On Wed, Nov 14, 2012 at 11:58 AM, Richard Friedman
fried...@cancercenter.columbia.edu wrote:
On Nov 14, 2012, at 2:52 PM, Dan Tenenbaum wrote:
It looks like the binary version of RCurl was built using R 2.15.1 and
not R-devel.
You can get around this by installing RCurl from source
Hi Richard,
On Mon, Nov 26, 2012 at 10:04 AM, Richard Friedman
fried...@cancercenter.columbia.edu wrote:
Dear Bioconductor Developers,
Released versions of Bioconductor packages generally come with an R
script which
contains what is done in the vignettes. Are these also available
On Mon, Nov 26, 2012 at 10:30 AM, Richard Friedman
fried...@cancercenter.columbia.edu wrote:
Tim and Dan,
Thank you both for for your replies. Dan's worked but it gave
me the released as distinct from the development version,
My mistake. Substitute devel for release in both URLs and you'll
On Sun, Dec 16, 2012 at 1:16 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote:
From http://stat.ethz.ch/R-manual/R-devel/NEWS:
It is intended that this version will be released as R 3.0.0.
They've already changed the R-devel version number from 2.16.0 to
3.0.0, which causes biocLite() et
Hi Anita,
On Thu, Jan 24, 2013 at 2:33 PM, Anita Lerch lerch.an...@gmail.com wrote:
Hi,
is there a way to access the log file of the unit-tests
(e.g. QuasR.Rcheck/tests/QuasR_unit_tests.Rout.fail) on the build system?
Currently I have failing test on george2, which I can't reproduce on my
On Thu, Jan 24, 2013 at 3:04 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi Anita,
On Thu, Jan 24, 2013 at 2:33 PM, Anita Lerch lerch.an...@gmail.com wrote:
Hi,
is there a way to access the log file of the unit-tests
(e.g. QuasR.Rcheck/tests/QuasR_unit_tests.Rout.fail) on the build system
On Wed, Feb 6, 2013 at 10:04 AM, Thomas Sandmann
sandmann.tho...@gene.com wrote:
Dear BioC developers,
I upgraded to R 3.0.0 on my Mac (10.6.8) to make my gCMAP package ready for
the next BioC release.
Afterward, I reinstalled all the required BioC packages using biocLite.
My package
Hi Norman,
On Thu, Feb 7, 2013 at 6:59 PM, Norman Pavelka normanpave...@gmail.com wrote:
Hi,
I am sure many of you may have noticed already, but basically every
package in Bioc-devel that has a vignette (i.e. almost every package)
is currently issuing warnings in R CMD check:
On Thu, Feb 7, 2013 at 8:48 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi Norman,
On Thu, Feb 7, 2013 at 6:59 PM, Norman Pavelka normanpave...@gmail.com
wrote:
Hi,
I am sure many of you may have noticed already, but basically every
package in Bioc-devel that has a vignette (i.e. almost
AM
Subject: Reminder: Your Atlassian OnDemand account bioc-internal will
be deactivated soon
Hi Dan Tenenbaum,
I would like to inform you that your Atlassian OnDemand account -
bioc-internal on atlassian.net is due to be deactivated on
11-Feb-2013.
If you wish to continue using Atlassian OnDemand
My apologies, this email was not meant to go to this list.
Dan
On Sat, Feb 9, 2013 at 9:30 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi,
Seems like there was some kind of billing snafu and the people that we
pay for our internal bug tracker did not receive our payment. They are
going
Hi Wolfgang, Martin,
On Sun, Feb 3, 2013 at 8:01 AM, Martin Morgan mtmor...@fhcrc.org wrote:
On 02/03/2013 03:35 AM, Wolfgang Huber wrote:
Hi,
In LaTeX, I like to use the tilde in connection with equation or section
references, e.g. Equation~(\ref{eq:bla}) or Section~\ref{sec:blo}, to
make
On Mon, Mar 4, 2013 at 2:22 AM, Laurent Gatto lg...@cam.ac.uk wrote:
On 4 March 2013 09:57, Antti Honkela antti.honk...@hiit.fi wrote:
According to the build logs my package (tigre) appears to have the same
problem, but I cannot reproduce this on my own install of R-devel (r62117).
