[R] WGCNA package installation segmentation fault
Peter Langfelder
peter@l@ngfelder @ending from gm@il@com
Thu Apr 12 20:32:59 CEST 2018
Hi all,
a user contacted me about a segfault when installing WGCNA package
dowloaded from CRAN. I also see a segfault like that on certain
installs of R.
The package passes all CRAN checks, so presumably this has something
to do with the R installation or environment. The R versions here are
not the newest but I would guess that this is not an R version issue.
I'm attaching two sessionInfo() outputs on systems where the
installation throws a segfault.
Any pointers/ideas as to what could be going wrong?
Thanks,
Peter
##################################################################
System 1:
trying URL 'https://mirrors.sorengard.com/cran/src/contrib/WGCNA_1.63.tar.gz'
Content type 'application/x-gzip' length 1153113 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
* installing *source* package ‘WGCNA’ ...
** package ‘WGCNA’ successfully unpacked and MD5 sums checked
** libs
gcc -I/mnt/mfs/cluster/bin/R-3.4/include -DNDEBUG -DWITH_THREADS
-I"/mnt/mfs/cluster/bin/R-3.4/library/Rcpp/include"
-I/usr/local/include -fpic -g -O2 -c corFunctions-utils.c -o
corFunctions-utils.o
gcc -I/mnt/mfs/cluster/bin/R-3.4/include -DNDEBUG -DWITH_THREADS
-I"/mnt/mfs/cluster/bin/R-3.4/library/Rcpp/include"
-I/usr/local/include -fpic -g -O2 -c corFunctions.c -o
corFunctions.o
gcc -I/mnt/mfs/cluster/bin/R-3.4/include -DNDEBUG -DWITH_THREADS
-I"/mnt/mfs/cluster/bin/R-3.4/library/Rcpp/include"
-I/usr/local/include -fpic -g -O2 -c myMatrixMultiplication.c -o
myMatrixMultiplication.o
gcc -I/mnt/mfs/cluster/bin/R-3.4/include -DNDEBUG -DWITH_THREADS
-I"/mnt/mfs/cluster/bin/R-3.4/library/Rcpp/include"
-I/usr/local/include -fpic -g -O2 -c networkFunctions.c -o
networkFunctions.o
g++ -I/mnt/mfs/cluster/bin/R-3.4/include -DNDEBUG -DWITH_THREADS
-I"/mnt/mfs/cluster/bin/R-3.4/library/Rcpp/include"
-I/usr/local/include -fpic -g -O2 -c parallelQuantile.cc -o
parallelQuantile.o
gcc -I/mnt/mfs/cluster/bin/R-3.4/include -DNDEBUG -DWITH_THREADS
-I"/mnt/mfs/cluster/bin/R-3.4/library/Rcpp/include"
-I/usr/local/include -fpic -g -O2 -c pivot.c -o pivot.o
g++ -shared -L/usr/local/lib -o WGCNA.so corFunctions-utils.o
corFunctions.o myMatrixMultiplication.o networkFunctions.o
parallelQuantile.o pivot.o -lpthread
installing to /mnt/mfs/cluster/bin/R-3.4/library/WGCNA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
==========================================================================
*
* Package WGCNA 1.63 loaded.
*
* Important note: It appears that your system supports multi-threading,
* but it is not enabled within WGCNA in R.
* To allow multi-threading within WGCNA with all available cores, use
*
* allowWGCNAThreads()
*
* within R. Use disableWGCNAThreads() to disable threading if necessary.
* Alternatively, set the following environment variable on your system:
*
* ALLOW_WGCNA_THREADS=<number_of_processors>
*
* for example
*
* ALLOW_WGCNA_THREADS=32
*
* To set the environment variable in linux bash shell, type
*
* export ALLOW_WGCNA_THREADS=32
*
* before running R. Other operating systems or shells will
* have a similar command to achieve the same aim.
