[Bioc-devel] Error in biocLite(groupName="all") - unused argument(s) (groupName="all") on Linux and MacOS X platform
Christian Kohler
christian.kohler at klinik.uni-regensburg.de
Wed Nov 9 09:49:20 CET 2011
On 11/08/2011 07:30 PM, Sean Davis wrote:
> 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
>
Hi Sean
I myself could not have said it better.
A full BioC installation makes admin life easier, less time consuming and is easy to script.
You'll never know what package your teammates wanna to play around with.
Thanks for all the replies and the quick implementation :-)
Best
Christian
>>>
>>> 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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>>
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--
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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