Bug#1041598: Needed for r-bioc-* transition, please give priority (Was: r-bioc-s4arrays_1.0.4+dfsg-1_amd64.changes is NEW)

2023-07-21 Thread Andreas Tille
Hi ftpmasters, since this package is a new precondition for a package in level 2 of the r-bioc- transition[1] (package r-bioc-biocneighbors has this new dependency) it would be really great if you could give this package priority over other packages I habe in new queue. Thanks in advance for

Bug#1040498: transition: r-bioc-biocgenerics - blocked by new package r-bioc-s4arrays

2023-07-21 Thread Andreas Tille
Control: block -1 by 1041598 Hi, it has turned out that there is a new dependency for the new version of package r-bioc-delayedarray. The new package r-bioc-s4arrays is uploaded to new but I record the ITP bug here as a blocker to record that issue. Usually ftpmaster is helpful and quick in

Bug#1041598: ITP: r-bioc-s4arrays -- foundation of array-like containers in Bioconductor

2023-07-21 Thread Andreas Tille
Package: wnpp Severity: wishlist Subject: ITP: r-bioc-s4arrays -- foundation of array-like containers in Bioconductor Package: wnpp Owner: Andreas Tille Severity: wishlist * Package name: r-bioc-s4arrays Version : 1.0.4 Upstream Author : Hervé Pagès * URL : https

Bug#1040498: Help for Bioconductor transition needed: using Debian packaged libraries in r-bioc-rhdf5filters

2023-07-21 Thread Andreas Tille
Hi, I've just pushed r-bioc-rhdf5filters to salsa[1]. We are replacing code copies of several compression related libs by the Debian equivalents. Seems upstream added zstd and thus I added libzstd-dev to Build-Depends and tried to fix the according patch. But it went more complex. The issues

Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets

2023-07-21 Thread Andreas Tille
Hi Bo, Am Fri, Jul 21, 2023 at 12:29:24AM +0800 schrieb Bo YU: > > [1]: https://med-team.pages.debian.net/policy/ > > > > If you agree to it, please feel free to proceed, git easily > > I have read the policy and accepted it. :-) > > Sounds good, let us know once you pushed your modification.

Bug#1038668: veryfasttree_4.0.1+dfsg-1_amd64.changes REJECTED

2023-07-20 Thread Andreas Tille
Hi Thorsten, Am Wed, Jul 19, 2023 at 07:05:32PM +0200 schrieb Thorsten Alteholz: > On 11.07.23 21:40, Andreas Tille wrote: > > uploaded with GPL-3. Thanks for quick checking > > as César confirmed, the code from  Stephane Guindon was already present in > fasttree-2.1.10.c an

Bug#1020473: Interest in patch?

2023-07-20 Thread Andreas Tille
Hi Soren, Am Wed, Jul 19, 2023 at 02:42:27PM -0700 schrieb Soren Stoutner: > Would you be interested in a patch implementing this functionality? Yes, for sure, as always. I'm quite busy with other stuff so a patch will always speed up things. Kind regards Andreas. -- http://fam-tille.de

Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets

2023-07-20 Thread Andreas Tille
Hi, Am Thu, Jul 20, 2023 at 12:57:11PM +0800 schrieb Bo YU: > ... > Oh, thanks you told me the background so today I learned many here. > > I think it is okay i push the update to the salsa repo directly as > your suggestion. Thank you for your contribution and welcome in the team Andreas.

Bug#1040566: let logol be removed

2023-07-18 Thread Andreas Tille
Hi Olivier, Am Mon, Jul 17, 2023 at 12:13:30PM +0200 schrieb olivier sallou: > logol is not maintained anymore for quite some time now > > effort to keep in line with swi-prolog updates (need to recompile on each > ABI break of swi-prolog) AND biojava requires frequent work for an old > software

Bug#1039910: r-cran-exactextractr_0.9.1-1_amd64.changes REJECTED

2023-07-18 Thread Andreas Tille
Hi Thorsten, Am Sun, Jul 16, 2023 at 12:00:09PM + schrieb Thorsten Alteholz: > according to the file header and DESCRIPTION, the only copyright holder is > ISciences, LLC., so I don't think Daniel Baston should be mentioned. > But please mention Martin Moene. Both fixed in new upload.

Bug#1040498: Fwd: Bug#1040498: transition: r-bioc-biocgenerics

2023-07-17 Thread Andreas Tille
regards Andreas. Am Mon, Jul 17, 2023 at 04:08:53PM +0200 schrieb Andreas Tille: > Hi, > > the BioC transition can be started now. I'm kind of offline-ish for a > couple of hours today and a bit tired. May be I'll start tomorrow. For > those who do not want to wait fee

Bug#1037603: marked as done (civetweb: ftbfs with GCC-13)

2023-07-15 Thread Andreas Tille
Hi Sebastien, seems you closed the wrong bug with your upload. The package you uploaded is orthanc-postgresql but the bug concerns civetweb. Kind regards Andreas. Am Sat, Jul 15, 2023 at 12:09:18PM + schrieb Debian Bug Tracking System: > Your message dated Sat, 15 Jul 2023 12:07:17