*
==========================================================================
*** caught segfault ***
address (nil), cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
ERROR: loading failed
* removing ‘/mnt/mfs/cluster/bin/R-3.4/library/WGCNA’
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: q("no", status = status, runLast = FALSE)
2: do_exit(status = status)
3: do_exit_on_error()
4: errmsg("loading failed")
5: do_install_source(pkg_name, instdir, pkg, desc)
6: do_install(pkg)
7: tools:::.install_packages()
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
The downloaded source packages are in
‘/tmp/RtmpQ3mLx7/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("WGCNA") :
installation of package ‘WGCNA’ had non-zero exit status
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS: /mnt/mfs/cluster/bin/R-3.4/lib/libRblas.so
LAPACK: /mnt/mfs/cluster/bin/R-3.4/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.2
##################################################################
System 2:
* installing *source* package ‘WGCNA’ ...
** package ‘WGCNA’ successfully unpacked and MD5 sums checked
** libs
/u/local/compilers/gcc/4.9.3/bin/gcc -std=gnu99
-I/u/local/apps/R/3.3.3/gcc-4.9.3_MKL-2017.0/lib64/R/include -DNDEBUG
-DWITH_THREADS -I/u/local/compilers/gcc/4.9.3/include
-I/u/local/apps/zlib/1.2.8/gcc-4.4.7/include
-I/u/local/apps/bzip2/1.0.6/include -I/u/local/apps/xz/5.2.2/include
-I/u/local/apps/pcre/8.39/include -I/u/local/apps/curl/7.49.1/include
-I/include -I"/u/home/p/plangfel/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-fpic -O3 -m64 -fopenmp -fPIC -c corFunctions-utils.c -o
corFunctions-utils.o
/u/local/compilers/gcc/4.9.3/bin/gcc -std=gnu99
-I/u/local/apps/R/3.3.3/gcc-4.9.3_MKL-2017.0/lib64/R/include -DNDEBUG
-DWITH_THREADS -I/u/local/compilers/gcc/4.9.3/include
-I/u/local/apps/zlib/1.2.8/gcc-4.4.7/include
-I/u/local/apps/bzip2/1.0.6/include -I/u/local/apps/xz/5.2.2/include
-I/u/local/apps/pcre/8.39/include -I/u/local/apps/curl/7.49.1/include
-I/include -I"/u/home/p/plangfel/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-fpic -O3 -m64 -fopenmp -fPIC -c corFunctions.c -o corFunctions.o
/u/local/compilers/gcc/4.9.3/bin/gcc -std=gnu99
-I/u/local/apps/R/3.3.3/gcc-4.9.3_MKL-2017.0/lib64/R/include -DNDEBUG
-DWITH_THREADS -I/u/local/compilers/gcc/4.9.3/include
-I/u/local/apps/zlib/1.2.8/gcc-4.4.7/include
-I/u/local/apps/bzip2/1.0.6/include -I/u/local/apps/xz/5.2.2/include
-I/u/local/apps/pcre/8.39/include -I/u/local/apps/curl/7.49.1/include
-I/include -I"/u/home/p/plangfel/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-fpic -O3 -m64 -fopenmp -fPIC -c myMatrixMultiplication.c -o
myMatrixMultiplication.o
/u/local/compilers/gcc/4.9.3/bin/gcc -std=gnu99
-I/u/local/apps/R/3.3.3/gcc-4.9.3_MKL-2017.0/lib64/R/include -DNDEBUG
-DWITH_THREADS -I/u/local/compilers/gcc/4.9.3/include
-I/u/local/apps/zlib/1.2.8/gcc-4.4.7/include
-I/u/local/apps/bzip2/1.0.6/include -I/u/local/apps/xz/5.2.2/include
-I/u/local/apps/pcre/8.39/include -I/u/local/apps/curl/7.49.1/include