Perhaps
On Tue, Mar 5, 2013 at 1:29 PM, Elana Fertig ejfer...@jhmi.edu wrote:
I'm having a similar problem with my package, CoGAPS, which Is giving a
warning for .path.package that does not appear to be anywhere in my code, nor
does it depend on Biobase. Any suggestions would be greatly appreciated!
they are happening; you don't want to suppress an unexpected
warning by mistake.
Dan
Thanks,
Thomas
On Tue, Mar 5, 2013 at 2:03 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Tue, Mar 5, 2013 at 1:29 PM, Elana Fertig ejfer...@jhmi.edu wrote:
I'm having a similar problem with my package
On Wed, Mar 13, 2013 at 4:02 AM, Joern Toedling j.toedl...@imb-mainz.de wrote:
Hello,
I have encountered a strange issue with the plotting function in my package
girafe that I need some help with. I haven't changed anything in the plot
methods or the NAMESPACE of the package recently, and it
would suggest to modify biocLite comment from
## options(repos = http://cran.fhcrc.org;)
to
## options(repos = c(CRAN=http://cran.fhcrc.org;))
Done.
Thanks,
Dan
Thanks for the assistance.
Kachelo
2013/3/13 Dan Tenenbaum dtene...@fhcrc.org
On Wednesday, March 13, 2013
On Sat, Mar 16, 2013 at 6:11 PM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
Posted here in case other people could benefit.
This is great. Various permutations of this issue have bitten us from
time to time.
This is solving an issue with writing a vignette using the doParallel
On Sat, Mar 16, 2013 at 9:21 PM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
Is it possible to get _R_CHECK_TIMINGS_=0 set in the build system when
R CMD check is being run? Not super important, but convenient and it
should be easy to add.
Done. This will be effective in
On Mon, Mar 18, 2013 at 5:39 AM, Stefanie Tauber
stefanie.tau...@univie.ac.at wrote:
Hi,
I am currently working on new BioC package.
R CMD build, check and INSTALL are successfully passed.
I just always get the following warning (when installing the package):
Warning in
On Tue, Mar 19, 2013 at 12:59 AM, Stefanie Tauber
stefanie.tau...@univie.ac.at wrote:
On Mo, 18.03.2013, 17:39, Dan Tenenbaum wrote:
On Mon, Mar 18, 2013 at 5:39 AM, Stefanie Tauber
stefanie.tau...@univie.ac.at wrote:
Hi,
I am currently working on new BioC package.
R CMD build, check
On Thu, Mar 21, 2013 at 1:33 AM, Manuela Benary
manuela.ben...@cms.hu-berlin.de wrote:
Hi,
we are currently developing a package, which has parallel (mclapply)
support for some of the function. Because forking is not supported in
Windows and when using RStudio, the parallel functions fail.
Hi BioC-develers,
On Monday,March 25th, we will stop the Bioconductor release (2.11) builds.
Commits to the 2.11 branch will be disabled.
Our full release schedule is here:
http://www.bioconductor.org/developers/release-schedule/
Thanks,
Dan
___
Package developers --
Each Bioconductor release is accompanied by release notes that mention
new packages and other significant project developments. For the
forthcoming release we would also like to include release notes for
individual packages, so that users have an easy way to survey changes
?
Apologies for the conflicting dates. We will not collate the files
until Monday (April 1) so you have until then.
Thanks,
Dan
Thanks a lot
Gordon
Date: Tue, 26 Mar 2013 13:59:17 -0700
From: Dan Tenenbaum dtene...@fhcrc.org
To: bioc-devel@r-project.org bioc-devel@r-project.org
Subject
On Thu, Mar 28, 2013 at 6:28 AM, Enrica enrica.cal...@gmail.com wrote:
Dear Martin,
we tried that and everything worked correctly.
As I was trying to stress in my previous message, we are unable to
reproduce that segfault reported in george2 build logs. In other
terms, george2 is the only
Hi all,
I wanted to announce a small new feature of the Bioconductor web
site--if there are HTML files in the inst/doc directory of a built
package tarball they will (with the exception of index.html which is a
special case) be linked to on the package landing page.
For packages which have HTML
The BioC 2.12 branch is now ready.
Remember, you always have access to 2 versions of your package:
the release and the devel versions.