Bug#1038668: veryfasttree_4.0.1+dfsg-1_amd64.changes REJECTED

2023-07-11 Thread Andreas Tille
Hi Thorsten, uploaded with GPL-3. Thanks for quick checking Andreas. Am Tue, Jul 11, 2023 at 07:00:10PM + schrieb Thorsten Alteholz: > > Hi Andreas, > > according to [1] the code from Stephane Guindon was added 2019-05-11 whereas > according to [2] the license of pyhml was already

Bug#1038668: veryfasttree_4.0.1+dfsg-1_amd64.changes REJECTED

2023-07-11 Thread Andreas Tille
Hi Thorsten, Am Sun, Jul 09, 2023 at 07:10:10PM + schrieb Thorsten Alteholz: > please also mention Stephane Guindon in your debian/copyright. Fixed in new upload. Thanks for thorough checking Andreas. -- http://fam-tille.de

Bug#1039562: [a...@debian.org: Bug#1039562: libchado-perl: fails to access database during installation]

2023-07-11 Thread Andreas Tille
Control: severity -1 minor Control: tags -1 wontfix Am Mon, Jul 10, 2023 at 11:19:52PM +0200 schrieb Étienne Mollier: > olivier sallou, on 2023-07-10: > > for me not a bug, just an information on setup, so bug should be > > closed/rejected. > > > > I do not understand very well why a bug is

Bug#1040766: RM: aeskulap -- ROM; Dead upstream, blocking removal of GTK+ 2 libraries

2023-07-10 Thread Andreas Tille
Package: ftp.debian.org Severity: normal User: ftp.debian@packages.debian.org Usertags: remove X-Debbugs-Cc: aesku...@packages.debian.org, 1038...@bugs.debian.org Control: affects -1 + src:aeskulap Hi, as in bug #1038453 reported this package is not maintained upstream any more and is

Bug#1040500: routine-update: Don't create d/salsa-ci.yml file

2023-07-10 Thread Andreas Tille
Hi Jochen, Am Fri, Jul 07, 2023 at 12:04:29PM +0200 schrieb Jochen Sprickerhof: > > echo "SALSA_TOKEN=" >> ~/.devscripts > echo 'SALSA_CI_CONFIG_PATH="recipes/debian.yml@salsa-ci-team/pipeline"' >> > ~/.devscripts > sudo apt install devscripts > salsa update_safe --group science-team --all

Bug#1040762: netpbm-free: Netpbm "make check" modifications

2023-07-10 Thread Andreas Tille
Source: netpbm-free Version: 2:11.01.00-2 Severity: normal X-Debbugs-Cc: Akira Urushibata Upstream Akira Urushibat wrote in private mail due to problems posting to Debian BTS: - I see that you have authored a patch file for

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-09 Thread Andreas Tille
Am Sat, Jul 08, 2023 at 10:35:17PM +0200 schrieb Paul Gevers: > Indeed, I think the pattern is that if we test in testing, with r-cran from > unstable and r-cran-tibble from testing it fails, but with r-cran from > unstable and r-cran-tibble from unstable, it works. > > I'm working my through the

Bug#1040001: adds unnecessarily strict versioned Depends on r-base-core

2023-07-07 Thread Andreas Tille
Control: reopen -1 Thanks for watching me, Bas. Am Fri, Jul 07, 2023 at 05:09:31PM +0200 schrieb Sebastiaan Couwenberg: > It seems that dh-r (20230707) should have closed #1040515 instead of the > transition bug report (#1040001). -- http://fam-tille.de

Bug#1040500: routine-update: Don't create d/salsa-ci.yml file

2023-07-07 Thread Andreas Tille
Hi Jochen, Am Fri, Jul 07, 2023 at 09:48:45AM +0200 schrieb Jochen Sprickerhof: > > I confirm routine-update is going beyond the recommendation but in those > > teams where I'm working (in CC) we have this de-facto standard to use > > this file. Before I change the behaviour of routine-update I

Bug#1040500: routine-update: Don't create d/salsa-ci.yml file

2023-07-07 Thread Andreas Tille
Control: severity -1 wishlist Hi Christopher, thanks you for the suggestion to enhance routine-update. Am Thu, Jul 06, 2023 at 09:03:23PM +0100 schrieb Christopher Obbard: > routine-update adds a file under the path "debian/salsa-ci.yml". Yes, this is intended. > According to the

Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing (Was: Bug#1040001: transition: r-base)

2023-07-06 Thread Andreas Tille
Am Fri, Jul 07, 2023 at 12:52:49AM +0530 schrieb Nilesh Patra: > > Andreas, if you remember, the code pointed out by Sébastien is > the exact same reason we had to t-p-u r-cran-shiny during freeze, See > > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1035428#15 >

Bug#1040001: To strict version restrictions injected by dh-r (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-06 Thread Andreas Tille
Hi Sébastien, Am Thu, Jul 06, 2023 at 09:13:46PM +0200 schrieb Sébastien Villemot: > > I'm not sure so please explain in more detail. dh-r was designed to put > > the lowest restriction regarding the versions. I remember some > > discussion some time ago that Dirk thought we should put stronger

Bug#1040001: Role of tibble? (Was: Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing)

2023-07-06 Thread Andreas Tille
Hi, Am Thu, Jul 06, 2023 at 08:28:45PM +0200 schrieb Paul Gevers: > On 06-07-2023 19:08, Paul Gevers wrote: > > Yes, we'll take care of that where it looks sane to do so (examples of > > that are r-cran-epi); I'll manually schedule the "combined" tests, such > > that they disappear from the

Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing (Was: Bug#1040001: transition: r-base)

2023-07-06 Thread Andreas Tille
Hi Paul, Am Thu, Jul 06, 2023 at 07:08:04PM +0200 schrieb Paul Gevers: > Yes, we'll take care of that where it looks sane to do so (examples of that > are r-cran-epi); I'll manually schedule the "combined" tests, such that they > disappear from the excuses if they then pass. OK. Thanks a lot

Bug#1040498: transition: r-bioc-biocgenerics

2023-07-06 Thread Andreas Tille
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition X-Debbugs-Cc: r-bioc-biocgener...@packages.debian.org, debia...@bugs.debian.org Control: affects -1 + src:r-bioc-biocgenerics Hi, BioConductor has released version 3.17 when we were in

Bug#1040001: Seeking advise how to proceed with the transition / move R stack to testing (Was: Bug#1040001: transition: r-base)

2023-07-06 Thread Andreas Tille
Hi again, Am Thu, Jul 06, 2023 at 09:56:31AM +0200 schrieb Andreas Tille: > > I've now re-uploaded all 6 packages that are known to be affected by the > graphics ABI change (and verified that it is set properly). I'll > continue now closing the open bugs. After rebuilding quite s

Bug#1040001: transition: r-base

2023-07-06 Thread Andreas Tille
Hi, Am Wed, Jul 05, 2023 at 04:07:12PM + schrieb Graham Inggs: > I don't think it's possible to set up a tracker for this first > "transition", as no packages currently depend on r-graphics-engine-*. Right, this makes perfectly sense. > Please wait until r-base and dh-r are built and in

Bug#1040001: transition: r-base

2023-07-05 Thread Andreas Tille
Hi, the just uploaded r-base 4.3.1-2 implements r-graphics-engine-* which is respected by dh-r 20230705 (also just uploaded). It would be great if you could setup transition tracker. Am I understanding things correctly that I can now start uploading those r-cran-* packages featuring bugs

Bug#1040038: r-base-core: Please provide r-graphics-api-*

2023-07-05 Thread Andreas Tille
Hi Dirk, Am Sat, Jul 01, 2023 at 10:55:25AM -0500 schrieb Dirk Eddelbuettel: > | The graphics engine version, R_GE_version, has been bumped to 16 > | and so packages that provide graphics devices should be > | reinstalled. > > Also see the nice compact history at > >

Bug#1040001: Add block by

2023-07-05 Thread Andreas Tille
Control: block -1 by 1040038

Bug#1040283: python3-csb: SyntaxWarning during package installation

2023-07-04 Thread Andreas Tille
Control: tags -1 pending Fixed in Git, upload blocked due to #1040316. -- http://fam-tille.de

Bug#1040282: python3-cgelib: SyntaxWarning during package installation

2023-07-04 Thread Andreas Tille
Control: tags -1 pending Fixed in git upload blocked by bug #1040316 -- http://fam-tille.de

Bug#1040316: python3-minimal fails to install

2023-07-04 Thread Andreas Tille
Hi, I can confirm this problem here in a clean unstable chroot. Kind regards Andreas. -- http://fam-tille.de

Bug#1040001: transition: r-base

2023-07-04 Thread Andreas Tille
Hi Paul, Am Sun, Jul 02, 2023 at 10:54:03AM +0800 schrieb Paul Wise: >    $ objdump -T debian/*/usr/lib/R/site-library/*/libs/*.so | grep > R_GE_checkVersionOrDie >      DF *UND*     Base    > R_GE_checkVersionOrDie Thanks for the hint. Its

Bug#1040001: transition: r-base

2023-07-03 Thread Andreas Tille
Hi Graham, Am Mon, Jul 03, 2023 at 05:24:19PM + schrieb Graham Inggs: > On Sun, 2 Jul 2023 at 19:57, Andreas Tille wrote: > > 45 > > > > serious bugs that are all caused by the non-transition while we should > > have done one. That's pretty annoying fo

Bug#1033907: numba: autopkgtest regression: segmentation fault on arm64

2023-07-03 Thread Andreas Tille
Hi On Sun, 21 May 2023 11:39:29 -0700 Diane Trout wrote: > Unfortunately it also wants llvmlite 0.40.0. Could you please be more verbose about this "unfortunately"? > It'd probably be easier to get upstream to help with debugging 0.57 I fully agree that we should target at latest upstream

Bug#1040001: transition: r-base

2023-07-02 Thread Andreas Tille
Hi Paul, Am Sat, Jul 01, 2023 at 05:21:16PM +0200 schrieb Paul Gevers: > > So per upstream ("R Core" for short), this is clearly on the package > > side. There is no ABI/API incompatibility: R offers graphics functions new > > functionality, to use it one needs a rebuild _if a package decides to

Bug#1040038: r-base-core: Please provide r-graphics-api-*

2023-07-02 Thread Andreas Tille
rsion-16 +Closes: #1040038 + + -- Andreas Tille Sat, 01 Jul 2023 13:45:57 +0200 + r-base (4.3.1-1) unstable; urgency=medium * New upstream release diff --git a/debian/control b/debian/control index 37d0cd042..2eae826af 100644 --- a/debian/control +++ b/debian/control @@ -49,7 +49,7 @@ Pack

