Makes sense. Thanks.
I'll update my code.
Florian
From: Marc Carlson mcarl...@fhcrc.orgmailto:mcarl...@fhcrc.org
Date: Friday, September 13, 2013 7:38 PM
To: Florian Hahne
florian.ha...@novartis.commailto:florian.ha...@novartis.com
Cc: bioc-devel@r-project.orgmailto:bioc-devel@r-project.org
Hi,
It seems the issue has been resolved with the latest bioc build.
Best wishes
Julian
On 09/15/2013 04:01 PM, Julian Gehring wrote:
Hi,
calling 'head' or 'tail' on a 'RangedData' objects fail with the lastest
builds (R: 2013-09-14 r63932, IRanges: 1.19.35). The cause seems to be
that
I agree that the profile or metagene plot is useful and widely applied.
Creating such a plot consists of several steps, including:
- quantifying and accumulating signal around sites of interest
- normalization
- visualization
The qProfile() function in QuasR was designed to do the
Hey Marc,
I think your move towards seqlevels is not quite working yet:
samplefile - system.file(extdata, UCSC_knownGene_sample.sqlite,
package=GenomicFeatures)
txdb - loadDb(samplefile)
## This works fine
fiveUTRsByTranscript(txdb)
## This breaks
seqlevels(txdb, force=TRUE) - chr6
Thanks Florian,
I just checked in a fix for this. Please let me know if you find any
other quirks.
Marc
On 09/16/2013 05:33 AM, Hahne, Florian wrote:
Hey Marc,
I think your move towards seqlevels is not quite working yet:
samplefile - system.file(extdata, UCSC_knownGene_sample.sqlite,
On 09/15/2013 07:12 AM, Wolfgang Huber wrote:
Dear Julian
thanks.
Since this has come up here and elsewhere, and since the next Bioc release is coming up,
let's remind ourselves that we should make development against 3.0.1 Patched (2013-09-03
r63824) -- Good Sport.
Martin - should this be
Bioconductor developers:
The Bioc release schedule is available
http://bioconductor.org/developers/release-schedule/
A reminder that version 2.13 of Bioconductor will be released on October 15, and
will work with R-3.0.2. Package authors should be testing the Bioc 'devel'
version of their
On Sep 16, 2013, at 01:46 PM, Brian Rowe wrote:
That reminds me: I once made a suggestion on how to automate some of the CRAN
deployment process, but it was shot down as not being useful to them. I do
recall a quote that was along the lines of as long as you don't need help,
do whatever you
Ben Bolker wrote :
Do you happen to remember what the technical difficulty was?
From memory I think it was that CRAN maintainers didn't have
access to Uwe's winbuilder machine. But often when I get OK
from winbuilder R-devel I don't want it to go to CRAN yet. So
procedures and software would
On 16.09.2013 01:04, Ben Bolker wrote:
Uwe Ligges ligges at statistik.tu-dortmund.de writes:
Setting
BuildVignettes: false
is fine if it is possible to build the vignettes, and the latter is
checked in CRAN incoming checks (but not the daily checks).
Uwe Ligges
Hmmm. I was told by
On 09/15/2013 11:09 AM, Matthew Dowle wrote:
I'm a little surprised by this thread.
I subscribe to the RSS feeds of changes to NEWS (as Dirk mentioned) and
that's been pretty informative in the past :
http://developer.r-project.org/RSSfeeds.html
Mainly though, I submit to winbuilder before
On 13-09-16 3:59 AM, Göran Broström wrote:
On 09/15/2013 11:09 AM, Matthew Dowle wrote:
I'm a little surprised by this thread.
I subscribe to the RSS feeds of changes to NEWS (as Dirk mentioned) and
that's been pretty informative in the past :
http://developer.r-project.org/RSSfeeds.html
On 13-09-15 9:58 PM, Yihui Xie wrote:
I've been watching this thread closely and trying not to chime in,
because as Brian Rowe mentioned about CRAN's mysterious absence in a
previous reply.
