Question: Error biocLite() newest version of ChAMP
1
gravatar for rosa_hegi
18 months ago by
rosa_hegi10
rosa_hegi10 wrote:

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?

champ bioclite R • 463 views
ADD COMMENTlink written 18 months ago by rosa_hegi10

Is your script complete? It looks like the segfault occurs in R, before any package is downloaded.

ADD REPLYlink written 18 months ago by Martin Morgan ♦♦ 23k

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 

ADD REPLYlink written 13 months ago by jim.chen0

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

ADD REPLYlink written 13 months ago by Yuan Tian120
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