Bug#1040038: r-base-core: Please provide r-graphics-api-*

2023-07-01 Thread Andreas Tille
Hi again, Am Sat, Jul 01, 2023 at 05:50:08PM +0200 schrieb Andreas Tille: > > That's a pretty good point. Dirk, do you want me to adapt the > patch or will you do the search and replace? I'll adapt dh-r > accordingly to the proper string. I've attached a patch implementing Graham

Bug#1040038: r-base-core: Please provide r-graphics-api-*

2023-07-01 Thread Andreas Tille
Hi Graham, Am Sat, Jul 01, 2023 at 03:26:44PM + schrieb Graham Inggs: > Your patch has 'rgraphicsapiversion' and 'r-graphics-api-4.3'. > > Upstream [1] refer to it as follows: > > The graphics engine version, R_GE_version, has been bumped to 16 > and so packages that provide graphics

Bug#1040001: transition: r-base

2023-07-01 Thread Andreas Tille
Hi again, just a status update: Am Sat, Jul 01, 2023 at 01:45:11PM +0200 schrieb Andreas Tille: > > I think my piece is ready. We just need to decide about a proper name > of the virtual package. I'll inject this into my proof of concept > change of dh-r. Than Dirk needs to uplo

Bug#1040038: r-base-core: Please provide r-graphics-api-*

2023-07-01 Thread Andreas Tille
+ + * Non-maintainer upload. + * Add r-graphics-api + + -- Andreas Tille Sat, 01 Jul 2023 13:45:57 +0200 + r-base (4.3.1-1) unstable; urgency=medium * New upstream release diff --git a/debian/control b/debian/control index 37d0cd042..d18e50c85 100644 --- a/debian/control +++ b/debian/control

Bug#1040037: r-base-dev: depends-on-obsolete-package Depends: libncurses5-dev => libncurses-dev

2023-07-01 Thread Andreas Tille
Package: r-base-dev Version: 4.3.1-1 Severity: normal Hi, as lintian says: E: r-base-dev: depends-on-obsolete-package Depends: libncurses5-dev => libncurses-dev Please do not depend from obsolete package but depend from libncurses-dev instead. Kind regards Andreas. -- System

Bug#1040001: transition: r-base

2023-07-01 Thread Andreas Tille
Hi Paul, Am Sat, Jul 01, 2023 at 07:48:16AM +0200 schrieb Paul Gevers: > Anytime is good to ask for a transition, particularly when the transition is > already ongoing. :-) > I don't think it should surprise anyone that we prefer it to be done right. > Our preference is for option 1. Thanks

Bug#1039926: Will file bug report for complete R transition (Was: Bug#1039926: svglite requires rebuild under R 4.3.*)

2023-06-30 Thread Andreas Tille
Hi Johannes, Am Fri, Jun 30, 2023 at 03:22:19PM +0200 schrieb Johannes Ranke: > I think option 1 from [1] is the way to go, i.e. make r-base provide a > graphics API version according to the R changelog, and have the relevant > packages depend on that graphics API version. How to identify them

Bug#1040001: transition: r-base

2023-06-30 Thread Andreas Tille
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition X-Debbugs-Cc: r-b...@packages.debian.org, debia...@lists.debian.org Control: affects -1 + src:r-base Hi, I'm not sure that we are in the right status to ask for a transition bug since

Bug#1039926: Will file bug report for complete R transition (Was: Bug#1039926: svglite requires rebuild under R 4.3.*)

2023-06-30 Thread Andreas Tille
Hi Dirk, Am Thu, Jun 29, 2023 at 05:52:34PM -0500 schrieb Dirk Eddelbuettel: > This accidentally omitted > > library(svglite) > > The package loads fine, but like the others will not create a graphics device > as it was built under the previous R 4.2.* series. Thanks a lot for your

Bug#1039912: ITP: r-cran-dials -- GNU R tools for creating tuning parameter values

2023-06-29 Thread Andreas Tille
Package: wnpp Severity: wishlist Subject: ITP: r-cran-dials -- GNU R tools for creating tuning parameter values Package: wnpp Owner: Andreas Tille Severity: wishlist * Package name: r-cran-dials Version : 1.2.0 Upstream Author : Max Kuhn, * URL : https://cran.r

Bug#1039910: ITP: r-cran-exactextractr -- GNU R fast extraction from raster datasets using polygons

2023-06-29 Thread Andreas Tille
Package: wnpp Severity: wishlist Subject: ITP: r-cran-exactextractr -- GNU R fast extraction from raster datasets using polygons Package: wnpp Owner: Andreas Tille Severity: wishlist * Package name: r-cran-exactextractr Version : 0.9.1 Upstream Author : Daniel Baston, * URL

Bug#1039909: ITP: r-cran-dicedesign -- GNU R designs of computer experiments

2023-06-29 Thread Andreas Tille
Package: wnpp Severity: wishlist Subject: ITP: r-cran-dicedesign -- GNU R designs of computer experiments Package: wnpp Owner: Andreas Tille Severity: wishlist * Package name: r-cran-dicedesign Version : 1.9 Upstream Author : Jessica Franco, Delphine Dupuy, Olivier Roustant

Bug#1039645: What kind of transition do we want (Was: Bug#1039645: r-cran-epi: autopkgtest failure with r-base (4.3.1-1))

