpp.o.d -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp
[ 26%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -MF CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o.d -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -MF CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o.d -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp
[ 30%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -MF CMakeFiles/kallisto_core.dir/H5Writer.cpp.o.d -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -MF CMakeFiles/kallisto_core.dir/GeneModel.cpp.o.d -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSData.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp
[ 34%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o
[ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -MF CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o.d -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -MF CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o.d -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E touch /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-mkdir
[ 42%] No download step for 'bifrost'
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E echo_append
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E touch /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-download
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
[ 46%] No update step for 'bifrost'
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E echo_append
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E touch /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-update
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
[ 50%] No patch step for 'bifrost'
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E echo_append
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E touch /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-patch
[ 53%] Performing configure step for 'bifrost'
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost && mkdir -p build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX= "-DCMAKE_CXX_FLAGS=-Wno-subobject-linkage -Wno-return-type"
Re-run cmake no build system arguments
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- The C compiler identification is AppleClang 15.0.0.15000040
-- The CXX compiler identification is AppleClang 15.0.0.15000040
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hppIn file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
-- Detecting C compiler ABI info
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hppIn file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config::87837::7041:: warning: note: unqualified call to 'std::move' [-Wunqualified-std-cast-call]expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp
: ^40
:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED:
41: note: 29 ^
expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator:
^warning:
unqualified call to 'std::move' [-Wunqualified-std-cast-call]
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
: note: /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here:
87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
bf = move(filter_out.second.first);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
bf = move(filter_out.second.first);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
bf = move(filter_out.second.first);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454:74: note: in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here
for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
bf = move(filter_out.second.first);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h: h_kmers_ccov.insert(move(km), move(it_s->ccov));
549 ^:
40 std:::
warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from h_kmers_ccov.insert(move(km), move(it_s->ccov));/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h
: ^17
:
std::In file included from
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
700:In file included from 22:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc8:
:In file included from 700/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:22:: warning: 7unqualified call to 'std::move' [-Wunqualified-std-cast-call]
:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
bf = move(filter_out.second.first);In file included from
bf = move(filter_out.second.first);35
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:700: ^ ^
std::22
:
warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc bf = move(filter_out.second.first); std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp
^
std::20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: :warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
40:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
:2771:31/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
bf = move(filter_out.second.first);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:5329:56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454:74: note: in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here
for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cppIn file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454:74: note: in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here
for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454:74: note: in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here
for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454:74: note: in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here
for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680:28: note: in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454:74: note: in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here
for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: :9: note: In file included from In file included from 'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc
:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
bf = move(filter_out.second.first);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:7000:28: note: in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454:74: note: in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here
for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:5329:56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:5329:56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from 5329:In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:8103:40: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here
if ((i == 4) && (j == 4)) tips.insert(km, 3);
^
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp810::149:
: note: In file included from expanded from macro '_LIBCPP_DEPRECATED'/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h
:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454:74: note: in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here
for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
29: note: class iterator_ : public std::iterator<std::forward_iterator_tag, T> {'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680:28: note: struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:5329:56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680:28: note: in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:5329:56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680:28: note: in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:7000:28: note: in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp1:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16In file included from In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp16::
1In file included from :
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:: 48note: :9: note: in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:8103:40: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here
:
if ((i == 4) && (j == 4)) tips.insert(km, 3);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
In file included from struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h
: ^13
:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED:
35 ^:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config::35: warning: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:5329:56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp::28: note: in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:7000:28: note: in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here
:
In file included from :74: if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.hIn file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:note: 6
:
in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here ^
:20:35: warning: 'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]
In file included from for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from class iterator_ : public std::iterator<std::forward_iterator_tag, T> {/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h
: ^
5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc::7000:28: note: in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here
In file included from if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7:
In file included from 10/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:
:In file included from 16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp: class iterator_ : public std::iterator<std::forward_iterator_tag, T> {35struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35# define _LIBCPP_DEPRECATED __attribute__((deprecated)):
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680:28: note: in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
29
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:5329:56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
: note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from :
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680:28: note: in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:7000:28: note: in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
_T1 first;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413:38: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config: if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:7000:28: note: in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680:28: note: in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
^
In file included from In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cppIn file included from :24:29/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:: 6In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:1:
:48In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
:
note: In file included from In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp17::In file included from In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h::316::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cppIn file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:118:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
:
9:: 1:
note: in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested hereIn file included from
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here _T1 first;
2:
In file included from :
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20: ^struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator:
^In file included from
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hppIn file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config::5837:
:In file included from 41/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h::35:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]
::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:8103:40 class iterator_ : public std::iterator<std::forward_iterator_tag, T> {:
^
note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h::16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp: note: 5expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17':
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:In file included from 35# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED:
if ((i == 4) && (j == 4)) tips.insert(km, 3);
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp ^:
20:35:7000::28: /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.hnote: :in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here11
:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.hIn file included from : ^24:2920:35:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h :warning: 16
