[BioC] problem with biocLite("Biobase") -- results in looping of download
Martin Morgan
mtmorgan at fhcrc.org
Wed May 20 23:58:58 CEST 2009
Hi Mark --
So the reproducible example is, I guess
% cat > .Rprofile
source("http://bioconductor.org/biocLite.R")
biocLite("Biobase")
^D
% R
There were extensive changes to package build / installation during the
last release. I'll forward this to R-devel, and look a little more my self.
One work-around might be to add something along the lines of
if (interactive()) {
source('http://bioconductor.org/biocLite.R')
biocLite('Biobase')
}
at least if you start from the command line; only the first invocation
is interactive.
Martin
Mark Kimpel wrote:
> Sorry took me a bit to get to this, was out of the office yesterday.
>
> The problem seems to only occur if I try to execute biocLite("Biobase")
> from within my .Rprofile OR if I have tried and failed with this,
> escaped, and then retry without rebooting R. If I completely leave it
> out of my .Rprofile it will run normally from within R. This is
> definitely new behavior as this has worked well for me for over a year.
> It actually doesn't run every time, it is actually wrapped in a function
> so that it only runs once a week (which I stripped out for diagnostic
> purposes, that wrapper is not the problem).
>
> It seems like something internal to R or biocLite has changed, any idea
> what it could be?
>
> Mark
> ------------------------------------------------------------
> 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
> ******************************************************************
>
>
> On Mon, May 18, 2009 at 10:48 PM, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> wrote:
>
> Hi Mark --
>
> Mark Kimpel <mwkimpel at gmail.com <mailto: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
> > ******************************************************************
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch <mailto:Bioconductor at stat.math.ethz.ch>
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> 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
>
>
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