Re: [Bioc-devel] how could I get new packages list

2013-10-11 Thread Dan Tenenbaum
- 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

Re: [Bioc-devel] how could I get new packages list

2013-10-11 Thread Dan Tenenbaum
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

[Bioc-devel] release builds have stopped

2013-10-09 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Emergent build and check errors on the Windows Server Re: release builds have stopped

2013-10-09 Thread Dan Tenenbaum
- 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

[Bioc-devel] Preparing package release notes

2013-10-08 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Is it too late to make an update to an existing package?

2013-10-07 Thread Dan Tenenbaum
- 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

Re: [Bioc-devel] build server

2013-10-05 Thread Dan Tenenbaum
- 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.

Re: [Bioc-devel] build server

2013-10-05 Thread Dan Tenenbaum
- 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

[Bioc-devel] Reminder: Warning deadline approaching

2013-10-04 Thread Dan Tenenbaum
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

Re: [Bioc-devel] oneChannelGUI devel

2013-10-03 Thread Dan Tenenbaum
- 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

Re: [Bioc-devel] Clarifying/simplifying on the SVN-Github mirroring

2013-09-26 Thread Dan Tenenbaum
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 -

Re: [Bioc-devel] org-mode vignettes

2013-08-28 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Package Build RSS feeds now available

2013-08-07 Thread Dan Tenenbaum
...@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

Re: [Bioc-devel] Package Build RSS feeds now available

2013-08-06 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Package Build RSS feeds now available

2013-08-06 Thread Dan Tenenbaum
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

Re: [Bioc-devel] shiny, Bioconductor, and reproducible research

2013-07-29 Thread Dan Tenenbaum
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

Re: [Bioc-devel] shiny, Bioconductor, and reproducible research

2013-07-29 Thread Dan Tenenbaum
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

[Bioc-devel] shiny, Bioconductor, and reproducible research

2013-07-26 Thread Dan Tenenbaum
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

Re: [Bioc-devel] best practice: verbose messages

2013-07-10 Thread Dan Tenenbaum
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

Re: [Bioc-devel] exp. data, updates

2013-07-10 Thread Dan Tenenbaum
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

Re: [Bioc-devel] best practice: verbose messages

2013-07-10 Thread Dan Tenenbaum
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

[Bioc-devel] BioC2013 Afternoon Lab schedule now online

2013-07-08 Thread Dan Tenenbaum
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

[Bioc-devel] svn and package version numbers

2013-06-30 Thread Dan Tenenbaum
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.

Re: [Bioc-devel] AnnotationHubServer requires AnnotationHubData of a particular vintage

2013-06-25 Thread Dan Tenenbaum
(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

Re: [Bioc-devel] Size limits of packages when including other executables

2013-06-07 Thread Dan Tenenbaum
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

Re: [Bioc-devel] BiocParallel: BatchJobs backend (Was: Re: BiocParallel)

2013-06-06 Thread Dan Tenenbaum
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'

Re: [Bioc-devel] R version in Bioc packages (was Re: [BioC] Package \'jmosaics\' not found)

2013-05-21 Thread Dan Tenenbaum
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

Re: [Bioc-devel] R version in Bioc packages (was Re: [BioC] Package \'jmosaics\' not found)

2013-05-21 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Bioconductor Package Builder and _R_CHECK_FORCE_SUGGESTS_

2013-05-17 Thread Dan Tenenbaum
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

Re: [Bioc-devel] broken links for curatedOvarianData package

2013-04-10 Thread Dan Tenenbaum
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

Re: [Bioc-devel] GLX extension missing on petty

2013-04-04 Thread Dan Tenenbaum
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

[Bioc-devel] BioC 2.12 branch created

2013-04-03 Thread Dan Tenenbaum
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

[Bioc-devel] Linking to HTML documents in a package on the BioC web site

2013-03-29 Thread Dan Tenenbaum
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

Re: [Bioc-devel] graphite build error on George2

2013-03-28 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Preparing package release notes

2013-03-27 Thread Dan Tenenbaum
? 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

[Bioc-devel] Preparing package release notes

2013-03-26 Thread Dan Tenenbaum
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

[Bioc-devel] Reminder: release builds will stop on Monday

2013-03-22 Thread Dan Tenenbaum
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 ___

Re: [Bioc-devel] parallel support for Windows and RStudio

2013-03-21 Thread Dan Tenenbaum
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.

Re: [Bioc-devel] Warning in .simpleDuplicateClass(def, prev)

2013-03-19 Thread Dan Tenenbaum
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

Re: [Bioc-devel] request: timings

2013-03-18 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Warning in .simpleDuplicateClass(def, prev)

2013-03-18 Thread Dan Tenenbaum
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

Re: [Bioc-devel] vignettes using foreach on Windows

2013-03-16 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Recent issue with plot method dispatch

2013-03-13 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Custom CRAN repository in biocLite.R not working

2013-03-13 Thread Dan Tenenbaum
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

Re: [Bioc-devel] avoiding call to .find.package

2013-03-07 Thread Dan Tenenbaum
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

Re: [Bioc-devel] avoiding call to .find.package

2013-03-05 Thread Dan Tenenbaum
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!

Re: [Bioc-devel] avoiding call to .find.package

2013-03-04 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Section~\ref{sec:bla} idiom in vignettes

2013-02-21 Thread Dan Tenenbaum
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

[Bioc-devel] bug tracker (was Fwd: Reminder: Your Atlassian OnDemand account bioc-internal will be deactivated soon)

2013-02-09 Thread Dan Tenenbaum
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

Re: [Bioc-devel] bug tracker (was Fwd: Reminder: Your Atlassian OnDemand account bioc-internal will be deactivated soon)

2013-02-09 Thread Dan Tenenbaum
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

Re: [Bioc-devel] R CMD build not copying PDF vignettes to inst\doc

2013-02-07 Thread Dan Tenenbaum
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:

Re: [Bioc-devel] R CMD build not copying PDF vignettes to inst\doc

2013-02-07 Thread Dan Tenenbaum
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

Re: [Bioc-devel] BioC question

2013-02-06 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Access UnitTests Log-File

2013-01-25 Thread Dan Tenenbaum
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

Re: [Bioc-devel] Access UnitTests Log-File

2013-01-24 Thread Dan Tenenbaum
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

Re: [Bioc-devel] R v3.0.0: It's now official and BioC devel needs some updates

2012-12-16 Thread Dan Tenenbaum
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

Re: [Bioc-devel] getting Rscript for development version packages

2012-11-26 Thread Dan Tenenbaum
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

Re: [Bioc-devel] getting Rscript for development version packages

2012-11-26 Thread Dan Tenenbaum
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

Re: [Bioc-devel] error message upon installing easyRNASeq

2012-11-14 Thread Dan Tenenbaum
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

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