: warning: 'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> { warning: note: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations] class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
:
^
'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator9
: ^
^
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:
:24/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:48:/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config20:
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'note: /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: :note: in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested here
837::in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested here29 _T1 first;
^
:9: 1641
: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
35: _T1 first;
warning: ^'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49:/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc :note: 8103expanded from macro '_LIBCPP_DEPRECATED':
40: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc if ((i == 4) && (j == 4)) tips.insert(km, 3);:
8103 ^note:
# define _LIBCPP_DEPRECATED __attribute__((deprecated))in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
^:
note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29 ^
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hppnote: expanded from macro '_LIBCPP_DEPRECATED'
:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:8103:40: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here
if ((i == 4) && (j == 4)) tips.insert(km, 3);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:7000:28: note: in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
:40: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here
if ((i == 4) && (j == 4)) tips.insert(km, 3);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
_T1 first;
^
: note: 'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413:38: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:5329:56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:8103:40: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here
if ((i == 4) && (j == 4)) tips.insert(km, 3);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.h:7In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:8103:40: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here
if ((i == 4) && (j == 4)) tips.insert(km, 3);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413:38: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680:28: note: in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
: note: 'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]
In file included from class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp:3:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.h:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:7000:28: note: in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413:38: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
_T1 first;
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413:38: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
:38: note: std::/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:40
: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:8103:40: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here
if ((i == 4) && (j == 4)) tips.insert(km, 3);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413:38: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.h:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
In file included from std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413:38: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/EMAlgorithm.h:5:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.h:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413:38: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.h:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.hpp:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/DataManager.hpp:4:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.hpp:37:57: warning: 'iterator<std::forward_iterator_tag, std::pair<unsigned long, unsigned long>>' is deprecated [-Wdeprecated-declarations]
class UnitigColors_const_iterator : public std::iterator<std::forward_iterator_tag, pair<size_t, size_t>> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::pair<unsigned long, unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.hpp:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/DataManager.hpp:10:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/DataStorage.tcc:345:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
color_names = move(o.color_names);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/DataStorage.tcc:347:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
overflow = move(o.overflow);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.hpp:10:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/DataManager.hpp:11:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/DataAccessor.tcc:153:19: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
*uc_ptr = move(uc_);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/DataAccessor.tcc:197:19: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
*uc_ptr = move(uc_);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/DataAccessor.tcc:276:52: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (!new_cs.isEmpty()) *(p.second.first) = move(new_cs); // Move extracted colors to new (inserted) UnitigColors
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/DataAccessor.tcc:299:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
*(p.second.first) = move(new_cs); // Move extracted colors to new (inserted) UnitigColors
^
std::
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/homebrew/Library/Homebrew/shims/mac/super/clang - skipped
-- Detecting C compile features
-- Detecting C compile features - done
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.hpp:369:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:505:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
*uc = move(r_uc);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:826:68: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (uc != nullptr) *(p.second.first) = move(*uc);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:44:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigIterator.hpp:36:36: warning: 'iterator<std::input_iterator_tag, UnitigMap<DataAccessor<>, DataStorage<>>, int>' is deprecated [-Wdeprecated-declarations]
class unitigIterator : public std::iterator<std::input_iterator_tag, UnitigMap<Unitig_data_t, Graph_data_t, is_const>, int> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:853:54: note: in instantiation of template class 'unitigIterator<DataAccessor<>, DataStorage<>>' requested here
typename ColoredCDBG<void>::iterator g_a = this->begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, UnitigMap<DataAccessor<>, DataStorage<>>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<DataAccessor<>>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigIterator.hpp:105:73: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<DataAccessor<>>>::iterator_<>' requested here
typename KmerHashTable<CompressedCoverage_t<U>>::const_iterator it_h_kmers_ccov;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:853:54: note: in instantiation of template class 'unitigIterator<DataAccessor<>, DataStorage<>>' requested here
typename ColoredCDBG<void>::iterator g_a = this->begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<DataAccessor<>>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:13:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.hpp:369:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1758:55: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
buffers_seq.push_back(move(s));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, tiny_vector<unsigned long, 1>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<tiny_vector<unsigned long, 1>>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1849:83: note: in instantiation of template class 'std::pair<KmerHashTable<tiny_vector<unsigned long, 1>>::iterator_<false>, bool>' requested here
pair<KmerHashTable<tiny_vector<size_t, 1>>::iterator, bool> it = km_h.insert(it_km->first.rep(), tiny_vector<size_t, 1>());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, tiny_vector<unsigned long, 1>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, tiny_vector<unsigned long, 1>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1865:73: note: in instantiation of template class 'KmerHashTable<tiny_vector<unsigned long, 1>>::iterator_<>' requested here
for (typename KmerHashTable<tiny_vector<size_t, 1>>::const_iterator it_km = km_h.begin(), it_km_end = km_h.end(); it_km != it_km_end; ++it_km){
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, tiny_vector<unsigned long, 1>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:44:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigIterator.hpp:36:36: warning: 'iterator<std::input_iterator_tag, UnitigMap<Node, void, true>, int>' is deprecated [-Wdeprecated-declarations]
class unitigIterator : public std::iterator<std::input_iterator_tag, UnitigMap<Unitig_data_t, Graph_data_t, is_const>, int> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:217:23: note: in instantiation of template class 'unitigIterator<Node, void, true>' requested here
for (const auto& um : dbg) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, UnitigMap<Node, void, true>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigIterator.hpp:105:73: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<Node>>::iterator_<>' requested here
typename KmerHashTable<CompressedCoverage_t<U>>::const_iterator it_h_kmers_ccov;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:217:23: note: in instantiation of template class 'unitigIterator<Node, void, true>' requested here
for (const auto& um : dbg) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:44:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigIterator.hpp:36:36: warning: 'iterator<std::input_iterator_tag, UnitigMap<Node>, int>' is deprecated [-Wdeprecated-declarations]
class unitigIterator : public std::iterator<std::input_iterator_tag, UnitigMap<Unitig_data_t, Graph_data_t, is_const>, int> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:604:17: note: in instantiation of template class 'unitigIterator<Node>' requested here
for (auto& um : dbg) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, UnitigMap<Node>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
-- Detecting CXX compiler ABI info
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigMap.tcc:274:47: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<Node>>::iterator_<>' requested here
if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig)->getData();
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigMap.tcc:253:12: note: in instantiation of function template specialization 'UnitigMap<Node, void, true>::getData_<false>' requested here
return getData_<is_void<U>::value>();
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:227:22: note: in instantiation of member function 'UnitigMap<Node, void, true>::getData' requested here
a.first.getData()->ec[a.first.dist] == b.first.getData()->ec[b.first.dist]) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:302:31: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<Node>>::iterator_<false>' requested here
return const_iterator(this);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigMap.tcc:274:47: note: in instantiation of member function 'KmerHashTable<CompressedCoverage_t<Node>>::find' requested here
if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig)->getData();
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigMap.tcc:253:12: note: in instantiation of function template specialization 'UnitigMap<Node, void, true>::getData_<false>' requested here
return getData_<is_void<U>::value>();
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp:227:22: note: in instantiation of member function 'UnitigMap<Node, void, true>::getData' requested here
a.first.getData()->ec[a.first.dist] == b.first.getData()->ec[b.first.dist]) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
39 warnings generated.
