Question: Error Installing Cluster Profiler
0
gravatar for heir_of_isildur88
11 months ago by
heir_of_isildur880 wrote:

Hi all,

I was trying to install clusterProfiler in my R Studio but I was unable to do it. As I am using my institute's server, I have only local access. The command I used to install is: 

biocLite("clusterProfiler", lib = "~/R/3.4/clusterProfiler")

The error I got is:

*** installing help indices
  converting help for package ‘DOSE’
    finding HTML links ... done
    DOSE-package                            html  
    DataSet                                 html  
    EXTID2NAME                              html  
    GSEA_internal                           html  
    barplot.enrichResult                    html  
    clusterSim                              html  
    cnetplot-methods                        html  
    cnetplot_internal                       html  
    computeIC                               html  
    doSim                                   html  
    dotplot-methods                         html  
    enrichDGN                               html  
    enrichDGNv                              html  
    enrichDO                                html  
    enrichMap                               html  
    enrichNCG                               html  
    enrichResult-class                      html  
    enricher_internal                       html  
    fortify.enrichResult                    html  
    gene2DO                                 html  
    geneID                                  html  
    geneInCategory                          html  
    geneSim                                 html  
    gsInfo                                  html  
    gseDGN                                  html  
    gseDO                                   html  
    gseNCG                                  html  
    gseaResult-class                        html  
    gseaplot                                html  
    gsfilter                                html  
    list2graph                              html  
    mclusterSim                             html  
    netplot                                 html  
    plot-methods                            html  
    rebuildAnnoData                         html  
    reexports                               html  
    ridgeplot                               html  
    scaleNodeColor                          html  
    setReadable                             html  
    setting.graph.attributes                html  
    show-methods                            html  
    simplot                                 html  
    summary-methods                         html  
    theme_dose                              html  
    upsetplot-methods                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
sh: line 1: 61860 Segmentation fault      (core dumped) '/usr/lib64/R/bin/R' --no-save --slave 2>&1 < '/tmp/Rtmp1c8RKq/filef19c7a7d05e9'

 *** caught segfault ***
address (nil), cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
* removing ‘/home/sato_y/R/3.4/DOSE’

 *** 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: 61851 Done                    echo 'tools:::.install_packages()'
     61852 Segmentation fault      (core dumped) | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
ERROR: dependency ‘DOSE’ is not available for package ‘clusterProfiler’
* removing ‘/home/sato_y/R/3.4/clusterProfiler’

The downloaded source packages are in
	‘/tmp/RtmpeVVmdz/downloaded_packages’
installation path not writeable, unable to update packages: ade4, amap, ape,
  bit, cluster, data.table, edgeR, fastcluster, glmnet, highr, htmlTable,
  httpuv, kernlab, later, lmtest, Matrix, mgcv, munsell, mvtnorm, nlme,
  pillar, pkgmaker, progress, purrr, quantreg, RcppArmadillo, rjson, rlang,
  rmarkdown, robustbase, rrcov, slam, sp, spam, statnet.common, stringi, tm,
  xgboost, xts, zoo
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DOSE’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘clusterProfiler’ had non-zero exit status

This is the details of my session info:

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    yaml_2.1.19  

Please advice on how I can solve this issue. Thank you very much.

ADD COMMENTlink modified 11 months ago • written 11 months ago by heir_of_isildur880
ADD REPLYlink written 11 months ago by Guangchuang Yu1.1k
Run these:
source("http://www.bioconductor.org/biocLite.R")
biocLite("DO.db")
biocLite("DOSE")
ADD REPLYlink modified 10 months ago • written 10 months ago by mario.zanfardino150
Run these:
source("http://www.bioconductor.org/biocLite.R")
biocLite("DO.db")
biocLite("DOSE")
ADD REPLYlink written 10 months ago by mario.zanfardino150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 106 users visited in the last hour