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Question: ReportingTools Segmentation fault
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gravatar for michael
5 months ago by
michael20
Germany
michael20 wrote:

I am getting a segfault when trying to install 'ReportingTools'. I already tried removing the package and reinstall, and the devel package (v 2.19.1), but no success... Any help appreciated!

 

R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite("ReportingTools")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘ReportingTools’
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/ReportingTools_2.17.3.tar.gz'
Content type 'application/x-gzip' length 2356046 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

* installing *source* package ‘ReportingTools’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'objectToHTML' with signature 'object="ggbio"': no definition for class "ggbio"
Note: no visible binding for '<<-' assignment to '.reportDirectory'
Note: no visible binding for '<<-' assignment to '.reportDirectory'
** help
*** installing help indices
  converting help for package 'ReportingTools'
    finding HTML links ... done
    BaseReportType-class                    html
    CSVFile-class                           html
    CSVFile                                 html
    DataPackage-class                       html
    DataPackage                             html
    HTMLReport-class                        html
    HTMLReport                              html
    HTMLReportRef-class                     html
    Link                                    html
    ReportHandlers-class                    html
    addReportColumns-methods                html
    custHeaderPanel                         html
    filename-methods                        html
    finish-methods                          html
    makeDESeqDF                             html
    mockRnaSeqData                          html
    objectToHTML-methods                    html
    publish-methods                         html
    finding level-2 HTML links ... done

    readReport                              html
    reporting.theme                         html
    reporting.theme.alternate               html
    toReportDF-methods                      html
    validConnection                         html
** building package indices
** installing vignettes
** testing if installed package can be loaded
sh: line 1: 14021 Segmentation fault      (core dumped) '/usr/lib64/R/bin/R' --no-save --slave 2>&1 < '/tmp/RtmphZyPd7/file36be259a6b2f'

 *** caught segfault ***
address (nil), cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
* removing '/home/mspohn/R/x86_64-redhat-linux-gnu-library/3.4/ReportingTools'

 *** 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 ...
/usr/lib64/R/bin/INSTALL: line 34: 14013 Done                    echo 'tools:::.install_packages()'
     14014 Segmentation fault      (core dumped) | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}

The downloaded source packages are in
    ‘/tmp/Rtmp9rt8fr/downloaded_packages’
installation path not writeable, unable to update packages: survival
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘ReportingTools’ had non-zero exit status

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
[1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C            
[3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8   
[5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8  
[7] LC_PAPER=en_GB.utf8       LC_NAME=C               
[9] LC_ADDRESS=C              LC_TELEPHONE=C          
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3  
>
ADD COMMENTlink modified 5 months ago by becker.gabriel0 • written 5 months ago by michael20
1

biocLite("ReportingTools", INSTALL_opts="--no-test-load") will load the package but you likely will still encounter segfault ERROR.

What is your results from running the following commands:


`R CMD config CC` --version 
`R CMD config CXX` --version
ADD REPLYlink modified 5 months ago • written 5 months ago by shepherl ♦♦ 730

The results are:

gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
ADD REPLYlink written 5 months ago by michael20

So I was also having segfault issues on my machine with a number of different packages including this one. My fix was a little drastic  but ...

I updated  my version of gcc and g++  to use 5.4.1  and then installed the appropriate version of libgfortran for version 5. 

I then deleted my local R library and reinstalled every package from scratch. 

This got rid of the segfaults for me ... 

Again this is not ideal and rather extreme and there should be a better solution somewhere ...  

ADD REPLYlink written 5 months ago by shepherl ♦♦ 730

It seems like getting a newer version of gcc/g++ is the only solution so far

ADD REPLYlink written 5 months ago by michael20
0
gravatar for becker.gabriel
5 months ago by
becker.gabriel0 wrote:

This is strange. ReportingTools does not have any C or C++ code in it at all, so it is difficult to imagine the segfault being due to our code. I'm also not able to reproduce this when installing from source on OS X El Capitan in R 3.4.4 patched. 

I will try to look into this more but I'm not sure how much I can do without being able to reproduce it. Will post again once I have more info.

ADD COMMENTlink written 5 months ago by becker.gabriel0

This looks a lot like this report, superficially a rogue finalizer from Rcpp but it could be almost anything, and the complexity of the package dependencies makes this hard to track down. The original poster could have fun by installing and then trying to catch the segfault

R -d valgrind -e "library(ReportingTools)"

and / or trying to narrow down to which package is problematic (it could well be that simpler examples fail to fail, because of the nature of segfaults).

ADD REPLYlink written 5 months ago by Martin Morgan ♦♦ 22k

Valgrind reported following:

==1640== Memcheck, a memory error detector
==1640== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==1640== Using Valgrind-3.12.0 and LibVEX; rerun with -h for copyright info
==1640== Command: /usr/lib64/R/bin/exec/R -e library(ReportingTools)
==1640==

R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ReportingTools)
Loading required package: knitr

>
>
==1640== Invalid read of size 4
==1640==    at 0xC3A9CB3: std::locale::~locale() (in /usr/lib64/libstdc++.so.6.0.19)
==1640==    by 0x24E2A762: ~basic_streambuf (streambuf:198)
==1640==    by 0x24E2A762: ~Rstreambuf (Rstreambuf.h:31)
==1640==    by 0x24E2A762: Rcpp::Rostream<false>::~Rostream() (Rstreambuf.h:44)
==1640==    by 0x84B3A68: __run_exit_handlers (in /usr/lib64/libc-2.17.so)
==1640==    by 0x84B3AB4: exit (in /usr/lib64/libc-2.17.so)
==1640==    by 0x5049F4D: ??? (in /usr/lib64/R/lib/libR.so)
==1640==    by 0x4F8150A: run_Rmainloop (in /usr/lib64/R/lib/libR.so)
==1640==    by 0x40080A: main (in /usr/lib64/R/bin/exec/R)
==1640==  Address 0x0 is not stack'd, malloc'd or (recently) free'd
==1640==

 *** caught segfault ***
address (nil), cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
==1640==
==1640== Process terminating with default action of signal 11 (SIGSEGV)
==1640==    at 0x826E4AB: raise (in /usr/lib64/libpthread-2.17.so)
==1640==    by 0x826E5DF: ??? (in /usr/lib64/libpthread-2.17.so)
==1640==    by 0xC3A9CB2: std::locale::~locale() (in /usr/lib64/libstdc++.so.6.0.19)
==1640==
==1640== HEAP SUMMARY:
==1640==     in use at exit: 524,553,645 bytes in 281,805 blocks
==1640==   total heap usage: 688,583 allocs, 406,778 frees, 1,223,999,733 bytes allocated
==1640==
==1640== LEAK SUMMARY:
==1640==    definitely lost: 0 bytes in 0 blocks
==1640==    indirectly lost: 0 bytes in 0 blocks
==1640==      possibly lost: 838,851 bytes in 3,486 blocks
==1640==    still reachable: 523,714,794 bytes in 278,319 blocks
==1640==                       of which reachable via heuristic:
==1640==                         length64           : 802,872 bytes in 1,581 blocks
==1640==         suppressed: 0 bytes in 0 blocks
==1640== Rerun with --leak-check=full to see details of leaked memory
==1640==
==1640== For counts of detected and suppressed errors, rerun with: -v
==1640== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)
Segmentation fault (core dumped)
ADD REPLYlink written 5 months ago by michael20
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