39 warnings generated.
[ 57%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -MF CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o.d -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp
[ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/common.cpp.o -MF CMakeFiles/kallisto_core.dir/common.cpp.o.d -o CMakeFiles/kallisto_core.dir/common.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/common.cpp
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigMap.tcc:274:47: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<Node>>::iterator_<>' requested here
if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig)->getData();
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigMap.tcc:253:12: note: in instantiation of function template specialization 'UnitigMap<Node, void, true>::getData_<false>' requested here
return getData_<is_void<U>::value>();
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:72:24: note: in instantiation of member function 'UnitigMap<Node, void, true>::getData' requested here
const Node* n = um.getData();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:6:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:302:31: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<Node>>::iterator_<false>' requested here
return const_iterator(this);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigMap.tcc:274:47: note: in instantiation of member function 'KmerHashTable<CompressedCoverage_t<Node>>::find' requested here
if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig)->getData();
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigMap.tcc:253:12: note: in instantiation of function template specialization 'UnitigMap<Node, void, true>::getData_<false>' requested here
return getData_<is_void<U>::value>();
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp:72:24: note: in instantiation of member function 'UnitigMap<Node, void, true>::getData' requested here
const Node* n = um.getData();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
39 warnings generated.
39 warnings generated.
39 warnings generated.
[ 65%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o -MF CMakeFiles/kallisto_core.dir/h5utils.cpp.o.d -o CMakeFiles/kallisto_core.dir/h5utils.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/h5utils.cpp
[ 69%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/hash.cpp.o -MF CMakeFiles/kallisto_core.dir/hash.cpp.o.d -o CMakeFiles/kallisto_core.dir/hash.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/hash.cpp
[ 73%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/main.cpp.o -MF CMakeFiles/kallisto_core.dir/main.cpp.o.d -o CMakeFiles/kallisto_core.dir/main.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<DataAccessor<>>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigMap.tcc:96:51: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<DataAccessor<>>>::iterator_<false>' requested here
if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig).getKey();
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/DataStorage.tcc:1600:30: note: in instantiation of member function 'UnitigMap<DataAccessor<>, DataStorage<>>::getUnitigHead' requested here
const Kmer head = um.getUnitigHead();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<DataAccessor<>>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:395:27: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<Node>>::iterator_<false>' requested here
const_iterator it(this);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigIterator.tcc:12:160: note: in instantiation of member function 'KmerHashTable<CompressedCoverage_t<Node>>::begin' requested here
it_h_kmers_ccov((cdbg_ == nullptr) || cdbg_->invalid ? typename KmerHashTable<CompressedCoverage_t<U>>::const_iterator() : cdbg_->h_kmers_ccov.begin()){
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2525:20: note: in instantiation of member function 'unitigIterator<Node, void, true>::unitigIterator' requested here
const_iterator it(this);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:217:23: note: in instantiation of member function 'CompactedDBG<Node>::begin' requested here
for (const auto& um : dbg) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<Node>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
bf = move(filter_out.second.first);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:522:7: note: in instantiation of member function 'CompactedDBG<Node>::build' requested here
dbg.build(c_opt);
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
bf = move(filter_out.second.first);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:620:44: note: in instantiation of member function 'CompactedDBG<>::build' requested here
construct_finished = graph_seq.build(opt_seq);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:522:7: note: in instantiation of member function 'CompactedDBG<Node>::build' requested here
dbg.build(c_opt);
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:630:45: note: in instantiation of member function 'CompactedDBG<>::toDataGraph' requested here
if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:620:44: note: in instantiation of member function 'CompactedDBG<>::build' requested here
construct_finished = graph_seq.build(opt_seq);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:522:7: note: in instantiation of member function 'CompactedDBG<Node>::build' requested here
dbg.build(c_opt);
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:94:16: note: in instantiation of member function 'KmerCovIndex<>::toData' requested here
km_unitigs.toData(std::move(o.km_unitigs), nb_threads);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:630:45: note: in instantiation of member function 'CompactedDBG<>::toDataGraph' requested here
if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:620:44: note: in instantiation of member function 'CompactedDBG<>::build' requested here
construct_finished = graph_seq.build(opt_seq);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:522:7: note: in instantiation of member function 'CompactedDBG<Node>::build' requested here
dbg.build(c_opt);
^
1 warning generated.
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
[ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/weights.cpp.o -MF CMakeFiles/kallisto_core.dir/weights.cpp.o.d -o CMakeFiles/kallisto_core.dir/weights.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:696:76: note: in instantiation of member function 'CompactedDBG<>::filter' requested here
pair<bool, pair<BlockedBloomFilter, Roaring>> filter_out = filter(opt, nb_unique_kmers, nb_non_unique_kmers);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:620:44: note: in instantiation of member function 'CompactedDBG<>::build' requested here
construct_finished = graph_seq.build(opt_seq);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:522:7: note: in instantiation of member function 'CompactedDBG<Node>::build' requested here
dbg.build(c_opt);
^
39 warnings generated.
