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

[Dan Tenenbaum]

On Wed, Jul 10, 2013 at 5:02 AM, sk [guest] <guest at bioconductor.org> wrote:
>
> 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
>
>

What command are you using to try and install the package?

Also, have you tried starting R with the --vanilla option?

Dan


>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor