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

[Cei Abreu-Goodger]

Maybe related... (probably not, though)

I had some problems with "looping" biocLite install errors, after a new 
R install.

The R --vanilla didn't work, but what did work was to simply rename my 
~/.Rprofile

Apparently at some point during the install R is called to install 
packages, and at that point my .Rprofile was being loaded and it would 
complain that Biobase wasn't already installed.

Cheers,

Cei

Martin Morgan wrote:
> 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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