41 warnings generated.
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:44:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigIterator.hpp:36:36: warning: 'iterator<std::input_iterator_tag, UnitigMap<>, int>' is deprecated [-Wdeprecated-declarations]
class unitigIterator : public std::iterator<std::input_iterator_tag, UnitigMap<Unitig_data_t, Graph_data_t, is_const>, int> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2132:27: note: in instantiation of template class 'unitigIterator<>' requested here
for (auto& unitig : *this) unitig.setFullCoverage();
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:628:52: note: in instantiation of member function 'CompactedDBG<>::merge' requested here
construct_finished = graph_seq.merge(std::move(graph_ref), opt.nb_threads, opt.verbose);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:522:7: note: in instantiation of member function 'CompactedDBG<Node>::build' requested here
dbg.build(c_opt);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, UnitigMap<>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:44:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/UnitigIterator.hpp:36:36: warning: 'iterator<std::input_iterator_tag, UnitigMap<void, void, true>, int>' is deprecated [-Wdeprecated-declarations]
class unitigIterator : public std::iterator<std::input_iterator_tag, UnitigMap<Unitig_data_t, Graph_data_t, is_const>, int> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2248:37: note: in instantiation of template class 'unitigIterator<void, void, true>' requested here
for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2134:13: note: in instantiation of member function 'CompactedDBG<>::annotateSplitUnitigs' requested here
if (annotateSplitUnitigs(o, nb_threads, verbose)){
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:628:52: note: in instantiation of member function 'CompactedDBG<>::merge' requested here
construct_finished = graph_seq.merge(std::move(graph_ref), opt.nb_threads, opt.verbose);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:522:7: note: in instantiation of member function 'CompactedDBG<Node>::build' requested here
dbg.build(c_opt);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, UnitigMap<void, void, true>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:630:45: note: in instantiation of member function 'CompactedDBG<Node>::toDataGraph' requested here
if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:522:7: note: in instantiation of member function 'CompactedDBG<Node>::build' requested here
dbg.build(c_opt);
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:94:16: note: in instantiation of member function 'KmerCovIndex<Node>::toData' requested here
km_unitigs.toData(std::move(o.km_unitigs), nb_threads);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:630:45: note: in instantiation of member function 'CompactedDBG<Node>::toDataGraph' requested here
if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:522:7: note: in instantiation of member function 'CompactedDBG<Node>::build' requested here
dbg.build(c_opt);
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:106:32: note: in instantiation of member function 'Unitig<Node>::Unitig' requested here
v_unitigs[i] = new Unitig<U>(std::move(o.v_unitigs[i]->getSeq()), std::move(o.v_unitigs[i]->getCov()));
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:630:45: note: in instantiation of member function 'CompactedDBG<Node>::toDataGraph' requested here
if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:522:7: note: in instantiation of member function 'CompactedDBG<Node>::build' requested here
dbg.build(c_opt);
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:696:76: note: in instantiation of member function 'CompactedDBG<Node>::filter' requested here
pair<bool, pair<BlockedBloomFilter, Roaring>> filter_out = filter(opt, nb_unique_kmers, nb_non_unique_kmers);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:522:7: note: in instantiation of member function 'CompactedDBG<Node>::build' requested here
dbg.build(c_opt);
^
1 warning generated.
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:955:61: note: in instantiation of member function 'CompactedDBG<Node>::readBinaryGraph' requested here
const pair<uint64_t, bool> p_readSuccess_checksum = readBinaryGraph(in);
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:599:7: note: in instantiation of member function 'CompactedDBG<Node>::readBinary' requested here
dbg.readBinary(in, mphf, opt.threads);
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp:8:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
Disabling AVX2 instructions on arm64
Disabling native architecture compilation (including AVX2)
Disabling AVX2 instructions
Build type: Release
Maximum k-mer size: 31
Maximum g-mer size: 31
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
1 warning generated.
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
bf = move(filter_out.second.first);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454:74: note: in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here
for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:5329:56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680:28: note: in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:7000:28: note: in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:8103:40: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here
if ((i == 4) && (j == 4)) tips.insert(km, 3);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413:38: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
bf = move(filter_out.second.first);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp:2:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.h:9:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454:74: note: in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here
for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:5:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/TinyBitmap.hpp:28:44: warning: 'iterator<std::input_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class TinyBitmapIterator : public std::iterator<std::input_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:18:57: warning: 'iterator<std::forward_iterator_tag, unsigned int>' is deprecated [-Wdeprecated-declarations]
class BitContainer_const_iterator : public std::iterator<std::forward_iterator_tag, uint32_t> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:34:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:157:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.tcc:85:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v_blocks[i]->bc_cov = move(o.v_blocks[i]->bc_cov);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:5329:56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:36:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerIterator.hpp:15:34: warning: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' is deprecated [-Wdeprecated-declarations]
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::input_iterator_tag, std::pair<Kmer, int>, int>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680:28: note: in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:18:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/minHashIterator.hpp:507:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
v = move(v_tmp);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:7000:28: note: in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:37:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1149:86: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
ReadHasherMinimizer(ReadQualityHasherMinimizer&& o) : k(o.k), g(o.g), sc_min(move(o.sc_min)) {
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1151:85: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
for (size_t i = 0; i < NB_STREAMCOUNTER_PER_READHASHER; ++i) sc_km[i] = move(o.sc_km[i]);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerStream.hpp:1673:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
rsh = move(rqh);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:8103:40: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here
if ((i == 4) && (j == 4)) tips.insert(km, 3);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:12:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:536:48: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("bit array of size %lu: \n",_size);
~~~ ^~~~~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:540:38: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf(" (%lu) ",ii);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:40: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~
%llu
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BooPHF.h:549:43: warning: format specifies type 'unsigned long' but the argument has type 'value_type' (aka 'unsigned long long') [-Wformat]
printf("%lu : %lu, ",ii,_ranks[ii]);
~~~ ^~~~~~~~~~
%llu
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:40:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/MinimizerIndex.hpp:19:35: warning: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, packed_tiny_vector> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, packed_tiny_vector>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:7:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:169:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.hpp:182:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
CompressedCoverage_t(CompressedCoverage&& c) : ccov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:43:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:28:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:70: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Unitig.hpp:87:84: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:85: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<false>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations]
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h class iterator_ : public std::iterator<std::forward_iterator_tag, T> {:
24 ^:
29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iteratornote:
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
_T1 first;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413:38: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:138:63: note: in instantiation of template class 'KmerHashTable<CompressedCoverage_t<void>>::iterator_<>' requested here
KmerHashTable<CompressedCoverage_t<void>>::const_iterator it_s = o.h_kmers_ccov.begin();
