problem with biocLite("Biobase") -- results in looping of download
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@martin-morgan-1513
Last seen 3 days ago
United States
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_IDEN TIFICATION=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 > 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
Cancer Biobase Cancer Biobase • 1.1k views
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@cei-abreu-goodger-4433
Last seen 9.1 years ago
Mexico
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;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=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 >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Mark W Kimpel ▴ 830
@mark-w-kimpel-2027
Last seen 9.6 years ago
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@fhcrc.org> wrote: > Hi Mark -- > > Mark Kimpel <mwkimpel@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_IDEN TIFICATION=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@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 > [[alternative HTML version deleted]]
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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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