It's no mystery that they don't discuss CRAN policies on this list.
That's been stated many times. I
Hi,
A colleague recently came across an R crash, which I can boil down to
the following, running under Rgui on Windows 7:
library(ggplot2)
ggplot(data.frame(x=1, y=1, z=4.7), aes(x, y, z=z)) + stat_summary2d()
This reliably causes a segmentation fault. sessionInfo() below.
What's happening is
On 09/16/2013 12:38 PM, Duncan Murdoch wrote:
On 13-09-16 3:59 AM, Göran Broström wrote:
On 09/15/2013 11:09 AM, Matthew Dowle wrote:
I'm a little surprised by this thread.
I subscribe to the RSS feeds of changes to NEWS (as Dirk mentioned) and
that's been pretty informative in the past
I haven't used rforge, but I will look check out the scripts. The reason it
would be a six-pack of work is that there are generic build systems that handle
most of this work. What they don't do is act as a repository, so rforge could
remain that while separating out the build process.
On Sep
On 16.09.2013 13:52, Göran Broström wrote:
On 09/16/2013 12:38 PM, Duncan Murdoch wrote:
On 13-09-16 3:59 AM, Göran Broström wrote:
On 09/15/2013 11:09 AM, Matthew Dowle wrote:
I'm a little surprised by this thread.
I subscribe to the RSS feeds of changes to NEWS (as Dirk mentioned)
Dear all,
my apologies for posting here instead of rcpp-devel (registration for
which did not seem to work). I try to use a Rcpp module outside a
package using the following code which should work according to posts on
this list/rcpp-devel.
library('Rcpp');
dlr = dyn.load('build/libtestlib.so');
On 16 September 2013 at 16:12, Stefan Boehringer wrote:
| my apologies for posting here instead of rcpp-devel (registration for
| which did not seem to work).
It is using the standard Python mailman software, as do lots of other lists.
Your From: field _must_ match you registration. That is the
(subject changed from Re: [Rd] declaring package dependencies )
...
Yes useful. But that includes a package build system (which is what
breaks on
R-Forge). If you could do that on a six-pack then could you fix R-Forge
on a
three-pack first please? The R-Forge build system is itself an open
On 16/09/13 16:11, Paul Gilbert wrote:
(subject changed from Re: [Rd] declaring package dependencies )
...
Yes useful. But that includes a package build system (which is what
breaks on
R-Forge). If you could do that on a six-pack then could you fix R-Forge
on a
three-pack first please? The
On 13-09-16 05:19 AM, Uwe Ligges wrote:
...
Yes, and I could see really rare circumstances where vignette building
takes a long time and the maintainer decides not to build vignettes as
part of the daily checks.
...
I thought 'BuildVignettes: FALSE' only turns of assembling the pdf, all
the
Any chance some improvements can be made on table()?
table() is probably one of the most used R functions when working
interactively. Unfortunately it can be incredibly slow, especially
on a logical vector where a simple sum() is hundred times faster
(I actually got into the habit of using sum()
Hello!
Over the weekend, I updated my RcmdrPlugin.qual package.
It works fine on a 64 bit Windows machine but not a 32 bit. This is very
strange. The new menu with all of the Quality Control stuff does not appear.
Have any of you run into this sort of thing before, please?
Thanks,
Dear Erin,
I noticed that your RcmdrPlugin.qual package declares qcc under Suggests, and
thus qcc isn't necessarily installed along with the plug-in. The menu file for
your plug-in requires the presence of qcc to install most of the menu items
under the Quality Control menu.
I installed your
Given:
$JAVA_HOME=~/jdk1.7.0_40
$R_SHELL=/bin/sh
$PATH=$R_HOME/bin:$JAVA_HOME/bin:...
which jar -- ~/jdk1.7.0_40/bin/jar
which javac -- ~/jdk1.7.0_40/bin/javac
which javah -- ~/jdk1.7.0_40/bin/javah
which java -- '', even though there is one in $JAVA_HOME/bin
whereis java --
java: /bin/java
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