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, CompressedCoverage_t<void>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:831:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:147:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
h_kmers_ccov.insert(move(km), move(it_s->ccov));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:700:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
bf = move(filter_out.second.first);
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:701:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
r = move(filter_out.second.second);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.h:17:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.h:11:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:2771:31: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
if (reference_mode) bf2 = move(bf1);
^
std::
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, bool>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<bool>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:3454:74: note: in instantiation of template class 'std::pair<KmerHashTable<bool>::iterator_<false>, bool>' requested here
for (const auto& km_tip : l_ignored_km_tips) ignored_km_tips.insert(km_tip, false);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, bool>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:5329:56: note: in instantiation of template class 'KmerHashTable<std::vector<unsigned long>>::iterator_<false>' requested here
KmerHashTable<vector<size_t>>::iterator it(kht.begin());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, std::vector<unsigned long>>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, Kmer>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:6680:28: note: in instantiation of template class 'KmerHashTable<Kmer>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, Kmer>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:7000:28: note: in instantiation of template class 'KmerHashTable<char>::iterator_<false>' requested here
if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned char>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.tcc:8103:40: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned char>::iterator_<false>, bool>' requested here
if ((i == 4) && (j == 4)) tips.insert(km, 3);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned char>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:35:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/KmerHashTable.hpp:20:35: warning: 'iterator<std::forward_iterator_tag, unsigned long>' is deprecated [-Wdeprecated-declarations]
class iterator_ : public std::iterator<std::forward_iterator_tag, T> {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__utility/pair.h:48:9: note: in instantiation of template class 'KmerHashTable<unsigned long>::iterator_<false>' requested here
_T1 first;
^
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:413:38: note: in instantiation of template class 'std::pair<KmerHashTable<unsigned long>::iterator_<false>, bool>' requested here
if (unitig.isAbundant) idmap.insert(Kmer(unitig.referenceUnitigToString().c_str()), labelA);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator.h:24:29: note: 'iterator<std::forward_iterator_tag, unsigned long>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:837:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
# define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:810:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.h:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.h:16:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:833:
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:1690:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2423:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/IO.tcc:2534:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
unitig = new Unitig<U>(move(cs), move(cc));
^
std::
39 warnings generated.
-- Found ZLIB: /opt/homebrew/lib/libzlibstatic.a (found version "1.2.12")
-- Configuring done (2.6s)
-- Generating done (0.0s)
-- Build files have been written to: /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost && /opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E touch /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-configure
[ 80%] Performing build step for 'bifrost'
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost && cd build && make
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -S/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost -B/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build --check-build-system CMakeFiles/Makefile.cmake 0
/opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E cmake_progress_start /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/CMakeFiles /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build//CMakeFiles/progress.marks
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/Makefile2 all
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/depend
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/CMakeFiles/bifrost_dynamic.dir/build.make src/CMakeFiles/bifrost_dynamic.dir/depend
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build && /opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src/CMakeFiles/bifrost_dynamic.dir/DependInfo.cmake "--color="
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build && /opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake "--color="
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/CMakeFiles/bifrost_dynamic.dir/build.make src/CMakeFiles/bifrost_dynamic.dir/build
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/build
[ 3%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o
[ 6%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o
[ 9%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.cpp
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedSequence.cpp
[ 12%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o
[ 21%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o
[ 21%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
[ 21%] Building CXX object src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp
[ 25%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_static.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.cpp
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp
[ 28%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.cpp
[ 31%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.cpp
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:111:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/equal.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/distance.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/concepts.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/concepts:133:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__concepts/arithmetic.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:421:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/invoke.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/apply_cv.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/remove_reference.h:13:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:519:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/max.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/comp_ref_type.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__debug:15:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:5:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/limits:107:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:421:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/invoke.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/apply_cv.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/remove_reference.h:13:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:519:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/max.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/comp_ref_type.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__debug:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl : public false_type {};
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:111:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/equal.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/distance.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/concepts.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/concepts:133:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__concepts/arithmetic.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl : public false_type {};
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:5:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/limits:107:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl : public false_type {};
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedSequence.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:841:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/copy.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/unwrap_iter.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/concepts:133:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__concepts/arithmetic.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:421:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/invoke.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/apply_cv.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/remove_reference.h:13:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
41 warnings generated.
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:5:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/limits:107:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:421:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/invoke.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/apply_cv.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/remove_reference.h:13:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.hpp:8:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:841:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/copy.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/unwrap_iter.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/concepts:133:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__concepts/arithmetic.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:421:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/invoke.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/apply_cv.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/remove_reference.h:13:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
39 warnings generated.
