Re: Please categorise your packages for the Debian Science metapackages

Hi Julien, On Thu, Jan 05, 2017 at 09:03:41AM +0100, Julien Puydt wrote: > Ah, thanks for the heads-up and taking care of the blends! You are welcome. > Those should clearly be mathematics : > - edge-addition-planarity-suite I added planarity since the tasks files contain *binary* packages.

Re: Please categorise your packages for the Debian Science metapackages

Hi Thibaut On Thu, Jan 05, 2017 at 07:07:16AM +0100, Thibaut Paumard wrote: > All my packages should really go to astronomy. Two sets of packages I > would hide in any case, the last one would need to fit in the right task > in the astronomy blend. > > (python|python3|yorick)-pyorick hide >

Repeaded warning: Published-* fields are deprecated in tasks files

Hi, since a long time the "Published-*" fields inside tasks files are deprecated[1] and will be ignored in the foreseable future. You should rather use Reference fields in debian/upstream/metadata[2]. To help users migrating these data I was usually touching Git or SVN of the relevant packages.

Re: Please categorise your packages for the Debian Science metapackages: fenics/dolfin

Hi Drew, I'm not sure whether I fully understand your suggestion. On Thu, Jan 05, 2017 at 01:26:46PM +0800, Drew Parsons wrote: > Hi Andreas, there are a couple more fenics components in the  > mathematics-dev task: > > python-dolfin (and dolfin-dev) > python-ffc > python-ufl > > I'm

Re: Please categorise your packages for the Debian Science metapackages

Hi, On Thu, Jan 05, 2017 at 02:46:55AM +, lumin wrote: > I'm holding 6 uncategorized d-science packages. > > * caffe and caffe-contrib are categorized into machine-learning task. > See the patch attached. Thanks for the patch. Please note that for packages that are either existing in

Re: pandas git Was: statsmodels: FTBFS: TypeError: 'float' object cannot be interpreted as an index

Hi Yaroslav, On Wed, Jan 04, 2017 at 09:37:34PM -0500, Yaroslav Halchenko wrote: > > I've also migrated pandas to Debian Science Git[1]. When trying to > > build I can not reproduce the actual error #845734 but the build fails > > with > > I did spend some time on pandas today and uploaded

Re: packaging Siconos

Hi, On Wed, Jan 04, 2017 at 04:07:42PM -0300, Stephen Sinclair wrote: > > Hmmm, I'd naively say please try later again. If this does not help > > you might need to contact alioth admins. > > Ok, I tried again and discovered it was automatically adding "-guest" > to my username. Now I managed

Better do not use strict Depends in metapackages [Was: ros-metapackages is marked for autoremoval from testing]

Hi, since we just discussed about ros metapackages I'd like to give the following hint here: Its best practice to not use Depends but rather Recommends in metapackages. One reason is that metapackages will not be removed for reasons like the ones below. Kind regards Andreas. -

Re: Please add ros packages to robotics tasks

Hi Jochen, On Mon, Jan 02, 2017 at 12:00:44AM +0100, Jochen Sprickerhof wrote: > * Andreas Tille <andr...@an3as.eu> [2017-01-01 23:27]: > > I added these metapackages as well as their first dependencies in the > > following patch: > > Thanks a lot, I had just cloned

Re: Please add ros packages to robotics tasks

Hi Jochen, On Fri, Dec 30, 2016 at 11:32:30PM +0100, Jochen Sprickerhof wrote: > thanks for asking how to integrate ROS into the science meta package. > As ROS is so big, we already created a special ros-metapackages package, > resembling to what upstream has as well. The top meta package,

Please add ros packages to robotics tasks

Hi maintainers of robotics related packages, I'm trying to prepares Debian Science meta packages and when doing so I tried to check what Debian Science packages are not yet categorised. I realised that no binary package out of the source packages ros-actionlib ros-angles ros-bloom

Re: upload of debian-science ?

On Thu, Dec 29, 2016 at 07:54:00PM +0100, Ralf Treinen wrote: > > OK. Does this mean that I can ask ftp@d.o for removal of confluence now, > or should I wait? Just go for it. Kind regards Andreas. -- http://fam-tille.de

Re: upload of debian-science ?

