Greetings all,
I am having trouble installing the ChAMP package. Briefly, there is a segmentation failure (line 1: 44538 Segmentation fault). All of the ChAMP package dependency is installed. Do you know how to solve this issue?
The output code is bellow.
Thank you so much for the help,
Nathan
installing to library â/home/cawten/R/x86_64-redhat-linux-gnu-library/3.3â
* installing *source* package âChAMPâ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import âigraph::edgesâ by âgraph::edgesâ when loading âFEMâ
Warning: replacing previous import âigraph::intersectionâ by âgraph::intersectionâ when loading âFEMâ
Warning: replacing previous import âigraph::degreeâ by âgraph::degreeâ when loading âFEMâ
Warning: replacing previous import âigraph::unionâ by âgraph::unionâ when loading âFEMâ
Warning: replacing previous import âMatrix::whichâ by âBiocGenerics::whichâ when loading âFEMâ
Warning: replacing previous import âlimma::plotMAâ by âBiocGenerics::plotMAâ when loading âFEMâ
Warning: replacing previous import âigraph::normalizeâ by âBiocGenerics::normalizeâ when loading âFEMâ
Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP'
Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP'
** help
*** installing help indices
converting help for package 'ChAMP'
finding HTML links ... done
Block.GUI html
ChAMP-package html
CpG.GUI html
DMP.GUI html
DMR.GUI html
QC.GUI html
champ.Block html
champ.CNA html
champ.DMP html
champ.DMR html
champ.EpiMod html
champ.GSEA html
champ.QC html
champ.SVD html
champ.ebayGSEA html
champ.filter html
champ.import html
champ.impute html
champ.load html
champ.norm html
champ.process html
champ.refbase html
champ.runCombat html
** building package indices
** installing vignettes
** testing if installed package can be loaded
sh: line 1: 44538 Segmentation fault (core dumped) '/usr/lib64/R/bin/R' --no-save --slave 2>&1 < '/tmp/RtmpSOWk1V/fileaddd6c6fe823'
Warning: replacing previous import âigraph::edgesâ by âgraph::edgesâ when loading âFEMâ
Warning: replacing previous import âigraph::intersectionâ by âgraph::intersectionâ when loading âFEMâ
Warning: replacing previous import âigraph::degreeâ by âgraph::degreeâ when loading âFEMâ
Warning: replacing previous import âigraph::unionâ by âgraph::unionâ when loading âFEMâ
Warning: replacing previous import âMatrix::whichâ by âBiocGenerics::whichâ when loading âFEMâ
Warning: replacing previous import âlimma::plotMAâ by âBiocGenerics::plotMAâ when loading âFEMâ
Warning: replacing previous import âigraph::normalizeâ by âBiocGenerics::normalizeâ when loading âFEMâ
Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP'
Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP'
*** caught segfault ***
address (nil), cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
* removing '/home/cawten/R/x86_64-redhat-linux-gnu-library/3.3/ChAMP'
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: q("no", status = 1, runLast = FALSE)
2: do_exit_on_error()
3: errmsg("loading failed")
4: do_install_source(pkg_name, instdir, pkg, desc)
5: do_install(pkg)
6: tools:::.install_packages()
An irrecoverable exception occurred. R is aborting now ...
/usr/lib64/R/bin/INSTALL: line 34: 44508 Done echo 'tools:::.install_packages()'
44509 Segmentation fault (core dumped) | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
Thank you Martin,
It was a combination of R being old, not having up to date biocInstaller, and not having the dependencies XML and RCurl (permission issues with IT).
Problem solved. Cheers,
Nathan