[BioC] Errors using biocLite on Apple OS X

[Herve Pages]

Hi Steven,

I can see warnings only in what you reported. These warnings
are well-known issues but are not biocLite problems: they are
Mac OS X install.packages() specific issues.

The first warning:
  1: number of rows of result
       is not a multiple of vector length (arg 2) in: cbind(1, res0, 
Repository = repos)
is issued by install.packages() when it is given a repos vector with 
length >= 4.
You can easily reproduce it with:
  > repos <- c("http://bioconductor.org/packages/1.8/bioc",
     "http://bioconductor.org/packages/1.8/data/annotation",
     "http://bioconductor.org/packages/1.8/data/experiment",
     "http://bioconductor.org/packages/1.8/omegahat",
     "http://bioconductor.org/packages/1.8/lindsey",
     "http://cran.fhcrc.org")
  > install.packages("Biobase", repos=repos)

The second warning is a permission issue specific to Mac OS X.

Anyway, these warnings should not prevent biocLite to install the requested
packages correctly.

Cheers,

H.


Steven McKinney wrote:
> I've recently started using R and Bioconductor
> on an Apple Mac running OS X (10.4). I've been
> installing packages from the *nix command line,
> one by one, no trouble.
>
> I would like to be able to update using
> biocLite from the R gui, but keep getting
> errors.
>
>
>> version
> _
> platform powerpc-apple-darwin8.6.0
> arch powerpc
> os darwin8.6.0
> system powerpc, darwin8.6.0
> status
> major 2
> minor 3.1
> year 2006
> month 06
> day 01
> svn rev 38247
> language R
> version.string Version 2.3.1 (2006-06-01)
>
>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("Biobase", destdir = 
>> "/Volumes/KilroyHD/kilroy/Software/BioConductor")
> Running getBioC version 0.1.6 with R version 2.3.1
> Running biocinstall version 1.8.4 with R version 2.3.1
> Your version of R requires version 1.8 of Bioconductor.
> trying URL 
> 'http://bioconductor.org/packages/1.8/bioc/bin/macosx/powerpc/contrib/2.3/Biobase_1.10.1.tgz'
> Content type 'application/x-gzip' length 1465858 bytes
> opened URL
> ==================================================
> downloaded 1431Kb
>
> Warning messages:
> 1: number of rows of result
> is not a multiple of vector length (arg 2) in: cbind(1, res0, 
> Repository = repos)
> 2: cannot create HTML package index in: make.packages.html()
>
>
> I am using version 1.10.1 of Biobase, I presume this is the
> version number for Bioconductor.
>
> I see a few others reporting similar errors
> when I google this issue, but I see no posted
> solutions. Can anyone see what I am doing wrong,
> and is there a solution?
>
> Any info appreciated
>
>
> Best regards
>
> Steven McKinney
>
> Statistician
> Molecular Oncology and Breast Cancer Program
> British Columbia Cancer Research Centre
>
> email: smckinney at bccrc.ca
>
>
>
> BCCRC
> Molecular Oncology
> 675 West 10th Ave, Floor 4
> Vancouver B.C.
> V5Z 1L3
> Canada
>
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Hervé Pagès
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