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

[Christian Kohler]

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


> 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