2023-06-29 Thread Andreas Tille
Am Thu, Jun 29, 2023 at 03:59:59PM +0530 schrieb Nilesh Patra: > > to pick the version from testing. But this should be dealt by a > > transition rather than picking a "random" (??? - that is my question > > about) package from the dependencies and make it versioned. > > Yes, but at the moment

Bug#1039645: r-cran-epi: autopkgtest failure with r-base (4.3.1-1)

2023-06-29 Thread Andreas Tille
Hi Nilesh, Am Thu, Jun 29, 2023 at 02:52:34PM +0530 schrieb Nilesh Patra: > > > > Why exactly do you think that actually dplyr should receive a versioned ^ > > Depends. It is not specified in DESCRIPTION explicitly and

Bug#1039645: r-cran-epi: autopkgtest failure with r-base (4.3.1-1)

2023-06-29 Thread Andreas Tille
Am Wed, Jun 28, 2023 at 08:18:57PM +0530 schrieb Nilesh Patra: > You are correct. A transition is all we need. However, in case of > r-cran-epi simply adding a versioned dep on dplyr should do the trick. > (epi is not a failure in excuses for dplyr). Why exactly do you think that actually dplyr

Bug#1039645: Seems we need a transition for r-base instead of lots of single bugs against single packages (Was: Bug#1039645: r-cran-epi: autopkgtest failure with r-base (4.3.1-1))

2023-06-28 Thread Andreas Tille
Hi Bas, (this is just an example bug out of a lot you filed) Am Wed, Jun 28, 2023 at 08:11:05AM +0200 schrieb Bas Couwenberg: > 189s DLL requires the use of native symbols I wonder, whether all those bugs against single r-* packages are sensible. As far as I can see we simply need a

Bug#1039633: r-bioc-bioccheck: autopkgtest failure with r-base (4.3.1-1)

2023-06-28 Thread Andreas Tille
Hi, just to give some update about those type of r-bioc-* related bugs: We need to do the transition to the next BioC release and upload every single r-bioc-* package. This will not happen this week due to time constraints (and updating r-cran-packages after the release). If it might help the

Bug#1039112: r-cran-chk_0.9.0-1_amd64.changes REJECTED

2023-06-28 Thread Andreas Tille
Hi Thorsten, Am Tue, Jun 27, 2023 at 07:10:09PM + schrieb Thorsten Alteholz: > according to LICENSE the only copyright holder is Poisson Consulting ... Fixed in new upload. Thanks a lot for your work as ftpmaster Andreas. PS: I've recently fixed the issue you mentioned in

Bug#1028132: now ready

2023-06-28 Thread Andreas Tille
Am Tue, Jun 27, 2023 at 06:31:28AM +0200 schrieb Rene Engelhard: > > Andreas, you can upload r-cran-hunspell. Uploaded. Thanks a lot for the ping Andreas. -- http://fam-tille.de

Bug#1039510: mvtnorm breaks r-cran-pammtools autopkgtest: missing Breaks and/or versioned (test) Depends?

2023-06-28 Thread Andreas Tille
Hi Paul, just as a hint for you who might have missed periodic blaming of Dirk about outdated R packages. Am Tue, Jun 27, 2023 at 02:02:43PM -0500 schrieb Dirk Eddelbuettel: > Life is too short: Yes, so I keep on updating r-cran- packages after freeze and save my time to repeat myself. Kind

Bug#1039501: r-bioc-biomart: autopkgtest regression: Failure ('test_ensembl_ssl_settings.R:71')

2023-06-28 Thread Andreas Tille
Hi Paul, thanks a lot for your bug report. We need to do a transition of all r-bioc-* packages soonish. We'll deal with this issue in this process with the new upstream version. Kind regards and thanks a lot for all your work Andreas. -- http://fam-tille.de

Bug#1039483: ITP: r-cran-diagram -- GNU R functions for visualising simple graphs (networks), plotting

2023-06-26 Thread Andreas Tille
Package: wnpp Severity: wishlist Subject: ITP: r-cran-diagram -- GNU R functions for visualising simple graphs (networks), plotting Package: wnpp Owner: Andreas Tille Severity: wishlist * Package name: r-cran-diagram Version : 1.6.5 Upstream Author : Karline Soetaert * URL

Bug#1039112: ITP: r-cran-chk -- GNU R check user-supplied function arguments

2023-06-25 Thread Andreas Tille
Package: wnpp Severity: wishlist Subject: ITP: r-cran-chk -- GNU R check user-supplied function arguments Package: wnpp Owner: Andreas Tille Severity: wishlist * Package name: r-cran-chk Version : 0.9.0 Upstream Author : Joe Thorley, * URL : https://cran.r

Bug#1037439: Opinions about removal of 32bit architecture for r-cran-rstan (Was: Bug#1037439: r-cran-rstan/armhf FTBFS with r-cran-bh 1.74)

2023-06-23 Thread Andreas Tille
Am Fri, Jun 23, 2023 at 05:26:15AM +0530 schrieb Nilesh Patra: > However pruning this off 32-bit archsn would also mean > removing a huge chunk of other R packages which transitively depend on rstan. > As far as I checked, not all of them are intensive to run, and it is > likely useful for people

Bug#1037439: Opinions about removal of 32bit architecture for r-cran-rstan (Was: Bug#1037439: r-cran-rstan/armhf FTBFS with r-cran-bh 1.74)

