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.
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.
> 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 >
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:
The results are:
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 ...
It seems like getting a newer version of gcc/g++ is the only solution so far