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rsangole/devtools_install_attempt.log

Created November 16, 2018 20:28
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Package install issues on new HDI cluster
Raw
devtools_install_attempt.log
hw831@ed0-rserve:~/common_setup_utils/R/Azure_HDI_Cluster_dev$
sudo R --no-save -q -e "install.packages('devtools',repo='https://mran.microsoft.com/snapshot/2018-11-01')"
> install.packages('devtools',repo='https://mran.microsoft.com/snapshot/2018-11-01')
Installing package into ‘/opt/microsoft/mlserver/9.3.0/libraries/RServer’
(as ‘lib’ is unspecified)
also installing the dependencies ‘fs’, ‘usethis’
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 780k 100 780k 0 0 960k 0 --:--:-- --:--:-- --:--:-- 960k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 318k 100 318k 0 0 448k 0 --:--:-- --:--:-- --:--:-- 448k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 379k 100 379k 0 0 474k 0 --:--:-- --:--:-- --:--:-- 474k
* installing *source* package ‘fs’ ...
** package ‘fs’ successfully unpacked and MD5 sums checked
** libs
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c id.cc -o id.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c utils.cc -o utils.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c file.cc -o file.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c path.cc -o path.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c link.cc -o link.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c fs.cc -o fs.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c dir.cc -o dir.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c error.cc -o error.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c unix/getmode.cc -o unix/getmode.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c bsd/setmode.c -o bsd/setmode.o
gcc -std=gnu99 -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c bsd/strmode.c -o bsd/strmode.o
gcc -std=gnu99 -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c bsd/reallocarray.c -o bsd/reallocarray.o
cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4
(cd libuv \
&& touch aclocal.m4 \
&& touch -r aclocal.m4 configure Makefile.in \
&& CC="gcc -std=gnu99" CFLAGS="-DU_STATIC_IMPLEMENTATION -g -O2 -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib" LDFLAGS="-L/usr/local/lib64" ./configure --quiet)
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make --directory=libuv \
HAVE_DTRACE=0
make[1]: Entering directory '/tmp/RtmpMoXvod/R.INSTALL38db34253a4c/fs/src/libuv'
CC src/libuv_la-fs-poll.lo
./libtool: line 552: CDPATH: command not found
libtool: Version mismatch error. This is libtool 2.4.2 Debian-2.4.2-1.7ubuntu1, but the
libtool: definition of this LT_INIT comes from an older release.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 Debian-2.4.2-1.7ubuntu1
libtool: and run autoconf again.
Makefile:1880: recipe for target 'src/libuv_la-fs-poll.lo' failed
make[1]: *** [src/libuv_la-fs-poll.lo] Error 63
make[1]: Leaving directory '/tmp/RtmpMoXvod/R.INSTALL38db34253a4c/fs/src/libuv'
Makevars:38: recipe for target 'libuv/.libs/libuv.a' failed
make: *** [libuv/.libs/libuv.a] Error 2
ERROR: compilation failed for package ‘fs’
* removing ‘/opt/microsoft/mlserver/9.3.0/libraries/RServer/fs’
ERROR: dependency ‘fs’ is not available for package ‘usethis’
* removing ‘/opt/microsoft/mlserver/9.3.0/libraries/RServer/usethis’
ERROR: dependency ‘usethis’ is not available for package ‘devtools’
* removing ‘/opt/microsoft/mlserver/9.3.0/libraries/RServer/devtools’
The downloaded source packages are in
‘/tmp/RtmpsLeW2F/downloaded_packages’
Warning messages:
1: In install.packages("devtools", repo = "https://mran.microsoft.com/snapshot/2018-11-01") :
installation of package ‘fs’ had non-zero exit status
2: In install.packages("devtools", repo = "https://mran.microsoft.com/snapshot/2018-11-01") :
installation of package ‘usethis’ had non-zero exit status
3: In install.packages("devtools", repo = "https://mran.microsoft.com/snapshot/2018-11-01") :
installation of package ‘devtools’ had non-zero exit status
>
>
hw831@ed0-rserve:~/common_setup_utils/R/Azure_HDI_Cluster_dev$
Raw
fs_install_attempt.log
hw831@ed0-rserve:~/common_setup_utils/R/Azure_HDI_Cluster_dev$ sudo R --no-save -q -e "install.packages('fs',repo='https://mran.microsoft.com/snapshot/2018-11-01')"
> install.packages('fs',repo='https://mran.microsoft.com/snapshot/2018-11-01')
Installing package into ‘/opt/microsoft/mlserver/9.3.0/libraries/RServer’
(as ‘lib’ is unspecified)
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 780k 100 780k 0 0 736k 0 0:00:01 0:00:01 --:--:-- 736k
* installing *source* package ‘fs’ ...
** package ‘fs’ successfully unpacked and MD5 sums checked
** libs
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c id.cc -o id.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c utils.cc -o utils.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c file.cc -o file.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c path.cc -o path.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c link.cc -o link.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c fs.cc -o fs.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c dir.cc -o dir.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c error.cc -o error.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c unix/getmode.cc -o unix/getmode.o
g++ -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c bsd/setmode.c -o bsd/setmode.o
gcc -std=gnu99 -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c bsd/strmode.c -o bsd/strmode.o
gcc -std=gnu99 -I/opt/microsoft/mlserver/9.3.0/runtime/R/include -DNDEBUG -I./libuv/include -I. -I"/opt/microsoft/mlserver/9.3.0/libraries/RServer/Rcpp/include" -I/usr/local/include -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c bsd/reallocarray.c -o bsd/reallocarray.o
cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4
(cd libuv \
&& touch aclocal.m4 \
&& touch -r aclocal.m4 configure Makefile.in \
&& CC="gcc -std=gnu99" CFLAGS="-DU_STATIC_IMPLEMENTATION -g -O2 -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib" LDFLAGS="-L/usr/local/lib64" ./configure --quiet)
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make --directory=libuv \
HAVE_DTRACE=0
make[1]: Entering directory '/tmp/Rtmp0kiyOM/R.INSTALL47aa2fe6e1b3/fs/src/libuv'
CC src/libuv_la-fs-poll.lo
./libtool: line 552: CDPATH: command not found
libtool: Version mismatch error. This is libtool 2.4.2 Debian-2.4.2-1.7ubuntu1, but the
libtool: definition of this LT_INIT comes from an older release.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 Debian-2.4.2-1.7ubuntu1
libtool: and run autoconf again.
Makefile:1880: recipe for target 'src/libuv_la-fs-poll.lo' failed
make[1]: *** [src/libuv_la-fs-poll.lo] Error 63
make[1]: Leaving directory '/tmp/Rtmp0kiyOM/R.INSTALL47aa2fe6e1b3/fs/src/libuv'
Makevars:38: recipe for target 'libuv/.libs/libuv.a' failed
make: *** [libuv/.libs/libuv.a] Error 2
ERROR: compilation failed for package ‘fs’
* removing ‘/opt/microsoft/mlserver/9.3.0/libraries/RServer/fs’
The downloaded source packages are in
‘/tmp/RtmphIzgoN/downloaded_packages’
Warning message:
In install.packages("fs", repo = "https://mran.microsoft.com/snapshot/2018-11-01") :
installation of package ‘fs’ had non-zero exit status
>
>
hw831@ed0-rserve:~/common_setup_utils/R/Azure_HDI_Cluster_dev$
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