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:5:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/limits:107:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl : public false_type {};
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1709:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__debug:15:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1709:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__debug:15:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.hpp:8:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:841:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/copy.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/unwrap_iter.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/concepts:133:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__concepts/arithmetic.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl : public false_type {};
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1709:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__debug:15:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedSequence.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:841:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/copy.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/unwrap_iter.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/concepts:133:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__concepts/arithmetic.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1709:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__debug:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl : public false_type {};
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1709:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__debug:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl : public false_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl : public false_type {};
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1709:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__debug:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl : public false_type {};
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:7:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstdlib:123:9: error: target of using declaration conflicts with declaration already in scope
using ::abs _LIBCPP_USING_IF_EXISTS;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include/stdlib.h:132:6: note: target of using declaration
int abs(int) __pure2;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cmath:339:1: note: conflicting declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:7:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstdlib:123:9: error: target of using declaration conflicts with declaration already in scope
using ::abs _LIBCPP_USING_IF_EXISTS;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include/stdlib.h:132:6: note: target of using declaration
int abs(int) __pure2;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cmath:339:1: note: conflicting declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:122:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/stdexcept:47:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:122:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/stdexcept:47:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.hpp:8:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.hpp:8:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/functional:510:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/bind.h:17:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/tuple:223:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/functional:510:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/bind.h:17:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/tuple:223:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedSequence.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedSequence.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/functional:510:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/bind.h:17:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/tuple:223:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/functional:510:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/bind.h:17:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/tuple:223:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:519:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/max.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/comp_ref_type.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__debug:15:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:549:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:549:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:519:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/max.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/comp_ref_type.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__debug:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl : public false_type {};
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.hpp:8:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.hpp:8:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.hpp:8:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/functional:515:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:22:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/functional:515:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:22:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/functional:515:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:22:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:610:45: error: unknown type name 'nullptr_t'
operator!=(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedSequence.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedSequence.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedSequence.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/iostream:41:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/ios:221:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
fatal error: too many errors emitted, stopping now [-ferror-limit=]
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:610:45: error: unknown type name 'nullptr_t'
operator!=(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:127:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:127:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:549:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:549:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:127:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:610:45: error: unknown type name 'nullptr_t'
operator!=(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.cpp:1:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:549:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
fatal error: too many errors emitted, stopping now [-ferror-limit=]
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:610:45: error: unknown type name 'nullptr_t'
operator!=(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:549:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:549:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:848:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/allocator.h:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/new:94:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/functional:515:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:22:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/functional:515:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:22:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/functional:515:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:22:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:549:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:549:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/string:549:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:610:45: error: unknown type name 'nullptr_t'
operator!=(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:610:45: error: unknown type name 'nullptr_t'
operator!=(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
fatal error: too many errors emitted, stopping now [-ferror-limit=]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:610:45: error: unknown type name 'nullptr_t'
operator!=(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.hpp:4:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/roaring.hh:10:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:610:45: error: unknown type name 'nullptr_t'
operator!=(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[5]: *** [src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o] Error 1
make[5]: *** Waiting for unfinished jobs....
[ 34%] Building CXX object src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp
20 errors generated.
make[5]: *** [src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o] Error 1
make[5]: *** Waiting for unfinished jobs....
20 errors generated.
make[5]: *** [src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o] Error 1
20 errors generated.
make[5]: *** [src/CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o] Error 1
20 errors generated.
make[5]: *** [src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o] Error 1
20 errors generated.
make[5]: *** [src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o] Error 1
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:111:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/equal.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/distance.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/concepts.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/concepts:133:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__concepts/arithmetic.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:421:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__functional/invoke.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/apply_cv.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/remove_reference.h:13:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/cstddef:50:9: error: no member named 'nullptr_t' in the global namespace
using ::nullptr_t;
~~^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:111:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__algorithm/equal.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/distance.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/concepts.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/concepts:133:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__concepts/arithmetic.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/type_traits:452:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_compound.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_fundamental.h:14:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: use of undeclared identifier 'nullptr_t'; did you mean 'nullptr'?
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:24:49: error: template argument for template type parameter must be a type
template <> struct __is_nullptr_t_impl<nullptr_t> : public true_type {};
^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__type_traits/is_null_pointer.h:23:17: note: template parameter is declared here
template <class _Tp> struct __is_nullptr_t_impl : public false_type {};
^
20 errors generated.
make[5]: *** [src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o] Error 1
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:122:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/stdexcept:47:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:45: error: field has incomplete type 'exception_ptr'
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:144:24: note: definition of 'std::exception_ptr' is not complete until the closing '}'
class _LIBCPP_TYPE_VIS exception_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:689:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
# define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:673:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
__attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER))))
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:122:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/stdexcept:47:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/exception:149:55: error: expected ';' at end of declaration list
_LIBCPP_INLINE_VISIBILITY exception_ptr(nullptr_t) _NOEXCEPT : __ptr_() {}
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:127:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:127:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:173:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:262:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:3: error: non-static data member cannot be constexpr; did you intend to make it const?
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__config:728:31: note: expanded from macro '_LIBCPP_CONSTEXPR'
# define _LIBCPP_CONSTEXPR constexpr
^
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp:1:
In file included from /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.hpp:4:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/array:127:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/algorithm:1712:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/memory:860:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:32: error: member 'nullptr_t' declared as a template
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:395:42: error: expected ';' at end of declaration list
_LIBCPP_CONSTEXPR unique_ptr(nullptr_t) _NOEXCEPT : __ptr_(__value_init_tag(), __value_init_tag()) {}
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:484:25: error: unknown type name 'nullptr_t'
unique_ptr& operator=(nullptr_t) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:14: error: unknown type name 'nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: error: cannot initialize a parameter of type 'int' with an rvalue of type 'std::nullptr_t'
void reset(nullptr_t = nullptr) _NOEXCEPT {
^ ~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:533:24: note: passing argument to parameter here
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:594:45: error: unknown type name 'nullptr_t'
operator==(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:602:12: error: unknown type name 'nullptr_t'
operator==(nullptr_t, const unique_ptr<_T1, _D1>& __x) _NOEXCEPT
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/include/c++/v1/__memory/unique_ptr.h:610:45: error: unknown type name 'nullptr_t'
operator!=(const unique_ptr<_T1, _D1>& __x, nullptr_t) _NOEXCEPT
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[5]: *** [src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1
20 errors generated.
make[5]: *** [src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o] Error 1
20 errors generated.
make[5]: *** [src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o] Error 1
make[4]: *** [src/CMakeFiles/bifrost_dynamic.dir/all] Error 2
make[4]: *** Waiting for unfinished jobs....
