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

[Sean Davis]

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
>
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