[R] WGCNA package installation segmentation fault
William Dunlap
wdun|@p @end|ng |rom t|bco@com
Thu Apr 12 21:38:33 CEST 2018
I get the seg-fault on exiting R after loading WGCNA into R-3.4.3 on
Linux. Valdgrind
shows the problem occurs when tearing down an Rstreambuf object:
% R --debugger valgrind --vanilla --quiet
==30889== Memcheck, a memory error detector
==30889== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==30889== Using Valgrind-3.12.0 and LibVEX; rerun with -h for copyright info
==30889== Command: /home/R/R-3.4.3/lib64/R/bin/exec/R --vanilla --quiet
==30889==
> library(WGCNA)
Loading required package: dynamicTreeCut
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
==========================================================================
*
* 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=12
*
* To set the environment variable in linux bash shell, type
*
* export ALLOW_WGCNA_THREADS=12
*
* before running R. Other operating systems or shells will
* have a similar command to achieve the same aim.
*
==========================================================================
Attaching package: ‘WGCNA’
The following object is masked from ‘package:stats’:
cor
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /usr/lib64/libblas.so.3.4.2
LAPACK: /home/R/R-3.4.3/lib64/R/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
other attached packages:
[1] WGCNA_1.63 fastcluster_1.1.24 dynamicTreeCut_1.63-1
loaded via a namespace (and not attached):
[1] robust_0.4-18 Rcpp_0.12.16 mvtnorm_1.0-7
[4] lattice_0.20-35 GO.db_3.4.1 digest_0.6.15
[7] foreach_1.4.4 plyr_1.8.4 backports_1.1.2
[10] acepack_1.4.1 pcaPP_1.9-73 stats4_3.4.3
[13] RSQLite_2.1.0 ggplot2_2.2.1 pillar_1.2.1
[16] rlang_0.2.0 lazyeval_0.2.1 rstudioapi_0.7
[19] data.table_1.10.4-3 blob_1.1.1 S4Vectors_0.16.0
[22] rpart_4.1-13 Matrix_1.2-13 checkmate_1.8.5
[25] preprocessCore_1.40.0 splines_3.4.3 stringr_1.3.0
[28] foreign_0.8-69 htmlwidgets_1.0 bit_1.1-12
[31] munsell_0.4.3 compiler_3.4.3 pkgconfig_2.0.1
[34] BiocGenerics_0.24.0 base64enc_0.1-3 htmltools_0.3.6
[37] nnet_7.3-12 tibble_1.4.2 gridExtra_2.3
[40] htmlTable_1.11.2 Hmisc_4.1-1 IRanges_2.12.0
[43] codetools_0.2-15 matrixStats_0.53.1 rrcov_1.4-3
[46] MASS_7.3-49 grid_3.4.3 gtable_0.2.0
[49] DBI_0.8 magrittr_1.5 scales_0.5.0
[52] stringi_1.1.7 impute_1.52.0 doParallel_1.0.11
[55] latticeExtra_0.6-28 robustbase_0.92-8 Formula_1.2-2
[58] RColorBrewer_1.1-2 iterators_1.0.9 tools_3.4.3
[61] bit64_0.9-7 Biobase_2.38.0 DEoptimR_1.0-8
[64] fit.models_0.5-14 parallel_3.4.3 survival_2.41-3
[67] AnnotationDbi_1.40.0 colorspace_1.3-2 cluster_2.0.7
[70] memoise_1.1.0 knitr_1.20
> q("no")
==30889== Invalid read of size 4
==30889== at 0x9A22CB3: std::locale::~locale() (in
/usr/lib64/libstdc++.so.6.0.19)
==30889== by 0x1B01E462: ~basic_streambuf (streambuf:198)
==30889== by 0x1B01E462: ~Rstreambuf (Rstreambuf.h:31)
==30889== by 0x1B01E462: Rcpp::Rostream<false>::~Rostream()
(Rstreambuf.h:44)
==30889== by 0x5AE3A68: __run_exit_handlers (in /usr/lib64/libc-2.17.so)
==30889== by 0x5AE3AB4: exit (in /usr/lib64/libc-2.17.so)
==30889== by 0x504282A: Rstd_CleanUp (sys-std.c:1200)
==30889== by 0x4F7D108: do_quit (main.c:1330)
==30889== by 0x4F45B1E: bcEval (eval.c:6473)
==30889== by 0x4F5450F: Rf_eval (eval.c:624)
==30889== by 0x4F5657E: R_execClosure (eval.c:1614)
==30889== by 0x4F546CB: Rf_eval (eval.c:747)
==30889== by 0x4F7D921: Rf_ReplIteration (main.c:258)
==30889== by 0x4F7DCF0: R_ReplConsole (main.c:308)
