[Bioc-sig-seq] BSgenome installation error from SVN
Wolfgang Huber
whuber at embl.de
Fri Feb 19 23:53:22 CET 2010
Hi all,
if you want to work with "devel" versions: on most days, I get good results by running the following shell script in the morning while I go get my coffee. (Important disclaimer: this procedure is not 100% safe and on some days, you'll have to do manually reinstall packages that rely on properties of R that have changed 'under them'; or, to "make distclean" instead of "make clean"; or wipe out and again check out the whole R svn tree):
## --------------------------------
## Update shell script
## --------------------------------
#!/bin/bash
set -e
set -o errexit
cd $HOME
svn up madman # https://hedgehog.fhcrc.org/bioconductor/trunk/madman
svn up R # https://svn.r-project.org/R/trunk
cd R
./tools/rsync-recommended
make clean
if [ "$(uname)" = "Darwin" ]; then
./configure --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib
else
./configure
fi
make
echo "update.packages(ask=F)" | R --no-save
## --------------------------------
## Furthermore, I have these lines in ~/.Rprofile:
## (you need to update this with every Bioconductor release)
## --------------------------------
Rvers = as.numeric(version$minor)
basename = "http://bioconductor.org/packages"
biocUrls = c("bioc", "data/annotation", "data/experiment", "extra")
if(Rvers >=11.0) repos=paste(basename, biocUrls, sep="/2.6/") else
if(Rvers >=10.0) repos=paste(basename, biocUrls, sep="/2.5/") else
stop("Zapperlot")
options(repos=c(CRAN="http://cran.fhcrc.org",
repos, OMEGAHT="http://www.omegahat.org/R"))
rm(list=c("Rvers", "basename", "biocUrls", "repos"))
Il giorno Feb 19, 2010, alle ore 5:07 PM, Nicolas Delhomme ha scritto:
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
>>>>
>>>> _______________________________________________
>>>> Bioc-sig-sequencing mailing list
>>>>
>>>> Bioc-sig-sequencing at r-project.org<mailto:Bioc-sig-sequencing at r-project.org
>>>> >
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>
>>>> _______________________________________________
>>>> Bioc-sig-sequencing mailing list
>>>> Bioc-sig-sequencing at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>
>>
>>
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Wolfgang Huber
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