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: [email protected]
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
<[email protected]> 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: [email protected]
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 <[email protected]
>
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: [email protected]<mailto:[email protected]>
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
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