[BioC] about org.Hs.eg.db package install on linux

sk [guest] guest at bioconductor.org
Wed Jul 10 14:02:01 CEST 2013


when I install "org.Hs.eg.db" package on Linux, there are some errors, I do not know why. Thanks!

 -- output of sessionInfo(): 

Warning in gzfile(file, mode) :
  cannot open compressed file '/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/org.Hs.eg.db/help/paths.rds', probable reason 'No such file or directory'
Error in gzfile(file, mode) : cannot open the connection
ERROR: installing Rd objects failed for package âorg.Hs.eg.dbâ
* removing â/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/org.Hs.eg.dbâ

The downloaded source packages are in
        â/tmp/RtmpHRvkWg/downloaded_packagesâ
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package âorg.Hs.eg.dbâ had non-zero exit status
2: installed directory not writable, cannot update packages 'class', 'foreign',
  'MASS', 'mgcv', 'nlme', 'nnet', 'spatial' 


>  sessionInfo() 
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

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=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] BiocInstaller_1.10.2  gcrma_2.32.0          affy_1.38.1          
[4] preprocessCore_1.22.0 plyr_1.8              GEOquery_2.26.1      
[7] Biobase_2.20.1        BiocGenerics_0.6.0   

loaded via a namespace (and not attached):
[1] affyio_1.28.0     Biostrings_2.28.0 IRanges_1.18.1    RCurl_1.95-4.1   
[5] splines_3.0.1     stats4_3.0.1      tools_3.0.1       XML_3.98-1.1     
[9] zlibbioc_1.6.0   



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