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

[Dan Tenenbaum]

Hi all,


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.
>

This has been added to BiocInstaller 1.2.1 (release) and 1.3.3 (devel).
You can install all Bioconductor software packages with
biocLite(all_group())

See ?all_group and ?biocLite for more info.

Thanks,
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
>> >
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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