Would be great if Sean's script could make it into BiocInstaller. The
admins here hit the same issue, and I wrote the exact same script for them.

Thanks,
Michael

On Tue, Nov 8, 2011 at 3:38 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Tue, Nov 8, 2011 at 5:14 AM, Christian Kohler
> <christian.kohler@klinik.uni-regensburg.de> wrote:
> > Dear Bioconductors,
> >
> > with the current BioC release, I observed the following error while
> running biocLite(groupName="all") on MacOS X - Snow Leopard as well as on a
> Linux
> > machine (x86_64-unknown-linux-gnu (64-bit)
> >
> >> source("http://www.bioconductor.org/biocLite.R")
> > BiocInstaller version 1.2.0, ?biocLite for help
> >> biocLite(groupName="all")
> > BioC_mirror: 'http://www.bioconductor.org'
> > Using R version 2.14, BiocInstaller version 1.2.0.
> > Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
> > Installing package(s) into ‘/Users/ckohler/Library/R/2.14/library’
> > (as ‘lib’ is unspecified)
> > also installing the dependencies ‘DBI’, ‘RSQLite’
> >
> > Error in download.file(url, destfile, method, mode = "wb", ...) :
> >  unused argument(s) (groupName = "all")
> > Warning in download.packages(pkgs, destdir = tmpd, available =
> available,  :
> >  download of package ‘DBI’ failed
> > Error in download.file(url, destfile, method, mode = "wb", ...) :
> >  unused argument(s) (groupName = "all")
> > Warning in download.packages(pkgs, destdir = tmpd, available =
> available,  :
> >  download of package ‘RSQLite’ failed
> > Error in download.file(url, destfile, method, mode = "wb", ...) :
> >  unused argument(s) (groupName = "all")
> > Warning in download.packages(pkgs, destdir = tmpd, available =
> available,  :
> >  download of package ‘Biobase’ failed
> > Error in download.file(url, destfile, method, mode = "wb", ...) :
> >  unused argument(s) (groupName = "all")
> > Warning in download.packages(pkgs, destdir = tmpd, available =
> available,  :
> >  download of package ‘IRanges’ failed
> > Error in download.file(url, destfile, method, mode = "wb", ...) :
> >  unused argument(s) (groupName = "all")
> > Warning in download.packages(pkgs, destdir = tmpd, available =
> available,  :
> >  download of package ‘AnnotationDbi’ failed
> >
>
> Hi, Christian.
>
> The groupName argument does not exist anymore.  Note that with the
> introduction the BiocInstaller package, you can read help for
> biocLite().
>
> To reproduce groupName="all", try the following:
>
> source('http://bioconductor.org/biocLite.R')
> pkglist =
> available.packages(contriburl=contrib.url(biocinstallRepos()['BioCsoft'],type='mac.binary.leopard'))
> pkgs = rownames(pkglist)
> biocLite(pkgs)
> # wait..........
>
> Hope that helps.
>
> Sean
>
> >> sessionInfo()
> > R version 2.14.0 (2011-10-31)
> > Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] BiocInstaller_1.2.0
> >
> > loaded via a namespace (and not attached):
> > [1] tools_2.14.0
> >
> >
> > with BioC 2.8, biocLite(groupName="all") behaves as expected:
> > ===========================================
> > source("http://www.bioconductor.org/biocLite.R")
> > BioC_mirror = http://bioconductor.org
> > Change using chooseBioCmirror().
> >> biocLite(groupName="all")
> > Using R version 2.13.2, biocinstall version 2.8.4.
> > Installing Bioconductor version 2.8 packages:
> >  [1] "ABarray"               "ACME"                  "ADaCGH2"
> >  [4] "AffyCompatible"        "AffyExpress"           "AffyTiling"
> > ... List continues until ....
> > [463] "xcms"                  "xmapbridge"            "xmapcore"
> > [466] "xps"                   "yaqcaffy"
> >
> >  sessionInfo()
> > R version 2.13.2 (2011-09-30)
> > Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> > locale:
> > [1] C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices datasets  utils     methods   base
> >
> > other attached packages:
> > [1] R.utils_1.7.4     R.oo_1.8.0        R.methodsS3_1.2.1
> >
> > loaded via a namespace (and not attached):
> > [1] tools_2.13.2
> >
> >
> > Did I miss an official announcment that tackles this kind of problem?
> >
> > Many Thanks for any hint(s).
> >
> > best
> > Christian
> >
> >
> >
> >
> > --
> >
> > Christian Kohler
> > Institute of Functional Genomics
> >  ~ Statistical Bioinformatics ~
> > University of Regensburg (BioPark I)
> > D-93053 Regensburg (Germany)
> >
> > Tel. +49 941 943 5055
> > Fax  +49 941 943 5020
> > christian.kohler@klinik.uni-regensburg.de
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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