Hi Ralf, On Thu, Dec 29, 2016 at 10:52:20AM +0100, Ralf Treinen wrote: > are there any plans of uploading debian-science for stretch ? I have > removed a Recommends from science-electronics in the git repo, the package > (confluence) is cruft and should be removed completely from the archive. > I

Re: Moving scikit-learn to Debian Science Git to let more people work on its issues

Hi, On Wed, Dec 28, 2016 at 08:13:37AM +0100, Andreas Tille wrote: > I intend to move scikit-learn to Debian Science to enable more people > working on issues like #848788 easily. Please tell me soon if you think > that it is not a good idea. Commited to Debian Science Git, fixed bug b

Re: Python-numpy transition breaks at least two packages

Hi Ghislain, On Fri, Dec 23, 2016 at 10:02:33AM +, Ghislain Vaillant wrote: > On Fri, 2016-12-23 at 10:43 +0100, Andreas Tille wrote: > > Hi, > > > > I have cloned bug #848758 where I suggested to revert the python-numpy > > transition which other posters agr

Python-numpy transition breaks at least two packages

Hi, I have cloned bug #848758 where I suggested to revert the python-numpy transition which other posters agreed upon. Besides breaking python-skbio I spotted another package python-skimage which fails with: == ERROR:

Re: Moving some R packages to Debian Science team

Hi again, On Thu, Dec 15, 2016 at 07:11:07PM -0500, lawre...@debian.org wrote: > On Mon, Dec 12, 2016 at 09:07:57AM +0100, Andreas Tille wrote: > > I'd volunteer to do the following if you agree: > > > > 1. Moving the said packages to Debian Science Git repository >

Re: Moving some R packages to Debian Science team

Hi Chris, On Thu, Dec 15, 2016 at 07:11:07PM -0500, lawre...@debian.org wrote: > On Mon, Dec 12, 2016 at 09:07:57AM +0100, Andreas Tille wrote: > > I'd volunteer to do the following if you agree: > > > > 1. Moving the said packages to Debian Science Git repository >

Moving some R packages to Debian Science team

Hi Chris and Julian, I'm currently busy updating all R packages of Debian Science team to the latest upstream version and making sure they have autopkgtests if possible. I checked UDD and found that some of your packages are also lagging behind upstream: udd=# select * from (select distinct

Re: Status of dh-r and problems building r-cran-yaml

Hi Gordon, On Tue, Dec 06, 2016 at 05:08:00PM +0100, Gordon Ball wrote: > >>> ** testing if installed package can be loaded > >>> Error in dyn.load(file, DLLpath = DLLpath, ...) :. > >>> unable to load shared object > >>>

Re: ITP: r-cran-bh -- GNU R package with Boost headers

Hi Dirk, I just realised that this ITP seems not to be closes. I somehow forgot this since the former requirement I had for this package seems to have vanished. However, my attempt to upgrade r-cran-rsqlite to its latest upstream version due to the missing r-cran-bh. Do you intend to upload

Status of dh-r and problems building r-cran-yaml

Hi Gordon, it seems you are quite busy currently since I have not heard from you since some time. I decided to upload a new version of dh-r which is fixing some nasty bug (#846239). I hope you are fine with the changes done by Dylan Aïssi and me. I have converted several packages from cdbs to

Pending team uploads for outdated R packages

Hi folks, I have migrated all those packages in Debian Science and Debian Med where I'm listed as Uploader. I found some R packages on my DM dashboard where I obviously committed something but are not Uploader. I plan to upgrade these to the latest upstream version and when doing so migrate

Re: [devteam-bioc] BioConductor phyloseq defines relation to not yet existing ade4 version

Hi Gordon, On Fri, Nov 18, 2016 at 02:56:16PM +0100, Gordon Ball wrote: > [only to andreas since I think this is effectively a debian > implementation detail rather than an issue for bioconductor] Involve Debian Science for wider audience - thus full quoting ... > On 17/11/16 16:14

Re: Please consider team maintenance for r-cran-jsonlite

On Tue, Nov 15, 2016 at 05:07:52PM -0500, Chris Lawrence wrote: > > this any more. If you agree I'd volunteer to commit r-cran-jsonlite > > packaging to Debian Science Git (or SVN if you prefer the latter) and > > upgrade to the new version as team upload. If you agree I could even > > switch

Re: new libgtkdatabox release

On Tue, Nov 15, 2016 at 09:21:54AM +0100, Petter Reinholdtsen wrote: > > I see from https://tracker.debian.org/pkg/libgtkdatabox > that the > package had some RC issues, fixed today, so that should not be a blocker > any more. I did an upload about 2 hours ago that should fix both issues. :-)

