[Bioc-devel] Error in biocLite(groupName="all") - unused argument(s) (groupName="all") on Linux and MacOS X platform

[Dan Tenenbaum]

On Tue, Nov 8, 2011 at 3:49 AM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> 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.


Christian and Michael,

Before changing BiocInstaller I'd want to understand why you are
attempting to install all Bioconductor software packages. I'm not sure
it's a good idea, even for a shared R installation with many users.
For one thing, many packages have external system dependencies, and
unless all those are set up just right, many of the packages you
download are guaranteed not to work.

Why not just install the packages you need, either before the fact or
as you need them?

Dan


>
> Thanks,
> Michael
>
> On Tue, Nov 8, 2011 at 3:38 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> On Tue, Nov 8, 2011 at 5:14 AM, Christian Kohler
>> <christian.kohler at 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 at klinik.uni-regensburg.de
>> >
>> > _______________________________________________
>> > Bioc-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>        [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>