20 errors generated.
make[5]: *** [src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o] Error 1
make[4]: *** [src/CMakeFiles/bifrost_static.dir/all] Error 2
make[3]: *** [all] Error 2
gmake[2]: *** [CMakeFiles/bifrost.dir/build.make:89: /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-build] Error 2
gmake[2]: Leaving directory '/private/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build'
gmake[1]: *** [CMakeFiles/Makefile2:105: CMakeFiles/bifrost.dir/all] Error 2
gmake[1]: *** Waiting for unfinished jobs....
39 warnings generated.
76 warnings generated.
[ 84%] Linking CXX static library libkallisto_core.a
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -P CMakeFiles/kallisto_core.dir/cmake_clean_target.cmake
cd /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build/src && /opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E cmake_link_script CMakeFiles/kallisto_core.dir/link.txt --verbose=1
/usr/bin/ar qc libkallisto_core.a CMakeFiles/kallisto_core.dir/BUSData.cpp.o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o CMakeFiles/kallisto_core.dir/common.cpp.o CMakeFiles/kallisto_core.dir/h5utils.cpp.o CMakeFiles/kallisto_core.dir/hash.cpp.o CMakeFiles/kallisto_core.dir/main.cpp.o CMakeFiles/kallisto_core.dir/weights.cpp.o
/usr/bin/ranlib libkallisto_core.a
gmake[2]: Leaving directory '/private/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build'
[ 84%] Built target kallisto_core
gmake[1]: Leaving directory '/private/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/build'
gmake: *** [Makefile:139: all] Error 2
HOMEBREW_VERSION: 4.1.16-17-g65da878
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Core tap origin: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 7475de6b7e560793c108d4d87aa812cf38de99e2
Core tap last commit: 3 minutes ago
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Raw
02.cmake.cc
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSData.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSData.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSData.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -MF CMakeFiles/kallisto_core.dir/MinCollector.cpp.o.d -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp
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superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -MF CMakeFiles/kallisto_core.dir/MinCollector.cpp.o.d -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/MinCollector.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSTools.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp
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superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSTools.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/BUSTools.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -MF CMakeFiles/kallisto_core.dir/GeneModel.cpp.o.d -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -MF CMakeFiles/kallisto_core.dir/GeneModel.cpp.o.d -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/GeneModel.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -MF CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o.d -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -MF CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o.d -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/KmerIndex.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -MF CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o.d -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -MF CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o.d -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/ProcessReads.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -MF CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o.d -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -MF CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o.d -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PlaintextWriter.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -MF CMakeFiles/kallisto_core.dir/H5Writer.cpp.o.d -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -MF CMakeFiles/kallisto_core.dir/H5Writer.cpp.o.d -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/H5Writer.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -MF CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o.d -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -MF CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o.d -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/Bootstrap.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang called with: CMakeCCompilerId.c
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang CMakeCCompilerId.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang++ called with: -Wno-subobject-linkage -Wno-return-type CMakeCXXCompilerId.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ -Wno-subobject-linkage -Wno-return-type CMakeCXXCompilerId.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang called with: -Wl,--help
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang -Wl,--help -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang called with: -Wl,--help
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang -Wl,--help -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang called with: -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -v -Wl,-v -MD -MT CMakeFiles/cmTC_805aa.dir/CMakeCCompilerABI.c.o -MF CMakeFiles/cmTC_805aa.dir/CMakeCCompilerABI.c.o.d -o CMakeFiles/cmTC_805aa.dir/CMakeCCompilerABI.c.o -c /opt/homebrew/Cellar/cmake/3.27.7/share/cmake/Modules/CMakeCCompilerABI.c
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -v -Wl,-v -MD -MT CMakeFiles/cmTC_805aa.dir/CMakeCCompilerABI.c.o -MF CMakeFiles/cmTC_805aa.dir/CMakeCCompilerABI.c.o.d -o CMakeFiles/cmTC_805aa.dir/CMakeCCompilerABI.c.o -c /opt/homebrew/Cellar/cmake/3.27.7/share/cmake/Modules/CMakeCCompilerABI.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang called with: -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTC_805aa.dir/CMakeCCompilerABI.c.o -o cmTC_805aa
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
superenv executed: clang -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTC_805aa.dir/CMakeCCompilerABI.c.o -o cmTC_805aa -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang++ called with: -Wl,--help
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ -Wl,--help -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang++ called with: -Wl,--help