Please consider team maintenance for r-cran-jsonlite

Hi Chris, I was stumbling upon r-cran-jsonlite since r-cran-rredlist has a dependency on version 1.1 but we only have 1.0. If r-cran-jsonlite would be maintained in Debian Science team I would have simply done the upgrade. Unfortunately it is not maintained in any VCS and you are a single

Re: Sponsor upload request for new package scram

similarly easy. Others here might help. Kind regards Andreas. > Thanks, > Olzhas > > > > On Mon, Nov 14, 2016 at 6:09 AM, Andreas Tille <andr...@an3as.eu> wrote: > > > Hi Olzhas, > > > > On Sun, Nov 13, 2016 at 03:04:28PM -0800, Olzhas Rakhimov

Re: Sponsor upload request for new package scram

Hi Olzhas, On Sun, Nov 13, 2016 at 03:04:28PM -0800, Olzhas Rakhimov wrote: > Hello, > I am new to packaging for debian. > I would appreciate any feedback and sponsorship > for this package: > https://mentors.debian.net/package/scram I have added scram to the engineering (according to your

Re: Sponsor upload request for new package scram

Hi, On Sun, Nov 13, 2016 at 03:04:28PM -0800, Olzhas Rakhimov wrote: > Hello, > I am new to packaging for debian. > I would appreciate any feedback and sponsorship > for this package: > https://mentors.debian.net/package/scram > > ITP: > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=842766 >

Re: Call for help: RC bugs of SageMath dependencies

On Sat, Nov 12, 2016 at 03:19:19PM +, Tobias Hansen wrote: > Hi Andreas, > > thanks for helping out! Meanwhile I packaged ppl 1.2 and asked for a > transition, which was granted (#844100). I have a package that fixes > both RC bugs. Let me merge the changes we both did (maybe I'll do a >

Re: Call for help: RC bugs of SageMath dependencies

Hi, On Fri, Nov 11, 2016 at 04:22:15PM +0100, Andreas Tille wrote: > On Fri, Nov 11, 2016 at 01:32:01AM +, Tobias Hansen wrote: > > https://wiki.debian.org/DebianScience/Sage#Other_packages: > > Suggested team maintenance for ppl. Bug #806865 should be simple to fix > - i

Re: Call for help: RC bugs of SageMath dependencies

On Fri, Nov 11, 2016 at 01:32:01AM +, Tobias Hansen wrote: > https://wiki.debian.org/DebianScience/Sage#Other_packages: Suggested team maintenance for ppl. Bug #806865 should be simple to fix - its a shame that we are to late for #811825 to fix it the most sensible way with upgrading to

Re: [ftpmas...@ftp-master.debian.org: dh-r_20160916_amd64.changes ACCEPTED into unstable, unstable]

Hi Gordon, On Thu, Oct 27, 2016 at 03:44:35PM +0200, Gordon Ball wrote: > >> > >> Quite a few are probably now out of date (bioconductor release in the > >> meanwhile), but yes, I can push some updates once I'm able to verify the > >> builds without needing to inject a local copy of dh-r. > > >

Re: [ftpmas...@ftp-master.debian.org: dh-r_20160916_amd64.changes ACCEPTED into unstable, unstable]

Hi Gordon, On Tue, Oct 25, 2016 at 03:31:47PM +0200, Gordon Ball wrote: > > Quite a few are probably now out of date (bioconductor release in the > meanwhile), but yes, I can push some updates once I'm able to verify the > builds without needing to inject a local copy of dh-r. Just to let you

Re: [ftpmas...@ftp-master.debian.org: dh-r_20160916_amd64.changes ACCEPTED into unstable, unstable]

On Tue, Oct 25, 2016 at 03:31:47PM +0200, Gordon Ball wrote: > > know and I'll work down the list of packages on my todo list. I just > > want to avoid duplicated work. > > > > Quite a few are probably now out of date (bioconductor release in the > meanwhile), but yes, I can push some updates

[ftpmas...@ftp-master.debian.org: dh-r_20160916_amd64.changes ACCEPTED into unstable, unstable]

Hi Gordon, good news that dh-r was accepted. You previously wrote that you had some packages converted and tested. Would you mind commiting at least the Debian Med packages to VCS. I'll notice the commits and will check and upload. If you have reasons not to push your changes just let me know

