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

[Nicolas Delhomme]

Hi folks, just to clarify.

1) I'm extensively working with Rsamtools and this package is in very  
active development (Thanks Martin!) which means that I do not want to  
wait for the package to be available through biocLite (which for me is  
1 and 1/2 day after any bug correction has been published on the  
mailing list). So, thanks Sean, but I need the SVN checkout , so a  
life with a production R and biocLite will remain an utopia for me...  
Luckily, I have no problem dealing with the dependancies by myself.

2) Kasper, maybe I was naive, but well, I expected that patching a  
"production" R with the latest development patch (the R- 
release.diff.gz) would result in the same as using a "development" R.  
I mean, that is the whole purpose of that diff file, right?

So, either I might have been expecting too much, or (thanks Arnaud for  
making me feel less alone and, well, possibly not that crazy ;-) )  
that might be an R related issue (r51142 fails for me, r51149 works  
for you).

Since I've "faith" in R, I got the latest R-release.diff.gz and I've  
patched my R 2.10.1 again. I'll let you know if that fixes the issue.  
Otherwise, I'll just get the R-devel; it's not like the download  
bandwidth would be an issue anyway.

Cheers,

Nico

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

High Throughput Functional Genomics Center

European Molecular Biology Laboratory

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



On 19 Feb 2010, at 15:30, Kasper Daniel Hansen wrote:

> You should _always_ use R-devel when using Bioc-devel.
>
> Kasper
>
> On Fri, Feb 19, 2010 at 9:20 AM, Droit Arnaud  
> <Arnaud.Droit at ircm.qc.ca> wrote:
>> 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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>> >
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