==30889== Address 0x0 is not stack'd, malloc'd or (recently) free'd
==30889==
*** caught segfault ***
address (nil), cause 'memory not mapped'
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 3
==30889== Invalid read of size 4
==30889== at 0x9A22CB3: std::locale::~locale() (in
/usr/lib64/libstdc++.so.6.0.19)
==30889== by 0x1B01E4D2: ~basic_streambuf (streambuf:198)
==30889== by 0x1B01E4D2: ~Rstreambuf (Rstreambuf.h:31)
==30889== by 0x1B01E4D2: Rcpp::Rostream<true>::~Rostream()
(Rstreambuf.h:44)
==30889== by 0x5AE3A68: __run_exit_handlers (in /usr/lib64/libc-2.17.so)
==30889== by 0x5AE3AB4: exit (in /usr/lib64/libc-2.17.so)
==30889== by 0x504282A: Rstd_CleanUp (sys-std.c:1200)
==30889== by 0x4F7B9E8: sigactionSegv (main.c:616)
==30889== by 0x589E5DF: ??? (in /usr/lib64/libpthread-2.17.so)
==30889== by 0x9A22CB2: std::locale::~locale() (in
/usr/lib64/libstdc++.so.6.0.19)
==30889== Address 0x0 is not stack'd, malloc'd or (recently) free'd
==30889==
==30889==
==30889== Process terminating with default action of signal 11 (SIGSEGV)
==30889== Access not within mapped region at address 0x0
==30889== at 0x9A22CB3: std::locale::~locale() (in
/usr/lib64/libstdc++.so.6.0.19)
==30889== by 0x1B01E4D2: ~basic_streambuf (streambuf:198)
==30889== by 0x1B01E4D2: ~Rstreambuf (Rstreambuf.h:31)
==30889== by 0x1B01E4D2: Rcpp::Rostream<true>::~Rostream()
(Rstreambuf.h:44)
==30889== by 0x5AE3A68: __run_exit_handlers (in /usr/lib64/libc-2.17.so)
==30889== by 0x5AE3AB4: exit (in /usr/lib64/libc-2.17.so)
==30889== by 0x504282A: Rstd_CleanUp (sys-std.c:1200)
==30889== by 0x4F7B9E8: sigactionSegv (main.c:616)
==30889== by 0x589E5DF: ??? (in /usr/lib64/libpthread-2.17.so)
==30889== by 0x9A22CB2: std::locale::~locale() (in
/usr/lib64/libstdc++.so.6.0.19)
==30889== If you believe this happened as a result of a stack
==30889== overflow in your program's main thread (unlikely but
==30889== possible), you can try to increase the size of the
==30889== main thread stack using the --main-stacksize= flag.
==30889== The main thread stack size used in this run was 8388608.
==30889==
==30889== HEAP SUMMARY:
==30889== in use at exit: 214,366,643 bytes in 111,859 blocks
==30889== total heap usage: 294,107 allocs, 182,248 frees, 507,439,997
bytes allocated
==30889==
==30889== LEAK SUMMARY:
==30889== definitely lost: 0 bytes in 0 blocks
==30889== indirectly lost: 0 bytes in 0 blocks
==30889== possibly lost: 0 bytes in 0 blocks
==30889== still reachable: 214,366,643 bytes in 111,859 blocks
==30889== of which reachable via heuristic:
==30889== length64 : 456,280 bytes in 769
blocks
==30889== suppressed: 0 bytes in 0 blocks
==30889== Rerun with --leak-check=full to see details of leaked memory
==30889==
==30889== For counts of detected and suppressed errors, rerun with: -v
==30889== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 0 from 0)
Segmentation fault (core dumped)
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Thu, Apr 12, 2018 at 11:32 AM, Peter Langfelder <
peter.langfelder using gmail.com> wrote:
> 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
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html <http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Thu, Apr 12, 2018 at 11:32 AM, Peter Langfelder <
peter.langfelder using gmail.com> wrote:
> 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
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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