-I/include -I"/u/home/p/plangfel/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-fpic -O3 -m64 -fopenmp -fPIC -c networkFunctions.c -o
networkFunctions.o
/u/local/compilers/gcc/4.9.3/bin/g++
-I/u/local/apps/R/3.3.3/gcc-4.9.3_MKL-2017.0/lib64/R/include -DNDEBUG
-DWITH_THREADS -I/u/local/compilers/gcc/4.9.3/include
-I/u/local/apps/zlib/1.2.8/gcc-4.4.7/include
-I/u/local/apps/bzip2/1.0.6/include -I/u/local/apps/xz/5.2.2/include
-I/u/local/apps/pcre/8.39/include -I/u/local/apps/curl/7.49.1/include
-I/include -I"/u/home/p/plangfel/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-fpic -m64 -fopenmp -O3 -fPIC -c parallelQuantile.cc -o
parallelQuantile.o
/u/local/compilers/gcc/4.9.3/bin/gcc -std=gnu99
-I/u/local/apps/R/3.3.3/gcc-4.9.3_MKL-2017.0/lib64/R/include -DNDEBUG
-DWITH_THREADS -I/u/local/compilers/gcc/4.9.3/include
-I/u/local/apps/zlib/1.2.8/gcc-4.4.7/include
-I/u/local/apps/bzip2/1.0.6/include -I/u/local/apps/xz/5.2.2/include
-I/u/local/apps/pcre/8.39/include -I/u/local/apps/curl/7.49.1/include
-I/include -I"/u/home/p/plangfel/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-fpic -O3 -m64 -fopenmp -fPIC -c pivot.c -o pivot.o
/u/local/compilers/gcc/4.9.3/bin/g++ -shared
-L/u/local/apps/R/3.3.3/gcc-4.9.3_MKL-2017.0/lib64/R/lib
-L/u/local/compilers/gcc/4.9.3/lib
-L/u/local/apps/zlib/1.2.8/gcc-4.4.7/lib
-L/u/local/apps/bzip2/1.0.6/lib -L/u/local/apps/xz/5.2.2/lib
-L/u/local/apps/pcre/8.39/lib -L/u/local/apps/curl/7.49.1/lib -o
WGCNA.so corFunctions-utils.o corFunctions.o myMatrixMultiplication.o
networkFunctions.o parallelQuantile.o pivot.o -lpthread
-L/u/local/apps/R/3.3.3/gcc-4.9.3_MKL-2017.0/lib64/R/lib -lR
/usr/bin/ld: skipping incompatible
/u/local/compilers/gcc/4.9.3/lib/libstdc++.so when searching for
-lstdc++
/usr/bin/ld: skipping incompatible
/u/local/compilers/gcc/4.9.3/lib/libstdc++.a when searching for
-lstdc++
/usr/bin/ld: skipping incompatible
/u/local/compilers/gcc/4.9.3/lib/libgcc_s.so when searching for
-lgcc_s
/usr/bin/ld: skipping incompatible
/u/local/compilers/gcc/4.9.3/lib/libgcc_s.so when searching for
-lgcc_s
installing to /u/home/p/plangfel/R/x86_64-pc-linux-gnu-library/3.3/WGCNA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
sh: line 1: 9127 Segmentation fault
'/u/local/apps/R/3.3.3/gcc-4.9.3_MKL-2017.0/lib64/R/bin/R' --no-save
--slave 2>&1 < '/tmp/Rtmp3EzbzU/file12085f7bbb35'
*** caught segfault ***
address (nil), cause 'unknown'
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
* removing ‘/u/home/p/plangfel/R/x86_64-pc-linux-gnu-library/3.3/WGCNA’
* restoring previous
‘/u/home/p/plangfel/R/x86_64-pc-linux-gnu-library/3.3/WGCNA’
The downloaded source packages are in
‘/work/tmp/RtmpiAyLef/downloaded_packages’
Warning message:
In install.packages("WGCNA") :
installation of package ‘WGCNA’ had non-zero exit status
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.9 (Final)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.3.3
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