[Bioc-sig-seq] BSgenome installation error from SVN

[Droit Arnaud]

Hi Nicolas,

I had the same problem with the BSgenome packages from SVN.
I tried different installation and desinstallation with different version of BSgenome, Biostrings, IRanges....

Finally, I resolved my problem by installing the latest build of R-dev (version.string R version 2.11.0 Under development (unstable) (2010-02-18 r51149).

Good luck,

Arnaud.

> sessionInfo()

R version 2.11.0 Under development (unstable) (2010-02-18 r51149)

x86_64-apple-darwin10.2.0

locale:

[1] fr_CA.UTF-8/fr_CA.UTF-8/C/C/fr_CA.UTF-8/fr_CA.UTF-8

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:

[1] BSgenome_1.15.7    Biostrings_2.15.21 IRanges_1.5.47

loaded via a namespace (and not attached):

[1] Biobase_2.7.4




Le 2010-02-19 à 08:51, Nicolas Delhomme a écrit :

Hi all,

Since a few days, I get the following error message when trying to
install BSgenome from my svn checkout directory (R CMD INSTALL --
preclean --clean BSgenome):

 installing *source* package ‘BSgenome’ ...
** R
** inst
** preparing package for lazy loading
Error in conformMethod(signature, mnames, fnames, f, fdef, definition) :
  in method for ‘start<-’ with signature ‘x="GRanges"’: formal
arguments (check = "NA") omitted in the method definition cannot be in
the signature
Error : unable to load R code in package 'BSgenome'
ERROR: lazy loading failed for package ‘BSgenome’

The details about the checkout are (svn info BSgenome/):

Path: BSgenome
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BSgenome
Repository Root: https://hedgehog.fhcrc.org/bioconductor
Repository UUID: bc3139a8-67e5-0310-9ffc-ced21a209358
Revision: 44766

My current sessionInfo:

R version 2.10.1 Patched (2010-02-14 r51142)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BSgenome_1.15.4    Biostrings_2.15.21 IRanges_1.5.47

loaded via a namespace (and not attached):
[1] Biobase_2.7.4 tools_2.10.1

Any idea what is happening there? Instead of patching my R with the R-
release.diff.gz, should I install R-devel?

Thanks for any help,

Cheers,

---------------------------------------------------------------
Nicolas Delhomme

High Throughput Functional Genomics Center

European Molecular Biology Laboratory

Tel: +49 6221 387 8426
Email: nicolas.delhomme at embl.de<mailto:nicolas.delhomme at embl.de>
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany

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