Re: new libgtkdatabox release

Hi Brent, On Tue, Oct 18, 2016 at 07:05:04PM -1000, Brent W. Baccala wrote: > Aloha - > > I released libgtkdatabox 0.9.3.0 about a week ago. > > It's mostly a bug fix release, but it's got one new feature (dotted grids) > that makes xoscope look a lot more aesthetically pleasing. It's

Re: Sponsor upload needed for updated packages: python-pynlpl, libticcutils, libfolia, uctodata, ucto

On Tue, Oct 18, 2016 at 07:24:59PM +0200, Anton Gladky wrote: > Hi Maarten, > > I will be able step by step to sponsor your packages. But I have > a very limited time, so if somebody is willing to help with it - please > go ahead. Maarten, feel free to try

Re: statistics: who maintains R packages in Debian (was: Re: Debhelper for R packages)

On Tue, Oct 18, 2016 at 06:27:13PM +0300, Michael Crusoe wrote: > > > r-other-hms-dbmi-spp > > > > > > It is _a lot_ easier for all of us if we only have top-level > > > > > > r-cran-* > > > r-bioc-* > > > r-other-* > > Sounds like a great plan. Where shall we document it? Its

Re: statistics: who maintains R packages in Debian (was: Re: Debhelper for R packages)

On Mon, Oct 10, 2016 at 09:05:11PM +0900, Charles Plessy wrote: > $ grep-aptavail -e -P 'r-cran|r-bioc|r-other' -s 'Maintainer' | > cut -d' ' -f3- | cut -d\< -f2 | sed 's/^/ 1 This query had the side effect to spot a package that should be Debian Med team maintained ...

Re: Packaging librsb

Hi Rafael, sorry for my late reply - I'm recovering from vacation backlog. On Sun, Oct 09, 2016 at 04:55:47PM +0200, Rafael Laboissière wrote: > >Thanks for working on this. Could you suggest a set of tasks in Debian > >Science[1] the package librsb-dev might fit into? > > It fits into

Re: Debhelper for R packages

On Sun, Oct 09, 2016 at 03:04:23PM +0200, Joost van Baal-Ilić wrote: > > I was not speaking about those packages that are just team maintained. > > There are a lot of others that are not - for these a Debian R team would > > make sense ... and for r-base for sure. > > I'm sorry but to me it's not

Re: Debhelper for R packages

On Sat, Oct 08, 2016 at 05:45:16PM +0200, Joost van Baal-Ilić wrote: > > IMHO that's not matter of personal preference but a matter of how to > > work together in a Debian maintainers team. There are tools working on > > git.debian.org but not elsewhere. I keep on thinking that a Debian R > >

Re: Debhelper for R packages

On Fri, Oct 07, 2016 at 10:24:30PM +0200, Dylan wrote: > > I have already pushed a small change in lintian to tag the uncanonical > homepage of CRAN [1]. Lintian displays only an info tag and not a > warning tag, so you can ignore it. The patch for tag the uncanonical > homepage of Bioconductor

Re: Debhelper for R packages

Hi, On Fri, Oct 07, 2016 at 04:25:40PM +0200, Gordon Ball wrote: > > You could generate a whole lot of extra substvars (eg, ${R:Homepage}) to > ensure the canonical versions are used, but I'm not really convinced > it's useful. ACK, that's not useful. > > Sure, and some people prefer GitHub

Re: Packaging librsb

Hi Raphael, On Fri, Sep 23, 2016 at 02:24:13AM +0200, Rafael Laboissière wrote: > I created a Git repository [1] for packaging librsb [2]. I intend to file > an ITP soon and any comments/suggestions/fixes will be welcome. Thanks for working on this. Could you suggest a set of tasks in Debian

Re: Debhelper for R packages

Hi, On Thu, Sep 29, 2016 at 02:39:05PM +0200, Gordon Ball wrote: > it's been in NEW for the last two weeks so hopefully the FTP masters > will have a chance to review it soon. I've sent an e-mail yesterday to ftpmaster giving reasons to handle dh-r with higher priority. > > Just a very small

Re: Debhelper for R packages

Hi Gordon, On Thu, Sep 15, 2016 at 04:12:35PM +0200, Gordon Ball wrote: > Moving forward with this, I propose to file an ITP for dh-r as a > standalone package shortly, barring any objections. Since this shouldn't > overlap with anything else, I would to go straight to unstable rather > than

