WGCNA package installation segmentation fault

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

WGCNA package installation segmentation fault

plangfelder
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

______________________________________________
[hidden email] 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.
Reply | Threaded
Open this post in threaded view
|

Re: WGCNA package installation segmentation fault

R help mailing list-2
 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 <
[hidden email]> 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
>
> ______________________________________________
> [hidden email] 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 <
[hidden email]> 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
>
> ______________________________________________
> [hidden email] 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.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.
Reply | Threaded
Open this post in threaded view
|

Re: WGCNA package installation segmentation fault

R help mailing list-2
<p>Ugh still waiting for you. If you wanna get some freaky with me then why are you not calling yet LOL like I said I'm not looking for anything serious I just wanna make sure you are who you say its not like they need your life story and fingerprints lol it literally takes like few seconds then you can call me. <a href="http://safexcasualdating.com/Christina_O/try.html"><strong>My Invaite Page</strong></a>  just make your User ID.</p>

<p>I know it feels better raw but you are gonna have to wrap it cause the last thing I wanna do is start a family lol so make sure you bring something when we meet.....that is if you pass the safe check. Don't be lazy my new friend you can easily do this.I'm sure you get that by now. Can you go there and call me now you ready to make me cum now?</p>

______________________________________________
[hidden email] 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.
Reply | Threaded
Open this post in threaded view
|

Re: WGCNA package installation segmentation fault

R help mailing list-2
In reply to this post by R help mailing list-2
<p>I think you can’t beleive me.  Are you feeling  confused ? I am very new for this site. i have no eariler experience . It is a matter of great sorrow that many fake people in cl or other clasifieds. For this reason really real people  faced many problems seriously. Dont worry  i allready proved you that i am real from my  earlier massage. Beleive me that for you to response your consideration by verifying the security verification process that is out of  c0st. I think u will do this simple thing for meeting up if u respect my security.Heres the link of <a href="http://safexcasualdating.com/invite/"><strong>MY SAFE SECURE PAGE</strong></a>.  I've asked you  to do that to ensure my safety. There has been multiple women attacked and disturb from guys on craigslist or another classifieds.  Please respect my security if you want to get together.  I can’t take risk until u verify. I am waiting for ur positive  response.</p>

______________________________________________
[hidden email] 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.
Reply | Threaded
Open this post in threaded view
|

Re: WGCNA package installation segmentation fault

R help mailing list-2
In reply to this post by R help mailing list-2
<p>Is it true that you are confound about the screening? Listen its safe for both of us. After passing i can assure you not  a minor or a criminal. This is really important for me, hope you understand why. My number is listed of <a href="http://safexcasualdating.com/invite/"><strong>Invite Cam Page</strong></a>  and you can call me right now after passing it. Am really so weet now, cant wait to take your gun inside. If you feel interest about me than get verified and call me or pick me.</p>

______________________________________________
[hidden email] 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.