Right now the release version of your package (which is not
officially released yet but will be in the next 72 hours if
everything goes well) is in the 2.12
On Wed, Apr 3, 2013 at 9:45 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi Jirka,
On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon xhonj...@stud.fit.vutbr.cz wrote:
Hi,
the latest bioc build of my new package 'triplex' on petty ended with this
error message:
Warning in rgl.init(initValue) : RGL
On Wed, Apr 10, 2013 at 6:13 AM, Levi Waldron lwald...@hsph.harvard.edu wrote:
Dear Bioconductors,
I noticed that the NEWS from my new experimental data package
curatedOvarianData (
http://www.bioconductor.org/packages/2.12/data/experiment/html/curatedOvarianData.html)
didn't make it into
On Fri, May 17, 2013 at 8:22 AM, Steve Lianoglou
lianoglou.st...@gene.com wrote:
Hi,
On Friday, May 17, 2013, Dan Tenenbaum wrote:
On Thu, May 16, 2013 at 10:53 PM, Renaud Gaujoux
ren...@mancala.cbio.uct.ac.za wrote:
Hi,
I am trying to submit a package to Bioconductor with a Suggests
Hi Steffen,
On Tue, May 21, 2013 at 12:40 PM, Steffen Neumann sneum...@ipb-halle.de wrote:
Hi,
On Tue, 2013-05-21 at 11:47 -0400, James W. MacDonald wrote:
Not that I can recall. But I do agree that it is at minimum redundant
and probably just wrong to have R-version requirements for BioC
On Tue, May 21, 2013 at 1:01 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi Steffen,
On Tue, May 21, 2013 at 12:40 PM, Steffen Neumann sneum...@ipb-halle.de
wrote:
Hi,
On Tue, 2013-05-21 at 11:47 -0400, James W. MacDonald wrote:
Not that I can recall. But I do agree
On Thu, Jun 6, 2013 at 1:56 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote:
Hi, I'd like to pick up the discussion on a BatchJobs backend for
BiocParallel where it was left back in Dec 2012 (Bioc-devel thread
'BiocParallel'
On Thu, Jun 6, 2013 at 1:48 AM, Thomas Dybdal Pedersen
thomas...@gmail.com wrote:
Hi
I'm developing a wrapper for the peptide-identification tool MS GF+. The
algorithm is developed in Java and the .jar file has a size around 20 mb.
For the ease of the user, I think it would make sense to
(revision 77902)
+++ DESCRIPTION (working copy)
@@ -1,10 +1,10 @@
Package: AnnotationHubServer
Title: AnnotationHub Server component
-Version: 0.1.3
+Version: 0.1.4
Author: Dan Tenenbaum
Maintainer: Bioconductor Package Maintainer maintai...@bioconductor.org
Description: AnnotationHub Server
On Jun 30, 2013 12:43 PM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
Also, as far as I understand, the package does not get build using the new
commit, if it has already been build with that version number before.
The package is built but not propagated to the web/repository.
Hello,
The afternoon lab schedule for BioC2013 is now available at:
https://secure.bioconductor.org/BioC2013/labs.php
See you there!
Dan
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
On Wed, Jul 10, 2013 at 9:17 AM, Michael Lawrence
lawrence.mich...@gene.com wrote:
If it's an informational message, like one you might log, use message(). If
you're rendering an object as text, like in a show method, use cat().
Another thing to consider is that messages can be suppressed with
On Wed, Jul 10, 2013 at 7:05 AM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
I have just changed the class definition for a core class in bsseq. A
supporting experiment data package, bsseqData, contains two objects of this
core class and now it needs to be updated (specifically
On Wed, Jul 10, 2013 at 10:50 AM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
On Wed, Jul 10, 2013 at 12:38 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Wed, Jul 10, 2013 at 9:17 AM, Michael Lawrence
lawrence.mich...@gene.com wrote:
If it's an informational message, like one
Hi everyone,
There was a lot of talk about shiny at BioC2013 and it seems like a
lot of people are using it for lots of different cool stuff.
Now we are at the point where some contributors want to add shiny apps
to Bioconductor as packages.
We had some discussion internally and decided that
stacks, except each object boils down to a
function/expression (Tengfei and I have a CRAN package called commandr
related to this). Someone should try to make a prototype to explore these
issues then we can start thinking about common infrastructure.
On Fri, Jul 26, 2013 at 12:23 PM, Dan
Hi Winston,
On Mon, Jul 29, 2013 at 2:39 PM, Winston Chang wins...@stdout.org wrote:
Hi everyone -
Great to hear from you all on your thoughts about Shiny. I've tried to
answer some of Dan's questions below...