Re: Debhelper for R packages

On Thu, Sep 08, 2016 at 05:12:28PM -0500, Dirk Eddelbuettel wrote: > | > | Yeah, I'd love to see this happen too; I actually started looking at > | supporting it, so you could just do: > | > | %: > | dh --with r $@ > | > | and get on with writing the rest of the bits. > > Exactly! Yes,

Re: Debhelper for R packages

Hi Gordon, R is not team maintained and Dirk is not reading all threads on Debian Science - make sure you CC him (as I did) if you want to be sure he notices your mail. On Thu, Sep 08, 2016 at 03:30:20PM +0200, Gordon Ball wrote: > I have written a prototype debhelper module for building R

Re: r-cran-rprotobuf 0.4.5-1 ready for upload

Uploaded, thanks for your preparation, Andreas. On Tue, Sep 06, 2016 at 08:20:33PM +1000, Jonathon Love wrote: > *bump* > > > On 3/09/2016 18:01, Jonathon Love wrote: > >hi folks, > > > >i've updated the r-cran-rprotobuf package to the latest version. > > > >could someone review and upload

What's the difference between CRAN Cairo and cairoDevice

Hi Dirk, I've got a request to install Cairo[1] which from the description sounds pretty similar to your package r-cran-cairodevice from[2]. Both R packages seem to be maintained. Could you explain the difference and do you think its sensible to package Cairo in addition? Kind regards

Re: bcolz for Debian Science

On Sun, Aug 14, 2016 at 08:59:29PM +0200, Daniel Stender wrote: > bcolz is a chunked compressed data container build on the top of Numpy, which > can be > used either on disk but also in-memory. For compression it uses blosc > (c-blosc). I would > say it belongs to Numerical Computation task,

Re: Jmol (Was: SageMath packaging status update)

On Wed, Aug 10, 2016 at 08:45:48AM +0100, Tobias Hansen wrote: > On 08/10/2016 07:43 AM, Andreas Tille wrote: > > Jmol is also a target for the Debian Med team (which closely works > > together with DebiChem team). I suggest that I move the latest status > > of packaging

Re: SageMath packaging status update

Hi Tobias, On Wed, Aug 10, 2016 at 12:17:07AM +0100, Tobias Hansen wrote: > More details can be found on the Wiki page [1]. Some remarks to the list on the Wiki page: ecl - Debian maintainer needs to apply this upstream patch This package is lagging behind upstream. What about

Jmol (Was: SageMath packaging status update)

Hi Tobias, On Wed, Aug 10, 2016 at 12:17:07AM +0100, Tobias Hansen wrote: > I thought I'd give you an update about the packaging of SageMath in Debian. Thanks for the update and in general for the effort. > We are currently working on packaging the last small dependencies and > making the

Re: Looking for sponsors to upload various updated packages

Hi Maarten, if you have trouble finding a sponsor please make sure the packages are mentioned on our tasks pages and use Sponsoring of Blends https://wiki.debian.org/DebianPureBlends/SoB Kind regards Andreas. On Fri, Aug 05, 2016 at 11:42:58AM +0200, Maarten van Gompel wrote: > Hi

Re: Sponsoring for new package inside debian-science

) here we go. > > On 04/08/16 01:43, Jose Luis Rivero wrote: > > On Fri, Jul 29, 2016 at 9:50 AM, Andreas Tille <andr...@an3as.eu > > <mailto:andr...@an3as.eu>> wrote: > > > > On Fri, Jul 29, 2016 at 09:18:49AM +0200, Andreas Tille wrote: >

Re: Fwd: ITP: form -- Symbolic manipulation system

Hi, I'd recommend to maintain this package in the Debian Science team. Kind regards Andreas. On Wed, Aug 03, 2016 at 03:51:14PM +0200, gurkan wrote: > forgot the cc during itp... > > Original Message > Subject: ITP: form -- Symbolic manipulation system > Date:

Re: Sponsoring for new package inside debian-science

On Fri, Jul 29, 2016 at 09:18:49AM +0200, Andreas Tille wrote: > Hi again, > > I had a look into kido and ignition-msgs. I removed some boilerplate in > d/rules from ignition-msgs (please git pull) and noticed that pristine-tar > branch is missing. Please push all branches or cre

