[Bioc-sig-seq] BSgenome installation error from SVN
Nicolas Delhomme
delhomme at embl.de
Fri Feb 19 17:07:41 CET 2010
Hi Kasper,
Thanks for refreshing my confused mind (not that I didn't know it);
seems like some of my synapses must have misfired one day because I
was convinced that the diff file had to do with devel. I'll RTFM more
attentively next time.
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 16:50, Kasper Daniel Hansen wrote:
> On Fri, Feb 19, 2010 at 10:26 AM, Nicolas Delhomme
> <delhomme at embl.de> wrote:
>> 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?
>
> Well, your expectation is completely wrong which is why you are
> running into this issue.
>
> Let me do a short recap of what happens, since you are clearly a bit
> confused.
>
> When R-2.10 was released, they immediately created two branches of R:
> 2.10-patched (known as R-patched) and devel. These branches are
> separate. The only things that enter into the 2.10 branch is bug
> fixes. When enough bug fixes has accumulated a minor version of R
> gets release (like R-2.10.1). All new functionality is in devel.
> This is an extremely big difference. All the release-diff does, is
> track the difference between the R-2.10 release and the patch branch
> of 2.10. So applying the diff means you essentially create the latest
> R-patched. Devel is completely different.
>
> All of this is done to make sure that a user of R-2.10 can get bug
> fixes, without getting new - perhaps non-compatible - functionality
> changes.
>
> Bioc-devel uses R-devel, not R-patched.
>
> Kasper
>
>> 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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>>>> >
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>>>>
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>>
>>
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