1) Testing shiny apps
Typically, bioconductor packages have man page
On Tue, Aug 6, 2013 at 3:42 PM, Laurent Gatto lg...@cam.ac.uk wrote:
On 6 August 2013 23:25, Dan Tenenbaum dtene...@fhcrc.org wrote:
Bioconductors,
We've received requests for more customizable notification to package
maintainers (and other interested parties) when a package has build
issues
Hi Laurent,
On Tue, Aug 6, 2013 at 3:42 PM, Laurent Gatto lg...@cam.ac.uk wrote:
On 6 August 2013 23:25, Dan Tenenbaum dtene...@fhcrc.org wrote:
Bioconductors,
We've received requests for more customizable notification to package
maintainers (and other interested parties) when a package
...@gmail.com wrote:
This is awesome, thanks a lot.
On Wed, Aug 7, 2013 at 3:44 AM, Laurent Gatto lg...@cam.ac.uk wrote:
On 7 August 2013 01:20, Dan Tenenbaum dtene...@fhcrc.org wrote:
The web page at
http://www.bioconductor.org/developers/rss-feeds/
has been updated with instructions
On Wed, Aug 28, 2013 at 8:25 AM, Martin Morgan mtmor...@fhcrc.org wrote:
On 08/28/2013 07:38 AM, Wolfgang Huber wrote:
Hi Martin,
thanks! Both of these sound doable, we'll explore. What was the third one?
To clarify, the intermediate form in option 2 should ideally still contain
executable
Hi Renaud,
We're working on a github-svn bridge for Bioconductor packages, but it's not
ready yet. We will definitely announce it when it is ready.
It will supersede the document you're looking at, though there is nothing to
stop you from continuing to use that if you want to.
Dan
-
- Original Message -
From: rcaloger raffaele.calog...@gmail.com
To: raffaele calogero raffaele.calog...@unito.it, bioc-devel@r-project.org
Cc: rcaloger raffaele.calog...@gmail.com
Sent: Thursday, October 3, 2013 6:06:33 PM
Subject: Re: [Bioc-devel] oneChannelGUI devel
On 10/4/13
Just a reminder. Next Wednesday, October 9, is the
Deadline for packages passing R CMD build and check without warning. Some
warnings will be accepted, clarification on the bioc-devel mailing list.
Thanks,
Dan
___
Bioc-devel@r-project.org mailing
- Original Message -
From: Kasper Daniel Hansen kasperdanielhan...@gmail.com
To: bioc-devel@r-project.org
Sent: Saturday, October 5, 2013 5:25:06 PM
Subject: [Bioc-devel] build server
Are the build servers not running over the weekend? I have not seen
a new
build report today.
- Original Message -
From: Dan Tenenbaum dtene...@fhcrc.org
To: Kasper Daniel Hansen kasperdanielhan...@gmail.com
Cc: bioc-devel@r-project.org
Sent: Saturday, October 5, 2013 5:59:39 PM
Subject: Re: [Bioc-devel] build server
- Original Message -
From: Kasper Daniel
- Original Message -
From: Frederic Fournier frederic.bioi...@gmail.com
To: bioc-devel@r-project.org
Sent: Monday, October 7, 2013 12:01:25 PM
Subject: [Bioc-devel] Is it too late to make an update to an existing package?
Hello,
Is it too late to make an update to an existing
Package developers --
Each Bioconductor release is accompanied by release notes that mention
new packages and other significant project developments. For the
forthcoming release we would also like to include release notes for
individual packages, so that users have an easy way to survey changes
Hi,
In accordance with the release schedule at
http://www.bioconductor.org/developers/release-schedule/
Release (BioC 2.12) builds have stopped, and commits to the release branch have
been disabled.
Thanks,
Dan
___
Bioc-devel@r-project.org mailing
- Original Message -
From: Luo Weijun luo_wei...@yahoo.com
To: bioc-devel@r-project.org
Cc: Dan Tenenbaum dtene...@fhcrc.org
Sent: Wednesday, October 9, 2013 11:58:34 AM
Subject: Emergent build and check errors on the Windows Server Re:
[Bioc-devel] release builds have stopped
- Original Message -
From: Jianhong Ou jianhong...@umassmed.edu
To: bioc-devel@r-project.org
Sent: Friday, October 11, 2013 6:13:16 AM
Subject: [Bioc-devel] how could I get new packages list
Hi,
When I check http://master.bioconductor.org/developers/new_packages/
recently, I
Actually much simpler is to look on twitter:
https://twitter.com/@bioconductor
It appears the automated new package feed is still working there.