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ -Wl,--help -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -MF CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o.d -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -MF CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o.d -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/PseudoBam.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/common.cpp.o -MF CMakeFiles/kallisto_core.dir/common.cpp.o.d -o CMakeFiles/kallisto_core.dir/common.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/common.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/common.cpp.o -MF CMakeFiles/kallisto_core.dir/common.cpp.o.d -o CMakeFiles/kallisto_core.dir/common.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/common.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -Wno-subobject-linkage -Wno-return-type -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -v -Wl,-v -MD -MT CMakeFiles/cmTC_71abe.dir/CMakeCXXCompilerABI.cpp.o -MF CMakeFiles/cmTC_71abe.dir/CMakeCXXCompilerABI.cpp.o.d -o CMakeFiles/cmTC_71abe.dir/CMakeCXXCompilerABI.cpp.o -c /opt/homebrew/Cellar/cmake/3.27.7/share/cmake/Modules/CMakeCXXCompilerABI.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -Wno-subobject-linkage -Wno-return-type -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -v -Wl,-v -MD -MT CMakeFiles/cmTC_71abe.dir/CMakeCXXCompilerABI.cpp.o -MF CMakeFiles/cmTC_71abe.dir/CMakeCXXCompilerABI.cpp.o.d -o CMakeFiles/cmTC_71abe.dir/CMakeCXXCompilerABI.cpp.o -c /opt/homebrew/Cellar/cmake/3.27.7/share/cmake/Modules/CMakeCXXCompilerABI.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o -MF CMakeFiles/kallisto_core.dir/h5utils.cpp.o.d -o CMakeFiles/kallisto_core.dir/h5utils.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/h5utils.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o -MF CMakeFiles/kallisto_core.dir/h5utils.cpp.o.d -o CMakeFiles/kallisto_core.dir/h5utils.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/h5utils.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/hash.cpp.o -MF CMakeFiles/kallisto_core.dir/hash.cpp.o.d -o CMakeFiles/kallisto_core.dir/hash.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/hash.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/hash.cpp.o -MF CMakeFiles/kallisto_core.dir/hash.cpp.o.d -o CMakeFiles/kallisto_core.dir/hash.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/hash.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/main.cpp.o -MF CMakeFiles/kallisto_core.dir/main.cpp.o.d -o CMakeFiles/kallisto_core.dir/main.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/main.cpp.o -MF CMakeFiles/kallisto_core.dir/main.cpp.o.d -o CMakeFiles/kallisto_core.dir/main.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/main.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -Wno-subobject-linkage -Wno-return-type -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTC_71abe.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_71abe
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
superenv executed: clang++ -Wno-subobject-linkage -Wno-return-type -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -Wl,-search_paths_first -Wl,-headerpad_max_install_names -v -Wl,-v CMakeFiles/cmTC_71abe.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_71abe -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang++ called with: -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/weights.cpp.o -MF CMakeFiles/kallisto_core.dir/weights.cpp.o.d -o CMakeFiles/kallisto_core.dir/weights.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -DNO_HTSLIB=ON -DUSE_HDF5=ON -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src -I/opt/homebrew/Cellar/hdf5/1.14.2/include -I/opt/homebrew/opt/libaec/include -O3 -DNDEBUG -std=c++17 -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -Wno-subobject-linkage -MD -MT src/CMakeFiles/kallisto_core.dir/weights.cpp.o -MF CMakeFiles/kallisto_core.dir/weights.cpp.o.d -o CMakeFiles/kallisto_core.dir/weights.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/src/weights.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang called with: -DCMAKE_HAVE_LIBC_PTHREAD -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -MD -MT CMakeFiles/cmTC_07abe.dir/src.c.o -MF CMakeFiles/cmTC_07abe.dir/src.c.o.d -o CMakeFiles/cmTC_07abe.dir/src.c.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/CMakeFiles/CMakeScratch/TryCompile-M0XUvv/src.c
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang -DCMAKE_HAVE_LIBC_PTHREAD -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -MD -MT CMakeFiles/cmTC_07abe.dir/src.c.o -MF CMakeFiles/cmTC_07abe.dir/src.c.o.d -o CMakeFiles/cmTC_07abe.dir/src.c.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/build/CMakeFiles/CMakeScratch/TryCompile-M0XUvv/src.c -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang called with: -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_07abe.dir/src.c.o -o cmTC_07abe
superenv added: -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
superenv executed: clang -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_07abe.dir/src.c.o -o cmTC_07abe -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/opt/homebrew/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
clang++ called with: -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_static.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp
superenv removed: -O3 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -DNDEBUG -mmacosx-version-min=13.6 -MD -MT src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_static.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp
superenv removed: -O3 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -DNDEBUG -mmacosx-version-min=13.6 -fPIC -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.cpp
superenv removed: -O3 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -DNDEBUG -mmacosx-version-min=13.6 -fPIC -MD -MT src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/ColorSet.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedSequence.cpp
superenv removed: -O3 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -DNDEBUG -mmacosx-version-min=13.6 -fPIC -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedSequence.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.cpp
superenv removed: -O3 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -DNDEBUG -mmacosx-version-min=13.6 -fPIC -MD -MT src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/FASTX_Parser.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp
superenv removed: -O3 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -DNDEBUG -mmacosx-version-min=13.6 -fPIC -MD -MT src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.cpp
superenv removed: -O3 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -DNDEBUG -mmacosx-version-min=13.6 -fPIC -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/CompressedCoverage.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp
superenv removed: -O3 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -DNDEBUG -mmacosx-version-min=13.6 -fPIC -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BitContainer.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp
superenv removed: -O3 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -O3
superenv added: -pipe -w -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -DNDEBUG -mmacosx-version-min=13.6 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.cpp
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superenv executed: clang++ -pipe -w -Os -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -DNDEBUG -mmacosx-version-min=13.6 -fPIC -MD -MT src/CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/GFA_Parser.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
clang++ called with: -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk -mmacosx-version-min=13.6 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp
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superenv executed: clang++ -pipe -w -Os -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.0.sdk/usr/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -mno-avx2 -DNDEBUG -mmacosx-version-min=13.6 -MD -MT src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -c /tmp/kallisto-20231104-51059-b8hmvt/kallisto-0.50.1/ext/bifrost/src/BlockedBloomFilter.cpp -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk --sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -isystem/opt/homebrew/include -isystem/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
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