I'm attempting to install Bioconductor under Debian following the instructions here: http://www.bioconductor.org/faq.html#getBioC Apparently, I don't have enough room in /tmp to untar the tar files. What is the "R way" to specify an alternate /tmp folder to use while installing Bioconductor? "export TMPDIR=" comes to mind. Also, can a failed install be "restarted" so that it will continue from where it failed? Regards, - Robert

Hi Robert, Sorry for the delay in response. We've been busy preparing the Bioconductor 1.6 release. Robert Citek <rwcitek@alum.calberkeley.org> writes: > I'm attempting to install Bioconductor under Debian following the > instructions here: > > http://www.bioconductor.org/faq.html#getBioC > > Apparently, I don't have enough room in /tmp to untar the tar files. > What is the "R way" to specify an alternate /tmp folder to use while > installing Bioconductor? "export TMPDIR=" comes to mind. Yes, exporting TMPDIR should result in files downloaded by getBioC being placed in TMPDIR. The new getBioC script for Bioconductor 1.6 will be modifed to accept an argument specifying where to download packages, but that isn't quite available yet (check back next week). > Also, can a failed install be "restarted" so that it will continue > from where it failed? Unfortunately, no, this isn't supported. + seth

You should also be able to install core parts of bioconductor you require providing the appropriate arguement for a subset of packages which hopefully wont fill up your assigned temp directory. e.g. getBioC("affy") ## - packages "affy", "affydata", ## "affyPLM", "annaffy", "matchprobes", ## "gcrma", "makecdfenv", plus exprs. see http://www.bioconductor.org/faq.html#getBioC, and the first few lines of getBioC. You can also download packages separately (e.g. development versions of packages) and install them from the command line, R CMD INSTALL [package].tar.gz, many packages have dependancies (usual installation path on linux is something like /usr/local/lib/R/library/[package]). Marcus >>> Robert Citek <rwcitek@alum.calberkeley.org> 20/05/2005 8:47:40 a.m. >>> On May 20, 2005, at 12:13 AM, Seth Falcon wrote: > Sorry for the delay in response. We've been busy preparing the > Bioconductor 1.6 release. No worries. Thanks for the reply. And thanks to you and everyone else involved in making 1.6. > Robert Citek <rwcitek@alum.calberkeley.org> writes: > >> I'm attempting to install Bioconductor under Debian following the >> instructions here: >> >> http://www.bioconductor.org/faq.html#getBioC >> >> Apparently, I don't have enough room in /tmp to untar the tar files. >> What is the "R way" to specify an alternate /tmp folder to use while >> installing Bioconductor? "export TMPDIR=" comes to mind. >> > > Yes, exporting TMPDIR should result in files downloaded by getBioC > being placed in TMPDIR. Great. I'll give that a shot in the morning. Since I last posted, my short-term work around was to create a soft- link, pointing /tmp to a partition with more room. Once I did that BioC seemed to hum along nicely. Since I did this on Thursday night, I suspect that I've already installed BioC 1.6. Regards, - Robert _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}

Robert Citek <rwcitek@alum.calberkeley.org> writes: > Since I last posted, my short-term work around was to create a soft- > link, pointing /tmp to a partition with more room. Once I did that > BioC seemed to hum along nicely. Since I did this on Thursday night, > I suspect that I've already installed BioC 1.6. The new-and-improved (famous last words) getBioC script detects your version of R and downloads Bioc 1.5 for R 2.0.x and Bioc 1.6 for R 2.1.x. So it would be prudent to verify your version of R and the version of a few Bioconductor packages. + seth