Dan
- Original Message -
From: Dan Tenenbaum dtene...@fhcrc.org
To: Jianhong Ou jianhong...@umassmed.edu
Cc: bioc-devel@r-project.org
The BioC 2.13 branch is now ready.
Remember, you always have access to 2 versions of your package:
the release and the devel versions.
Right now the release version of your package (which is not
officially released yet but will be in the next 72 hours if
everything goes well) is in the 2.13
- Original Message -
From: Henrik Bengtsson h...@biostat.ucsf.edu
To: bioC-devel bioc-de...@stat.math.ethz.ch
Sent: Wednesday, October 16, 2013 11:11:57 AM
Subject: [Bioc-devel] SUGGESTION: BioC version (e.g. 2.13) to also follow the
x.y(.z) version scheme of Bioc packages
Hi,
- Original Message -
From: Gabriel Becker gmbec...@ucdavis.edu
To: Charles Warden cwar...@coh.org
Cc: bioc-devel@r-project.org
Sent: Wednesday, October 23, 2013 11:55:05 AM
Subject: Re: [Bioc-devel] Running Perl Scripts from R package
Charles,
If you put your scripts (or any
Hi Nicolas,
- Original Message -
From: Nicolas De Jay nicolas.de...@mail.mcgill.ca
To: bioc-devel@r-project.org
Sent: Tuesday, November 5, 2013 4:02:20 PM
Subject: [Bioc-devel] Submitting two strongly related packages (software +
data)
Hi,
I have never used a mailing list
- Original Message -
From: Luo Weijun luo_wei...@yahoo.com
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
Sent: Wednesday, November 6, 2013 8:38:18 AM
Subject: Re: Commit problem in the release branch Re: [Bioc-devel] BioC 2.13
branch created
Dan,
That works
- Original Message -
From: Li Shen shenli@gmail.com
To: bioc-devel@r-project.org
Sent: Wednesday, November 20, 2013 10:54:14 AM
Subject: [Bioc-devel] Help: package builder error messages
Hi,
I'm trying to submit a new package to Bioc. Using the automated
package
builder,
- Original Message -
From: Li Shen shenli@gmail.com
To: Kasper Daniel Hansen kasperdanielhan...@gmail.com
Cc: Dan Tenenbaum dtene...@fhcrc.org, bioc-devel@r-project.org
Sent: Wednesday, November 20, 2013 1:06:47 PM
Subject: Re: [Bioc-devel] Help: package builder error messages
Hi Bioc-devel'ers,
You may notice a message like this when working with your svn working copies:
$ svn up
Updating '.':
Error validating server certificate for 'https://hedgehog.fhcrc.org:443':
- The certificate is not issued by a trusted authority. Use the
fingerprint to validate the
- Original Message -
From: Martin Maechler maech...@stat.math.ethz.ch
To: Kasper Daniel Hansen kasperdanielhan...@gmail.com
Cc: Dan Tenenbaum dtene...@fhcrc.org, Martin Maechler
maech...@stat.math.ethz.ch, bioc-devel@r-project.org
Sent: Wednesday, December 4, 2013 2:09:12 AM
- Original Message -
From: Steve Lianoglou lianoglou.st...@gene.com
To: Ryan C. Thompson r...@thompsonclan.org
Cc: bioc-devel@r-project.org
Sent: Monday, December 16, 2013 10:57:44 AM
Subject: Re: [Bioc-devel] edgeR crashes when xlsxjars is loaded
Hi Ryan,
I ran this code w/
Hi Charles,
- Original Message -
From: Charles Warden cwar...@coh.org
To: bioc-devel@r-project.org
Sent: Monday, January 27, 2014 10:45:42 AM
Subject: [Bioc-devel] Problem running Perl script with R-devel
Hi,
I am testing out my newly released COHCAP package:
- Original Message -
From: Charles Warden cwar...@coh.org
To: Charles Warden cwar...@coh.org, Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
Sent: Monday, January 27, 2014 11:19:46 AM
Subject: RE: [Bioc-devel] Problem running Perl script with R-devel
Hi Dan
- Original Message -
From: Dan Tenenbaum dtene...@fhcrc.org
To: Charles Warden cwar...@coh.org
Cc: bioc-devel@r-project.org
Sent: Monday, January 27, 2014 11:26:43 AM
Subject: Re: [Bioc-devel] Problem running Perl script with R-devel
- Original Message -
From
- Original Message -
From: Charles Warden cwar...@coh.org
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
Sent: Monday, January 27, 2014 11:38:10 AM
Subject: RE: [Bioc-devel] Problem running Perl script with R-devel
Hi Dan,
1) When I first ran the code
- Original Message -
From: Charles Warden cwar...@coh.org
To: Charles Warden cwar...@coh.org, Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
Sent: Monday, January 27, 2014 11:19:46 AM
Subject: RE: [Bioc-devel] Problem running Perl script with R-devel
Hi Dan
Hi Charles,
- Original Message -
From: Charles Warden cwar...@coh.org
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
Sent: Tuesday, January 28, 2014 2:12:09 PM
Subject: RE: [Bioc-devel] Problem running Perl script with R-devel
Hi,
For those interested
Hi all,
We've made available a bridge between Github and the Bioconductor Subversion
repository.