Re: Sponsoring for new package inside debian-science

Hi again, I had a look into kido and ignition-msgs. I removed some boilerplate in d/rules from ignition-msgs (please git pull) and noticed that pristine-tar branch is missing. Please push all branches or create the missing branch. Kind regards Andreas. -- http://fam-tille.de

Re: Sponsoring for new package inside debian-science

Hi Jose, On Fri, Jul 29, 2016 at 03:01:17AM +0200, Jose Luis Rivero wrote: > Hello Andreas: > > Sorry for the direct mail Sorry for the public response since I do not see any reason to keep such discussion private. > I hope that your are doing well. I added a > couple of new packages to the

Re: Blends naming in the Debian installer

stallation, and also maintains > the list of tasks to be installed by default, we can easily revert this. > > Best regards > > Ole > > Andreas Tille <andr...@an3as.eu> writes: > > On Wed, Jul 27, 2016 at 06:31:50PM +0200, Ole Streicher wrote: > >> We

Re: Science Typesetting: IDE overhaul

On Wed, Jul 20, 2016 at 02:08:52PM +0200, Jan Groenewald wrote: > On 20 July 2016 at 14:07, Jan Groenewald wrote: > > > On a final note, if this does seem reasonable, can we place TeXStudio > >> into the suggests as well? > >> > >> > > If this route is chosen, please add

Re: Bug#830343: Taking over cvxopt into Debian Science maintenance

Hi thanks for the quick confirmation. I've just created a Git repository of latest upstream and will push this soon. Kind regards Andreas. On Wed, Jul 20, 2016 at 09:30:29AM +0200, Soeren Sonnenburg wrote: > Thanks. Please do. > > On Wed, 2016-07-20 at 08:18 +0200, Andreas Ti

Re: science-statistics package suggestion: ggplot2

rately it might make sense to add it explicitly to the task. Kind regards Andreas. > On Wed, Jul 13, 2016 at 7:41 AM, Andreas Tille <andr...@an3as.eu> wrote: > > Hi Michael, > > > > I just added r-cran-ggplot2 to the statistics task. Thanks for your > >

Re: flann package

Hi On Fri, Jul 15, 2016 at 08:55:33AM +0200, Leopold Palomo-Avellaneda wrote: > Hi, > > flann has some serious bug (#822717) that affects several packages that I co- > maintain or are under debian-science team: fcl ompl pcl ros-metapackages ros- > pcl-conversions > > I have seen that the

Re: science-statistics package suggestion: ggplot2

Hi Michael, I just added r-cran-ggplot2 to the statistics task. Thanks for your long explanation. This kind of hints are *very* helpful - please come up with more of them. ;-) Kind regards Andreas. On Tue, Jul 12, 2016 at 09:41:42PM +0800, Michael Wilson wrote: > I propose the inclusion

Re: R package CI test failures

On Fri, Jun 17, 2016 at 04:18:40PM +0200, Gordon Ball wrote: > Pushed some fixes to git/svn: > > * r-cran-doparallel: extra test dependency r-cran-rpart, patch which > removes an attempt to write a report within the (read-only) package dir Uploaded. > * r-cran-matrixstats: cp and rm in

Re: R package CI test failures

On Thu, Jun 09, 2016 at 03:07:35PM +0200, Andreas Tille wrote: > > > missing test dependency on mlmrev (not packaged) for the "conception" > > > dataset > > > > Any volunteer for mlmrev? > > ITPed and in SVN, will upload today to new. Both pac

Re: R package CI test failures

Hi again, On Wed, Jun 08, 2016 at 05:05:15PM +0200, Andreas Tille wrote: > > Returning a few weeks later: CRAN packages. > > > > r-cran-adegraphics: > > r-cran-surveillance: > > > > waiting for r-cran-spdep > > Its the fourth time in n

Re: R package CI test failures

Hi, On Wed, Jun 08, 2016 at 03:50:18PM +0200, Gordon Ball wrote: > Returning a few weeks later: CRAN packages. > > r-cran-adegraphics: > r-cran-surveillance: > > waiting for r-cran-spdep Its the fourth time in new queue and I tried to convince ftpmaster that it is urgend (with no success for

Re: Committed some fixes to libf2c2

Hi Barak, my current pressure to add another upload to libf2c2 has vanished since I found a clue to build clapack with the current version (a copy of f2c.h just needed to be removed from there). I think your clone would fit my needs since the only different filename (i_ceiling.c in clapack is

