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