When i try to install the newest version of ChAMP I get the following error:
> biocLite("ChAMP")
*** caught segfault ***
address (nil), cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
* removing '/home/r.hegi/R/x86_64-redhat-linux-gnu-library/3.4/ChAMP'
*** 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: 10039 Done echo 'tools:::.install_packages()'
10040 Segmentation fault (core dumped) | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
The downloaded source packages are in
\u2018/tmp/RtmplKVP4H/downloaded_packages\u2019
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package \u2018ChAMP\u2019 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_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] BiocInstaller_1.28.0
loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3
Could someone pleas help me?
Is your script complete? It looks like the segfault occurs in R, before any package is downloaded.
Hi,
While trying to install 'Champ' on R version 3.3.1, I got the same 'segmentation fault' as the original post: Have anyone figured out the reason/solution?
The commands I used to do the installation:
> source("https://bioconductor.org/biocLite.R")
> biocLite("ChAMP")
Then I get the segfault:
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loadi ng 'ChAMP'
*** caught segfault ***
address (nil), cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
* removing '/usr/lib64/R/library/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: 37846 Done echo 'tools:::. install_packages()'
37847 Segmentation fault (core dumped) | R_DEFAULT_PACKAGES= LC_COLLAT E=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
Thank you.
Jim
Hello:
Based on my experience, I don't this is a problem with ChAMP, but could be some error related to R environment. I just tried to install ChAMP on R 3.5.1 and it works. Could you try R 3.5.1, because R 3.3.1 is a little bit too old.
Best
Yuan Tian