2023-06-22 Thread Andreas Tille
Hi Nilesh, Am Thu, Jun 22, 2023 at 10:06:02PM +0530 schrieb Nilesh Patra: > 1. rstan has got a lot of reverse-build-deps and reverse-deps > and those reversd-deps have further more of them. rstan is kind of an > important package in that sense, and dropping 32-bit arch for this would > mean

Bug#1037439: Opinions about removal of 32bit architecture for r-cran-rstan (Was: Bug#1037439: r-cran-rstan/armhf FTBFS with r-cran-bh 1.74)

2023-06-22 Thread Andreas Tille
Hi Adrian and Dirk, thanks a lot to Adrian for taking the time to dig into R source code for a fix. Am Mon, Jun 19, 2023 at 12:04:02PM -0500 schrieb Dirk Eddelbuettel: > | > Not sure that it is fair to point at BH / Boost though. Anyway. > | > > | > CRAN no longer checks / compiles 32 bit so

Bug#1013153: camitk: vtk[6,7] removal

2023-06-22 Thread Andreas Tille
Hi Emmanuel, Am Thu, Jun 22, 2023 at 09:57:48AM +0200 schrieb Emmanuel Promayon: > CamiTK is now fully compatible with VTK9 upstream [1], but there is no > official release yet. The new version of CamiTK with VTK9 support should be > available before the end of July, and my objective is to have

Bug#1013153: camitk: vtk[6,7] removal

2023-06-22 Thread Andreas Tille
Am Mon, Jun 19, 2023 at 10:26:02AM +0200 schrieb Sebastiaan Couwenberg: > Would you consider doing a nocheck upload to unstable to unblock the vtk7 > removal? > > The FTBFS on the buildds and autopkgtest failures would keep blocking > testing migration until the vtk9 support is fully fixed. I've

Bug#1034387: update youtube-dl control file to reflect? transitional package

2023-06-21 Thread Andreas Tille
Am Wed, Jun 21, 2023 at 06:13:27PM -0400 schrieb Andres Salomon: > > Andreas, were you planning to do an upload? Because I was about to open a > bug against ftp.debian.org to request removal of the package now that > bookworm is released. I can wait if you want, but I don't see much point in >

Bug#1031999: r-cran-mclogit_0.9.6-1_amd64.changes REJECTED

2023-06-21 Thread Andreas Tille
Hi Thorsten, On Tue Feb 28 19:06:49 GMT 2023 Thorsten Alteholz wrote: > please add the README.source for the data files. sorry, I've totally missed this reject despite the package is needed for upgrading some CRAN packages - specifically now since we can upgrade something again. I've added the

Bug#1038453: Anyone interested in aeskulap DICOM viewer (Was: Bug#1038453: aeskulap: Is this package still desirable to have in Debian?)

2023-06-19 Thread Andreas Tille
Hi, aeskulap is dead upstream for a long time Alexander Pipelka (in CC) maintained a Github repository to enable maintaining the code but the last commit was a Debian patch. So it seems we will not see any relevant upstream work in the foreseable future. Since the package is blocking removal of

Bug#1029203: r-cran-gfonts_0.2.0-1_amd64.changes REJECTED

2023-06-14 Thread Andreas Tille
Hi Thorsten, Am Thu, Jun 08, 2023 at 07:00:10PM + schrieb Thorsten Alteholz: > > is there a reason why these fonts are located in /usr/lib/R ? Well, since the R install procedure does it this way. ;-) > Wouldn't it make sense to move them to the normal fonts directories and just >

Bug#1037439: r-cran-rstan/armhf FTBFS with r-cran-bh 1.74

2023-06-14 Thread Andreas Tille
Am Tue, Jun 13, 2023 at 03:30:18PM -0500 schrieb Dirk Eddelbuettel: > On 13 June 2023 at 13:15, Steve Langasek wrote: > | Unfortunately, at least in Ubuntu it appears the r-cran-rstan build still > | exhausts the 32-bit memory space even with boost 1.81. > | > |

Bug#1034387: update youtube-dl control file to reflect transitional package

2023-06-04 Thread Andreas Tille
Control: tags -1 pending Am Sat, Jun 03, 2023 at 12:54:33PM -0400 schrieb Jesse Rhodes: > The debian/control fields for youtube-dl still have a lot of leftover > information from when it was a binary package, which should be cleaned > up to reflect what the package actually does at present.

Bug#1036988: crashes with TypeError: _ScrolledWindowBase.SetScrollbars(): argument 3 has unexpected type 'float'

2023-05-31 Thread Andreas Tille
Am Wed, May 31, 2023 at 05:35:46PM +0300 schrieb Konstantin L. Metlov: > Thank you for reporting this bug ! > > It is already fixed by the commit > > https://github.com/metlov/cycle/commit/e86d72ec1a2a05c46ccde2f607f142cef7dbabb2 > > I should, probably, make a new bugfix release. A bugfix

Bug#1036776: release-notes: Release notes paragraph from Debian Med team

2023-05-26 Thread Andreas Tille
Hi Justin, Am Sat, May 27, 2023 at 04:42:32AM +0100 schrieb Justin B Rye: > Andreas Tille wroteL > > Please add the following patch from the Debian Med team to the release > > notes: > > Some English-usage suggestions: Thanks a lot for looking onto the text in &quo

