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

Tue Nov 8 19:30:44 CET 2011

On Tue, Nov 8, 2011 at 11:22 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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?

I see you already implemented the change--thanks.  Just to answer your
question, it is just convenient and is definitely useful in a shared
environment (where I serve as system admin and don't want to hear
about package installation).  For those packages with external
dependencies, I let those fail and ignore them unless there is a
pressing need.

Sean

>>
>> 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
>>>
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