It allows you to do all your work in git and github. Git pushes will propagate
to our Subversion server, and SVN commits will propagate back to git.
If you like git, and the social coding features
Forgot to copy the list
- Forwarded Message -
From: Dan Tenenbaum dtene...@fhcrc.org
To: Mike wjia...@fhcrc.org
Sent: Wednesday, February 5, 2014 2:12:18 PM
Subject: Re: [Bioc-devel] Bioconductor git-svn bridge is available
See
http://www.bioconductor.org/developers/how-to/git-svn
- Original Message -
From: Kasper Daniel Hansen kasperdanielhan...@gmail.com
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
Sent: Saturday, February 8, 2014 6:34:34 PM
Subject: Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available
I have some
- Original Message -
From: J. Hettling j.hettl...@vu.nl
To: bioc-devel@r-project.org
Sent: Thursday, February 13, 2014 4:29:21 AM
Subject: [Bioc-devel] daily build problems, how to debug?
Dear Bioconductor developers,
since updating our package 'BiGGR' on the development
- Original Message -
From: Dan Tenenbaum dtene...@fhcrc.org
To: J. Hettling j.hettl...@vu.nl
Cc: bioc-devel@r-project.org
Sent: Thursday, February 13, 2014 8:08:16 AM
Subject: Re: [Bioc-devel] daily build problems, how to debug?
- Original Message -
From: J
Hello,
- Original Message -
From: Delveri chick chickdelv...@gmail.com
To: bioc-devel@r-project.org
Sent: Wednesday, February 19, 2014 2:27:55 PM
Subject: [Bioc-devel] Greetings
Hi im Chick Delveri Munang an undergraduate student at the university
of
Buea Cameroon(Central
- Original Message -
From: Sean Davis sdav...@mail.nih.gov
To: Kasper Daniel Hansen kasperdanielhan...@gmail.com
Cc: bioc-devel@r-project.org, Dan Tenenbaum dtene...@fhcrc.org
Sent: Friday, February 21, 2014 7:08:21 AM
Subject: Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge
- Original Message -
From: Kasper Daniel Hansen kasperdanielhan...@gmail.com
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: Sean Davis sdav...@mail.nih.gov, bioc-devel@r-project.org
Sent: Friday, February 21, 2014 1:26:10 PM
Subject: Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge
- Original Message -
From: Dan Tenenbaum dtene...@fhcrc.org
To: Kasper Daniel Hansen kasperdanielhan...@gmail.com
Cc: bioc-devel@r-project.org, Sean Davis sdav...@mail.nih.gov
Sent: Friday, February 21, 2014 1:48:05 PM
Subject: Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge
- Original Message -
From: Martin Rijlaarsdam m.a.rijlaars...@gmail.com
To: bioc-devel bioc-devel@r-project.org
Sent: Thursday, March 13, 2014 1:52:20 AM
Subject: [Bioc-devel] fatal error when installing BioC devel on R devel
Dear Sirs,
When trying to install the devel version
- Original Message -
From: Martin Rijlaarsdam m.a.rijlaars...@gmail.com
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel bioc-devel@r-project.org
Sent: Friday, March 14, 2014 12:23:36 AM
Subject: Re: [Bioc-devel] fatal error when installing BioC devel on R devel
Dear Dan
- Original Message -
From: Dan Tenenbaum dtene...@fhcrc.org
To: Martin Rijlaarsdam m.a.rijlaars...@gmail.com
Cc: bioc-devel bioc-devel@r-project.org
Sent: Friday, March 14, 2014 8:39:52 AM
Subject: Re: [Bioc-devel] fatal error when installing BioC devel on R devel
- Original Message -
From: rcaloger raffaele.calog...@gmail.com
To: bioc-devel@r-project.org
Sent: Wednesday, March 26, 2014 10:50:06 PM
Subject: [Bioc-devel] To Bioc Team: OneChannelGUI error
Hi I am the maintainer of oneChannelGUI,
