[BioC] problem with biocLite("Biobase") -- results in looping of download

[Martin Morgan]

Hi Mark -- 

Mark Kimpel <mwkimpel at gmail.com> writes:

> The code below results in a looping behavior with Biobase downloaded over
> and over again until escaped, then each downloaded instance (all in
> different temp folders) is installed. This behavior began about the time

Weird! Does it help to start

   R --vanilla

to avoid reading profile / etc information? What about unusual
environment variables / symbolic links in the file system?

Martin

> that R-2.9.0 was released, but I had been using R-devel prior to that
> without problem. My system is Debian Lenny AMD64. Output and sessionInfo()
> follows below.
>
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("Biobase")
>
>> source("http://www.bioconductor.org/biocLite.R")
> biocLite("Biobase")
> source("http://www.bioconductor.org/biocLite.R")
> Warning messages:
> 1: In safeSource() : Redefining ‘biocinstall’
> 2: In safeSource() : Redefining ‘biocinstallPkgGroups’
> 3: In safeSource() : Redefining ‘biocinstallRepos’
>>          biocLite("Biobase")
> Running biocinstall version 2.4.10 with R version 2.9.0
> Your version of R requires version 2.4 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   argument 'lib' is missing: using '/home/mkimpel/R_HOME/site-library-2.9.0'
> trying URL '
> http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz'
> Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
> opened URL
> ==================================================
> downloaded 1.9 Mb
>
> Loading required package: utils
> Running biocinstall version 2.4.10 with R version 2.9.0
> Your version of R requires version 2.4 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   argument 'lib' is missing: using '/home/mkimpel/R_HOME/site-library-2.9.0'
> trying URL '
> http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz'
> Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
> opened URL
> ==================================================
> ## REPEATS UNTIL ESCAPED
> ==================================================
> downloaded 1.9 Mb
>
> Loading required package: utils
> Running biocinstall version 2.4.10 with R version 2.9.0
> Your version of R requires version 2.4 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   argument 'lib' is missing: using '/home/mkimpel/R_HOME/site-library-2.9.0'
>   C-c C-c
> Execution halted
>
> The downloaded packages are in
>     ‘/tmp/RtmpkGuMs0/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   installation of package 'Biobase' had non-zero exit status
> * Installing *source* package ‘Biobase’ ...
> ** libs
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.9.0
> ------------------------------------------------------------
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN  46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 399-1219  Home
> Skype:  mkimpel
>
> "The real problem is not whether machines think but whether men do." -- B.
> F. Skinner
> ******************************************************************
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793