Re: Committed some fixes to libf2c2

Hi Barak, could we agree to keep debian-science in CC to make sure our discussion about f2c is somewhere archived. Considering there are so many clones of f2c and netlib with a code copy of f2c (as well as clapack where I'm fighting desperately with) we should stick to an open discussion to

Re: Committed some fixes to libf2c2

nce most probably we are dealing with dependencies that are maintained by Debian Science anyway. Kind regards Andreas. On Wed, May 25, 2016 at 09:55:37PM +0200, Andreas Tille wrote: > Hi Barak, > > On Wed, May 25, 2016 at 08:22:58PM +0100, Barak A. Pearlmutter wrote: > > Go for

Committed some fixes to libf2c2

Hi Barak, since I would like to get rid of the code copy of f2c in clapack which I'd like to package[1] I needed to do some changes in libf2c2. Basically there were some files missing that are contained in the clapack repository and I also needed to add some CFLAGS otherwise clapack test suite

Re: [devteam-bioc] BioConductor interactiveDisplayBase can't connect to bioconductor.org

Hi Dan, thanks for your quick response. On Fri, May 13, 2016 at 10:07:27AM -0700, Dan Tenenbaum wrote: > > > I wonder whether there is any chance to make this error non-critical > > and add a warning to enable passing this step without breaking the > > build on a disconnected box. > > I have

Re: R package CI test failures

On Sat, May 14, 2016 at 03:56:40PM +0200, Andreas Tille wrote: > > > > Patch (git format-patch for the repository) is attached. It > > suppress_test_writing_to_usr.patch, which removed some of the pre-amble > > to each vignette with one which modifies the p

Re: R package CI test failures

On Fri, May 13, 2016 at 05:37:35PM +0200, Gordon Ball wrote: > I don't have permissions for debian-med, nor am I a DM/DD, so I'm afraid > I haven't committed any patches or uploaded them, but a couple should be > attached here. In any case I've added you to the Debian Med team to enable you

BioConductor interactiveDisplayBase can't connect to bioconductor.org

Hi, I intend to package BioConductor interactiveDisplayBase as a new dependency for biovizBase version 1.20.0 (of BioConductor 3.3) as a Debian package. The Debian packaging process involves loading the package and since the packaging process needs to work on a machine disconnected from the

Re: Request for sponsoring r-cran-tgp and r-cran-maptree

Hi Pablo, On Tue, May 10, 2016 at 12:18:31PM +0200, Pablo Oliveira wrote: > Thanks Andreas for your feedback and upload of r-cran-maptree ! You are welcome. > The next step for fixing #820866 is uploading the new version of > r-cran-tgp. Should we try to get r-cran-tgp uploaded to unstable now

Re: Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)

Hi Dirk, On Mon, May 09, 2016 at 02:37:37PM -0500, Dirk Eddelbuettel wrote: > > Sorry, meant whichever version (of rtracklayer) gave you that issue. I would > rather not remove configure wholesale. > > I am reasonably fluent at writing these so I may be able to help you just > modify the

Re: Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)

Hi Dirk, On Mon, May 09, 2016 at 01:55:42PM -0500, Dirk Eddelbuettel wrote: > > On 9 May 2016 at 20:37, Andreas Tille wrote: > | Hi again, > | > | I solved this by simply removing the whole configure script in a quilt > patch. > > That sounds crazy so I took a look

Re: Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)

Hi again, I solved this by simply removing the whole configure script in a quilt patch. Kind regards Andreas. On Mon, May 09, 2016 at 05:01:52PM +0200, Andreas Tille wrote: > Hi, > > usually R packages are building without problems but I faced an issue > now which I have n

Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)

Hi, usually R packages are building without problems but I faced an issue now which I have no clue about. I try to upgrade r-bioc-rtracklayer[1] and I have updated SVN to something that should build version 1.32.0. Unfortunately when using pbuilder I get: dh_testroot dh_prep dh_installdirs -A

Re: Bug#819392: ITP: geg -- GTK+ Equation Grapher

Hi Georges, On Sun, May 08, 2016 at 09:10:59PM +0200, Georges Khaznadar wrote: > > The new repository seems to be well shaped from my point of view. Please > can you check it? It is my first repository there. I did some changes in the control file - please git pull. Kind regards

Re: toulbar2: another try ?