Bug#1036776: release-notes: Release notes paragraph from Debian Med team

2023-05-25 Thread Andreas Tille
Package: release-notes Severity: normal X-Debbugs-Cc: debian-...@lists.debian.org Please add the following patch from the Debian Med team to the release notes: News from Debian Med Blend As in every release new packages in the field of life sciences and medicine were added. The

Bug#1036743: [Debian-med-packaging] Bug#1036743: kleborate: debsums reports modified files after apt-get upgrade && apt-get dist-upgrade

2023-05-25 Thread Andreas Tille
Hi Étienne, Am Thu, May 25, 2023 at 10:34:10AM +0200 schrieb Étienne Mollier: > > Installation of kleborate from sid and testing shown no issues. > Installation of kleborate from bullseye on bullseye is okay too. Good. Maybe we should reflect in BTS that this bug is not relevant for bookworm?

Bug#1036753: unblock: debian-science/1.14.5

2023-05-25 Thread Andreas Tille
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: unblock X-Debbugs-Cc: debian-scie...@packages.debian.org, debian-scie...@lists.debian.org Control: affects -1 + src:debian-science Please unblock package debian-science [ Reason ] This is the

Bug#1021396: ITP: batterylog -- laptop battery logging tool

2023-05-25 Thread Andreas Tille
Hi, since I keep on tracking down issues when my battery drains to zero when in suspend mode I stumbled upon your discussion on framework community[1] and this ITP. Did you pushed something on salsa regarding the packaging I might be able to try? Kind regards Andreas. [1]

Bug#1031726: HDF5 - how about removing gif2h5 subject to several CVE?

2023-05-24 Thread Andreas Tille
Hi Gilles, since nobody responded to your question (I did not respond as well since none of my packages uses this tool) here some opinion from me: No contradiction means agreement - thus just go for it. Thanks a lot for caring for hdf5 libraries Andreas. Am Sat, Feb 25, 2023 at 10:37:58PM

Bug#1036227: bookworm-pu: package r-cran-shiny/1.7.4+dfsg-3~deb12u1

2023-05-23 Thread Andreas Tille
Hi Paul, Am Tue, May 23, 2023 at 01:52:38PM +0200 schrieb Paul Gevers: > Control: tags -1 confirmed Thanks. > On 17-05-2023 19:48, Andreas Tille wrote: > > I'd like to announce an upload to testing-proposed-updates > > You confused me here. I don't see traces of the uploa

Bug#1036557: unblock: debian-med/3.8.1

2023-05-22 Thread Andreas Tille
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: unblock X-Debbugs-Cc: debian-...@packages.debian.org, debian-...@lists.debian.org Control: affects -1 + src:debian-med Please unblock package debian-med [ Reason ] This is the final update of the

Bug#1036227: bookworm-pu: package r-cran-shiny/1.7.4+dfsg-3~deb12u1

2023-05-17 Thread Andreas Tille
iny (1.7.4+dfsg-3~deb12u1) bookworm; urgency=medium + + * Upload to testing-proposed-updates "bookworm" due to the fact that +there was an accidental upload of a new version of r-base to unstable + + -- Andreas Tille Wed, 17 May 2023 07:56:25 +0200 + r-cran-shiny (1.7.4+dfsg-3) unst

Bug#1035428: Test suite issues due to new upstream version of r-core in unstable (Was: r-cran-shiny: broken symlink: ...)

2023-05-17 Thread Andreas Tille
Am Wed, May 17, 2023 at 02:07:22PM +0530 schrieb Nilesh Patra: > On Wed, May 17, 2023 at 08:58:58AM +0200, Andreas Tille wrote: > > I hope I was following developers reference about t-p-u[6] correctly > > and pushed > > I've choosen the version 1.7.4+dfsg-3~deb12u1 to matc

Bug#1035428: Test suite issues due to new upstream version of r-core in unstable (Was: r-cran-shiny: broken symlink: ...)

2023-05-17 Thread Andreas Tille
hangelog @@ -1,3 +1,10 @@ +r-cran-shiny (1.7.4+dfsg-3~deb12u1) bookworm; urgency=medium + + * Upload to testing-proposed-updates "bookworm" due to the fact that +there was an accidental upload of a new version of r-base to unstable + + -- Andreas Tille Wed, 17 May 2023 07:56:

Bug#1035428: Test suite issues due to new upstream version of r-core in unstable (Was: r-cran-shiny: broken symlink: ...)

2023-05-16 Thread Andreas Tille
Am Tue, May 16, 2023 at 07:49:55PM +0530 schrieb Nilesh Patra: > On Tue, May 16, 2023 at 07:25:15PM +0530, Nilesh Patra wrote: > > I personally prefer "1" over 2 as it is less noise (and effort). > > On second thoughts, I think sending it via testing-proposed-updates > would be a better thing to

Bug#1035428: Test suite issues due to new upstream version of r-core in unstable (Was: r-cran-shiny: broken symlink: ...)