Robert Citek <rwcitek@alum.calberkeley.org> writes: > I used TMPDIR this time and it's working great. I pointed it to a > nice large partition. Glad to hear it. > As for the version, I did an 'apt-get install r-base libxml2-dev g77 > atlas3-base-dev' which installed R v2.1.0. So, I assume I'm now > installing BioC 1.6. How can I tell? That is, how can I display > what version of BioC is installed? Well, there isn't a global Bioc version that you get query. The best thing to do is to compare the version numbers of a few packages against what is on the Bioconductor website. For example, > library(Biobase) > sessionInfo() R version 2.1.0, 2005-04-29, x86_64-unknown-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: Biobase "1.5.12" And then verify the version here: http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/ > BTW, for notes on what I'm doing: > > http://www.cwelug.org/cgi-bin/wiki.cgi?BioConductor That looks quite interesting. If you get this working I would love to try it out! + seth

The following lookup in R may also be useful as an alternative to lookup from the http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/ url. You can obtain a list of dependancies (and more). a <- CRAN.packages(CRAN=getOption("BIOC")) a[,c("Package","Version","Depends")] Package Version Depends aCGH "aCGH" "1.1.4" "R (>= 1.8.0), cluster, repeated, rmutil, survival, multtest,\nsma" affy "affy" "1.5.8-1" "R (>= 1.9.0), Biobase (>= 1.4.22), reposTools" affycomp "affycomp" "1.4.3" "R (>= 1.8.1), Biobase (>= 1.1.0)" affydata "affydata" "1.4.0" "R (>= 1.6.2), affy (>= 1.2)" affylmGUI "affylmGUI" "1.2.5" "limma, tcltk, affy" ... > packageDescription("affy", field="Version") [1] "1.5.8-1" This list should be querying the current release packages of Biocondcutor 1.6. Can somebody verify that? Marcus >>> Kasper Daniel Hansen <k.hansen@biostat.ku.dk> 20/05/2005 10:21:18 p.m. >>> It could in principle be scritable and might even be a little worthwhile to do it. But basically the BioC version number is corresponds to a whole list of individual package numbers. As sson as you move away from the getBioC script you can have a big mix of development and release level packages. Kasper On Fri, May 20, 2005 at 02:40:04PM -0500, Robert Citek wrote: > > On May 20, 2005, at 11:52 AM, Seth Falcon wrote: > >Well, there isn't a global Bioc version that you get query. The best > >thing to do is to compare the version numbers of a few packages > >against what is on the Bioconductor website. > > > >For example, > > > >>library(Biobase) > >>sessionInfo() > >> > >R version 2.1.0, 2005-04-29, x86_64-unknown-linux-gnu > > > >attached base packages: > >[1] "tools" "methods" "stats" "graphics" "grDevices" > >"utils" > >[7] "datasets" "base" > > > >other attached packages: > > Biobase > >"1.5.12" > > > >And then verify the version here: > >http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/ > > I'm not that familiar with R, but I imagine that the above is > scriptable. That is, I should be able to traverse the package > dependency tree and query each package for its version. Is that > possible within R? > > Regards, > - Robert > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}

Hi Marcus, "Marcus Davy" <mdavy@hortresearch.co.nz> writes: > The following lookup in R may also be useful as an alternative to > lookup from the > http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/ > url. You can obtain a list of dependancies (and more). > > a <- CRAN.packages(CRAN=getOption("BIOC")) Yes, that's a good way to get detail on packages available in the Bioconductor repositories. > This list should be querying the current release packages of > Biocondcutor 1.6. Can somebody verify that? Actually, it depends... If you are running an R that installes source packages (a unix-like R), then yes, you will get a listing of the Bioc 1.6 packages. OTOH, if you are running an R that wants binary packages by default (Windows R, some OSX R), then the listing you will get depends on the version of R you have --- this is a good thing because Bioconductor releases are designed for a particular version of R. We hope to have this automatic selection working for source packages in the next release. Best, + seth

getBioC has been updated: When using R 2.1.x, it accepts a destdir argument, similar to install.packages and friends, that will be used as the path to write downloaded packages to. This provides an alternative to setting TMPDIR. We'll be working on an improvement to allow a "resume" after an interupted installation. Best, + seth