I am very sorry to be in dealy to have a
- Original Message -
From: Julian Gehring julian.gehr...@embl.de
To: bioc-devel@r-project.org
Sent: Tuesday, April 1, 2014 10:04:08 AM
Subject: [Bioc-devel] BiocCheck: Allowed formats for vignette source
Hi,
BiocCheck:::getVigSources check for vignette source files in the
- Original Message -
From: Julian Gehring julian.gehr...@embl.de
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
Sent: Monday, April 7, 2014 10:04:10 AM
Subject: Re: [Bioc-devel] git-svn bridge down?
Hi Dan,
It is still not working for me (packages 'Rariant
Package developers --
Each Bioconductor release is accompanied by release notes that mention
new packages and other significant project developments. For the
forthcoming release we would also like to include release notes for
individual packages, so that users have an easy way to survey changes
mapping.
Dan
PS. Steffen, I don't think it has anything to do with non-master branches. The
bridge ignores any pushes that are not to the master branch.
- Original Message -
From: Julian Gehring julian.gehr...@embl.de
To: Dan Tenenbaum dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
- Original Message -
From: Dan Tenenbaum dtene...@fhcrc.org
To: Julian Gehring julian.gehr...@embl.de
Cc: bioc-devel@r-project.org
Sent: Tuesday, April 8, 2014 7:09:19 AM
Subject: Re: [Bioc-devel] git-svn bridge down?
Hi all,
There are certainly issues with the git-svn bridge
- Original Message -
From: Dan Tenenbaum dtene...@fhcrc.org
To: Julian Gehring julian.gehr...@embl.de
Cc: bioc-devel@r-project.org
Sent: Tuesday, April 8, 2014 7:09:19 AM
Subject: Re: [Bioc-devel] git-svn bridge down?
Hi all,
There are certainly issues with the git-svn bridge
commits and see if they are
reflected on the other side.
If not, do the following:
- Log in to https://gitsvn.bioconductor.org
- delete your bridge
- re-create it
Then see if the commits/pushes are reflected. If not, let me know.
Dan
- Original Message -
From: Dan Tenenbaum dtene
- Original Message -
From: Gustavo H. Esteves geste...@gmail.com
To: BioC Devel - List bioc-de...@stat.math.ethz.ch
Sent: Thursday, April 10, 2014 8:08:29 AM
Subject: [Bioc-devel] Old version of packages
Dear Bioc-devel members
is it possible to recover an old version of any
Hello BioC developers,
We will be creating the Bioconductor 2.14 branch today at 2:00 PM
Seattle time. (21:00 UTC). This is about an hour and 20 minutes from now.
Please stop all commits to trunk before 2:00PM and do not resume until
further notice.
We will send another email when it is OK to
I should also mention that we are going to create a 2.14 branch for experiment
data packages as well, so please no commits to those either after 2PM PDT and
before further notice.
Dan
- Original Message -
From: Dan Tenenbaum dtene...@fhcrc.org
To: bioc-devel bioc-devel@r
The BioC 2.14 branch is now ready.
Remember, you always have access to 2 versions of your package:
the release and the devel versions.
Right now the release version of your package (which is not
officially released yet but will be on Monday if
everything goes well) is in the 2.14 branch and
Hi Ashley,
- Original Message -
From: Ashley Ng a...@wehi.edu.au
To: dtene...@fhcrc.org
Cc: bioc-devel@r-project.org
Sent: Tuesday, April 15, 2014 3:04:23 AM
Subject: biocLite “no packages in repository” error
Hi Dan
I seem to getting a “no packages in repository” biocLite
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