2023-05-16 Thread Andreas Tille
Hi, when fixing bug #1035428 I realised test suite issues with r-cran-thematic [1] -> Error in `svglite_(filename, bg, width, height, pointsize, standalone, always_valid)`: Graphics API version mismatch r-cran-treescape [2] r-cran-treespace [3] -> error is given if lambda is

Bug#1033366: resteasy3.0: should migrate to tomcat10

2023-04-21 Thread Andreas Tille
Am Fri, Apr 21, 2023 at 03:02:10PM +0200 schrieb Markus Koschany: > Am Freitag, dem 21.04.2023 um 14:50 +0200 schrieb Andreas Tille: > > > > Ahhh, right, the repository went over to source package resteasy.  So > > well, the CI log is not helpful for this bug log.  What I ra

Bug#1033366: resteasy3.0: should migrate to tomcat10

2023-04-21 Thread Andreas Tille
Hi Markus, Am Fri, Apr 21, 2023 at 01:39:17PM +0200 schrieb Markus Koschany: > Am Freitag, dem 21.04.2023 um 12:23 +0200 schrieb Andreas Tille: > > I tried to rebuild this package which does not work as you can > > see in Salsa CI: > > > >     https://salsa.debian.or

Bug#1033366: resteasy3.0: should migrate to tomcat10

2023-04-21 Thread Andreas Tille
Hi, I tried to rebuild this package which does not work as you can see in Salsa CI: https://salsa.debian.org/java-team/resteasy/-/jobs/4105287 Unfortunately I have no idea how to fix this. Kind regards Andreas. -- http://fam-tille.de

Bug#1032902: Numba issues for genx for other architectures than amd64 and ppc64el (Was: genx won't start: TypeError: Pen(): arguments did not match any overloaded call)

2023-04-18 Thread Andreas Tille
Hi, I've found genx in the "Cleaner view"[1] due to missing builds[2]. It turns out that for instance for arm64[3] the build fails with tests/test_numba_equivalency.py Fatal Python error: Segmentation fault For armel[4] (and armhf) we get dh_auto_test -a -O--buildsystem=pybuild I:

Bug#999526: Taking over package into Debian Python Team maintenance and fixing bug (Was: mdp: FTBFS with numpy 1.21 (in experimental): dh_auto_test: error: pybuild --test --test-pytest -i python{versi

2023-04-18 Thread Andreas Tille
Hi Yaroslav, Am Mon, Apr 17, 2023 at 05:59:23PM -0400 schrieb Yaroslav Halchenko: > Hi Andreas, > > Thank you very much for offering help. I think Tiziano would not mind, > so please feel very welcome to a) for the sake of b) or any other > goodness you would like to bring ;)

Bug#999526: Taking over package into Debian Python Team maintenance and fixing bug (Was: mdp: FTBFS with numpy 1.21 (in experimental): dh_auto_test: error: pybuild --test --test-pytest -i python{versi

2023-04-17 Thread Andreas Tille
Hi Tiziano and Yaroslav, I'd volunteer to a) take over package into Debian Python Team (including using Salsa Git and Maintainer address of DPT) and b) apply the patch and upload the package I'm not interested in just doing b) and hope you will find the time to care for the package

Bug#1033424: Please upload to delayed (Was: image-factory: FTBFS in testing: AssertionError: pylint found issues)

2023-04-17 Thread Andreas Tille
Hi Josef, thanks for finding a patch for this problem. I'd recommend to upload to DELAYED (may be with 3 or up to 7 days). We are in deep freeze and having RC bugs closed helps everybody. Kind regards Andreas. -- http://fam-tille.de

Bug#1031909: RC Bug tagged patch since more than one month (Was: python3-tk: bytecode not removed on upgrade)

2023-04-17 Thread Andreas Tille
Hi Matthias, thanks to James Addison this RC bug is tagged patch. It would help if you could comment on this patch (either in Bug report or MR[1]). Kind regards Andreas. [1] https://salsa.debian.org/cpython-team/python3-stdlib/-/merge_requests/5 -- http://fam-tille.de

Bug#1034369: C++ help needed (Was: Bug#1034369: libcereal: autopkgtest regression on non x86: cc1plus: all warnings being treated as errors)

2023-04-13 Thread Andreas Tille
Control: tags -1 help Hi, I guess the fix will boil down to a type casting in this line https://salsa.debian.org/med-team/libcereal/-/blob/master/unittests/map.hpp#L65 o_esplmap.insert({random_value(gen), { random_value(gen), random_value(gen) }}); unfortunately my C++ knowledge is

Bug#1034349: bedtools: autopkgtest fails on bookworm kernel: ulimit: error setting limit (Operation not permitted)

2023-04-13 Thread Andreas Tille
Hi Paul, Am Thu, Apr 13, 2023 at 10:28:13PM +0200 schrieb Paul Gevers: > Thanks for the quick fix. There is good news. Thanks to discussions on IRC > we found a change to the lxc configuration that will enable us to circumvent > the issue. Which means that you can drop the workaround in a future

Bug#1034288: RM: igdiscover/0.11-3

2023-04-12 Thread Andreas Tille
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: rm X-Debbugs-Cc: igdisco...@packages.debian.org, 1032...@bugs.debian.org, steffen_moel...@gmx.de Control: affects -1 + src:igdiscover According to bug #1032975 the package is non-functional and

Bug#1032975: Steffen, please raise your opinion about igdiscover

2023-04-11 Thread Andreas Tille
Hi Steffen, we really need your insight into the package created by you. Please raise your opinion whether this package is sensible at all as it is now. If not I'd ask for removal from testing immediately (since this mail refreshed the autoremoval counter.) Thanks a lot Andreas. --

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