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tseemann/# kmc - 2016-02-13_15-49-58.txt

Created February 13, 2016 05:06
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kmc (homebrew/science/kmc) on x86_64-linux - Homebrew build logs
Raw
# kmc - 2016-02-13_15-49-58.txt
Homebrew build logs for homebrew/science/kmc on x86_64-linux
Build date: 2016-02-13 15:49:58
Raw
00.config.out
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew
HEAD: d1c54fad11721c17d9c24557561ed91608e2338a
Last commit: 7 hours ago
HOMEBREW_PREFIX: /bio/linuxbrew
HOMEBREW_REPOSITORY: /bio/linuxbrew
HOMEBREW_CELLAR: /bio/linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 72-core 64-bit haswell
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: 2.7.8 => /usr
System Ruby: 2.2.2 => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Perl: /usr/bin/perl
Python: /bio/linuxbrew/bin/python => /bio/linuxbrew/Cellar/python/2.7.11/bin/python2.7
Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Java: openjdk version "1.8.0_65"
Raw
00.doctor.out
Your system is ready to brew.
Raw
00.tap.out
Formula: kmc
Tap: homebrew/science
Path: /bio/linuxbrew/Library/Taps/homebrew/homebrew-science/kmc.rb
Raw
01.make
2016-02-13 15:49:58 +1100
make
CC=/bio/linuxbrew/bin/g++-5
-fmakefile
makefile:73: target 'kmc_api/mmer.o' given more than once in the same rule
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/kmer_counter.cpp -o kmer_counter/kmer_counter.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/mmer.cpp -o kmer_counter/mmer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/mem_disk_file.cpp -o kmer_counter/mem_disk_file.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/rev_byte.cpp -o kmer_counter/rev_byte.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/bkb_writer.cpp -o kmer_counter/bkb_writer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/bkb_reader.cpp -o kmer_counter/bkb_reader.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/fastq_reader.cpp -o kmer_counter/fastq_reader.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/timer.cpp -o kmer_counter/timer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/radix.cpp -o kmer_counter/radix.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/kb_completer.cpp -o kmer_counter/kb_completer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/kb_storer.cpp -o kmer_counter/kb_storer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/kmer.cpp -o kmer_counter/kmer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmer_counter/prob_qual.cpp -o kmer_counter/prob_qual.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmc_dump/nc_utils.cpp -o kmc_dump/nc_utils.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmc_api/mmer.cpp -o kmc_api/mmer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmc_dump/kmc_dump.cpp -o kmc_dump/kmc_dump.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmc_api/kmc_file.cpp -o kmc_api/kmc_file.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -c kmc_api/kmer_api.cpp -o kmc_api/kmer_api.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/kmc_header.cpp -o kmc_tools/kmc_header.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/kmc_tools.cpp -o kmc_tools/kmc_tools.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/nc_utils.cpp -o kmc_tools/nc_utils.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/parameters_parser.cpp -o kmc_tools/parameters_parser.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/parser.cpp -o kmc_tools/parser.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/tokenizer.cpp -o kmc_tools/tokenizer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/fastq_filter.cpp -o kmc_tools/fastq_filter.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/fastq_reader.cpp -o kmc_tools/fastq_reader.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/fastq_writer.cpp -o kmc_tools/fastq_writer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/percent_progress.cpp -o kmc_tools/percent_progress.o
kmc_api/kmc_file.cpp: In member function 'bool CKMCFile::BinarySearch(int64, int64, const CKmerAPI&, uint64&, uint32)':
kmc_api/kmc_file.cpp:1360:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (index_start >= total_kmers)
^
mkdir -p bin
/bio/linuxbrew/bin/g++-5 -lm -static -fopenmp -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -o bin/kmc_dump kmc_dump/nc_utils.o kmc_api/mmer.o kmc_dump/kmc_dump.o kmc_api/kmc_file.o kmc_api/kmer_api.o
/bio/linuxbrew/bin/ld: cannot find -lpthread
/bio/linuxbrew/bin/ld: cannot find -lm
/bio/linuxbrew/bin/ld: cannot find -ldl
/bio/linuxbrew/bin/ld: cannot find -lpthread
/bio/linuxbrew/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
makefile:84: recipe for target 'kmc_dump' failed
make: *** [kmc_dump] Error 1
make: *** Waiting for unfinished jobs....
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew
HEAD: d1c54fad11721c17d9c24557561ed91608e2338a
Last commit: 7 hours ago
HOMEBREW_PREFIX: /bio/linuxbrew
HOMEBREW_REPOSITORY: /bio/linuxbrew
HOMEBREW_CELLAR: /bio/linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 72-core 64-bit haswell
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: 2.7.8 => /usr
System Ruby: 2.2.2 => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Perl: /usr/bin/perl
Python: /bio/linuxbrew/bin/python => /bio/linuxbrew/Cellar/python/2.7.11/bin/python2.7
Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Java: openjdk version "1.8.0_65"
CC: /bio/linuxbrew/bin/gcc-5 => /bio/linuxbrew/Cellar/gcc/5.3.0/bin/gcc-5
CXX: /bio/linuxbrew/bin/g++-5 => /bio/linuxbrew/Cellar/gcc/5.3.0/bin/g++-5
OBJC: /bio/linuxbrew/bin/gcc-5
OBJCXX: /bio/linuxbrew/bin/g++-5
CFLAGS: -Os -w -pipe -march=core2
CXXFLAGS: -Os -w -pipe -march=core2
CPPFLAGS: -isystem/bio/linuxbrew/include
LDFLAGS: -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib
MAKEFLAGS: -j72
CMAKE_PREFIX_PATH: /bio/linuxbrew
PKG_CONFIG_LIBDIR: /bio/linuxbrew/lib/pkgconfig:/bio/linuxbrew/share/pkgconfig
HOMEBREW_BUILD_FROM_SOURCE: 1
PATH: /home/tseemann/perl5/bin:/bio/perl5/bin:/bio/linuxbrew/bin:/bio/linuxbrew/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/home/agoncalves/bin:/bio/sw/hierBAPS:/bio/sw/brat:/bio/sw/mauve:/bio/sw/splitstree4:/bio/sw/vbc/fqa-tools:/bio/sw/vbc/misc:/bio/sw/MUMmer:/bio/sw/tablet:/home/tseemann/git/wombac/bin:/home/tseemann/git/snippy/bin:/home/tseemann/git/barrnap/bin:/home/tseemann/git/nullarbor/bin:/home/tseemann/git/prokka/bin:/home/tseemann/git/mlst/bin:/home/tseemann/git/abricate/bin:/home/tseemann/git/mdu-tools/bin:/usr/local/sbin:/usr/sbin:/home/tseemann/.local/bin:/home/tseemann/bin:/bio/linuxbrew/Library/ENV/scm
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