[BioC] Problem while installing \"org.At.tair.db\" and \"ath1121501.db\"

[Sean Davis]

On Tue, Feb 7, 2012 at 8:03 AM, Reetu [guest] <guest at bioconductor.org> wrote:
>
> Hi All,
>
> I am trying to install "org.At.tair.db" and "ath1121501.db" packages on working
> node of my server and getting the following problems. Except these two packages
> I successfully installed few other packages from R on the same node. I am not
> getting where exactly the problem is. Can someone please help.
>
> Thanks,
> RT
>
>  -- output of sessionInfo():
>
> Session Info:
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-redhat-linux-gnu
>
> 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=C              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
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
>
>
>> source("http://www.bioconductor.org/biocLite.R")
> BioC_mirror = http://www.bioconductor.org
> Change using chooseBioCmirror().
>> biocLite("org.At.tair.db")
> Using R version 2.11.0, biocinstall version 2.6.10.
> Installing Bioconductor version 2.6 packages:
> [1] "org.At.tair.db"
> Please wait...
>
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
>  argument 'lib' is missing: using
> '/home/XXX/R/x86_64-redhat-linux-gnu-library/2.11'
> trying URL
> 'http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib/org.At.tair.db_2.4.3.tar.gz'
> Content type 'application/x-gzip' length 26130925 bytes (24.9 Mb)
> opened URL
> ==================================================
> downloaded 24.9 Mb
>
> ERROR: failed to lock directory
> ‘/home/XXX/R/x86_64-redhat-linux-gnu-library/2.11’ for modifying
> Try removing ‘/home/XXX/R/x86_64-redhat-linux-gnu-library/2.11/00LOCK’

Did you remove the file noted above?  I'd do that and then try the
installation again.

Sean

> The downloaded packages are in
>    ‘/tmp/Rtmphd9Etx/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package 'org.At.tair.db' had non-zero exit status
>
> --
> 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