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

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

       [[alternative HTML version deleted]]