Hi, I agree with Gianfranco. PLease fix this in Git - but the package is in the new queue since this morning. Kind regards Andreas. On Fri, May 06, 2016 at 10:43:08AM +, Gianfranco Costamagna wrote: > Hi, lets see again > > > there is an extra space in VCS-fields, triggering a

Re: RFS for toulbar2

On Wed, May 04, 2016 at 02:48:35PM +0200, Thomas Schiex wrote: > Dear all, > > Anything we could do now to facilitate sponsorship for toulbar2 at > > https://anonscm.debian.org/cgit/debian-science/packages/toulbar2.git/ Please next time normalise your control file by cme fix dpkg-control

Re: R 3.3.0 for Debian jessie on the way to CRAN, not for wheezy

gt; It will hit the CRAN mirrors shortly. :-) > On another note, the backport of R 3.2.5 that Andreas Tille prepared, was > just > accepted to jessie-backports. In my mind, this is a first step towards > complementing the CRAN backports (which feature only three architectures) and >

Re: Request for sponsoring r-cran-tgp and r-cran-maptree

Hi Pablo, On Wed, May 04, 2016 at 11:16:43AM +0200, Pablo Oliveira wrote: > Thanks for the review! You are welcome. > I just fixed it on the git. I've noticed the fix. Unfortunately there is another slight issue: Per Debian Science policy we also keep pristine-tar information inside the Git

Re: Request for sponsoring r-cran-tgp and r-cran-maptree

Hi Pablo, On Tue, May 03, 2016 at 05:50:39PM +0200, Pablo Oliveira wrote: > I have updated r-cran-tgp [1] to the latest upstream version (2.4-14), > which fixes #820866. > > The new upstream version requires a new dependency, r-cran-maptree [2], > which I just packaged (ITP #823320). > > Could

Re: R package CI test failures

Hi Gordon, thanks for your investigation. On Tue, May 03, 2016 at 04:05:22PM +0200, Gordon Ball wrote: > Having had a better look at some of the less obvious failings: > > r-bioc-biocparallel > --- > > Non-deterministic? Seems to fail about 80% of the time in >

Re: SuperLU

Hi Nico, On Tue, May 03, 2016 at 09:30:03AM +, Nico Schlömer wrote: > > So if you have a real question rather than this meta-question you should > ask it here. > > Yup, well, SuperLU in Debian is pretty outdated and the new version allows > for a much simpler build process. That's worth a

Re: SuperLU

On Tue, May 03, 2016 at 10:18:23AM +0200, Johannes Ring wrote: > On Tue, May 3, 2016 at 10:07 AM, Nico Schlömer > wrote: > > Does anyone know who is the current maintainer for SuperLU [1] and where to > > find the debian repo? > > The maintainer is Debian Science

Re: R package CI test failures

More fixes below: On Thu, Apr 28, 2016 at 12:22:22AM +0200, Andreas Tille wrote: > My only idea is to rather use > >pkg=r-bioc-`echo $oname | tr '[A-Z]' '[a-z]'` > > and so I try this even if I think this is equivalent. This seems to work. > > r-bioc-aroma.light: atte

Re: R package CI test failures

On Thu, Apr 28, 2016 at 10:42:45AM +0200, Gordon Ball wrote: > > me. My only idea is to rather use > > > >pkg=r-bioc-`echo $oname | tr '[A-Z]' '[a-z]'` > > > > and so I try this even if I think this is equivalent. > > Hmm, yes. I can't obviously see why this fails. (Aside - `tr A-Z a-z` >

Re: R package CI test failures

Continued my previous mail: > r-cran-sp: missing dep rgeos (unpackaged?) As far as I can see rgeos is not yet packaged. Any volunteer? Otherwise tweaking the tests requiring this package might be an intermediate solution. > r-cran-surveillance: unsatisfyable dependencies New upstream version

Re: R package CI test failures

On Thu, Apr 28, 2016 at 01:38:54PM +1000, Jonathon Love wrote: > hi andreas, > > i've pushed fixes to: > > - r-cran-bms Did you really push? r-cran-bms(master) $ git log commit 4de85fa06d10e6aa3181b63efd35e70239fff861 Author: Jonathon Love Date: Sat Dec 19 14:48:39 2015

Re: Post-Receive Hooks

Hi James, thanks for your investigation. I'd welcome if you fix the issues you've found in a manner looking sensible to you. If you need permissions for those repositories you can not access please ping the according team. Kind regards Andreas. On Wed, Apr 27, 2016 at 11:20:02PM

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