Bug#1076245: lintian-brush: hangs and when killed leaved lock in Git repository

2024-07-17 Thread Andreas Tille
Am Tue, Jul 16, 2024 at 12:33:25PM + schrieb Jelmer Vernooij: > Yeah, I have managed to. > > This appears to be some weird issue in the reqwest crate used in > upstream-ontologist, which causes it to hang. > > Seems similar to >

Bug#1076314: qiime hard-codes python 3.11 without depending on it

2024-07-16 Thread Andreas Tille
Hi Matthias, Am Tue, Jul 16, 2024 at 12:52:56PM +0200 schrieb Matthias Klose: > > Just to let me understand correctly: Its definitely a mistake to > > (Build-)Depend: python3-all. However, am I understand you correctly > > that (Build-)Depend from python3.11 could save the packag in testing? >

Bug#1076314: qiime hard-codes python 3.11 without depending on it

2024-07-16 Thread Andreas Tille
Hi Matthias, Am Sun, Jul 14, 2024 at 10:57:14AM +0200 schrieb Matthias Klose: > Package: src:qiime > Version: 2024.5.0-1 > Severity: serious > Tags: sid trixie > > * Only build for Python 3.11 until upstream catches up with Python > 3.12. > > dear debian-med, please don't do that. It

Bug#1076245: lintian-brush: hangs and when killed leaved lock in Git repository

2024-07-13 Thread Andreas Tille
Hi Jelmer, Am Sat, Jul 13, 2024 at 02:13:24PM + schrieb Jelmer Vernooij: > > This is not only true for this specific package but for *all* packages > > I tried in the last couple of weeks. > > It looks like it's an issue with one of the fixers that seems to hang. I > think there's three

Bug#1076245: lintian-brush: hangs and when killed leaved lock in Git repository

2024-07-12 Thread Andreas Tille
Package: lintian-brush Version: 0.155 Severity: grave Justification: renders package unusable Hi, I'm currently do not use lintian-brush extensively currently (since I reduced my packaging work in DPL) term but *always* when using it hangs. Not even some ^C in terminal kann bring back some

Bug#1074222: pycorrfit FTBFS with Python 3.12 as default

2024-07-04 Thread Andreas Tille
Control: tags -1 pending Am Tue, Jul 02, 2024 at 05:07:08PM +0200 schrieb Andreas Tille: > I'm fine with whatever solution you might find and you can > perfectly skip me when doing some team upload. Could someone please fix W: pycorrfit: file-in-unusual-dir [usr/pycorrfit_doc/CHANGE

Bug#1071355: In how far are several packages affected by bug #1071355 of maptools

2024-07-04 Thread Andreas Tille
Hi, there was a series of testing removals due to bug #1071355 of r-cran-maptools. Since maptools was removed from CRAN[1] we intend to remove this package. However, before doing so I would like to understand why packages like r-cran-factominer, r-cran-ggpubr, r-cran-vim, r-cran-systemfit,

Bug#1074529: Bug#1074529: r-cran-dimred: autopkgtest regression with r-base 4.4.1 (i386)

2024-07-03 Thread Andreas Tille
Hi Charles, Am Tue, Jul 02, 2024 at 08:29:13AM +0900 schrieb Charles Plessy: > > For what it is worth version 0.2.6 is in good standing at CRAN with tests > > using "r-release" (ie now 4.4.1) as well as "r-devel" and "r-oldrel", see > >

Bug#1071523: r-cran-spatstat.geom: autopkgtest regression in testing

2024-07-02 Thread Andreas Tille
Am Tue, Jul 02, 2024 at 09:32:43PM + schrieb Graham Inggs: > > We did not implemented any hooks to realise this yet. > > Wouldn't removing the following line from debian/control do it? > > Testsuite: autopkgtest-pkg-r Well, sure. But our tooling will add this for the next upstream version

Bug#1071523: r-cran-spatstat.geom: autopkgtest regression in testing

2024-07-02 Thread Andreas Tille
Hi Graham, Am Tue, Jul 02, 2024 at 04:15:26PM + schrieb Graham Inggs: > > r-cran-spatstat.core was removed from Debian. R-cran-spatstat.geom does > > not depend from this package any more and the autopkgtest in Salsa CI is > > fine[1]. Any hint why it fails in testing would be welcome. > >

Bug#1074222: pycorrfit FTBFS with Python 3.12 as default

2024-07-02 Thread Andreas Tille
Am Tue, Jul 02, 2024 at 05:01:27PM +0800 schrieb Bo YU: > > I can confirm it works(still during build but pass the failed stage on > the issue). > > It seems tille had worked a lot on this, so hope this helps. I'm fine with whatever solution you might find and you can perfectly skip me when

Bug#1071523: r-cran-spatstat.geom: autopkgtest regression in testing

2024-06-30 Thread Andreas Tille
Control: tags -1 help Hi, r-cran-spatstat.core was removed from Debian. R-cran-spatstat.geom does not depend from this package any more and the autopkgtest in Salsa CI is fine[1]. Any hint why it fails in testing would be welcome. Kind regards Andreas. [1]

Bug#1071860: not fixed in 7.0-005-2

2024-06-30 Thread Andreas Tille
Hi Andreas, Am Sat, Jun 29, 2024 at 03:55:37PM +0200 schrieb Andreas Metzler: > I have now uploaded a NMU to delayed/7-days using the attached patch. I > have gone for the mininal change, dropping the respective code instead > of switching to pkgconf. It simpler, does not make a difference on >

Bug#1071106: r-cran-sf: autopkgtest regression in testing

2024-06-30 Thread Andreas Tille
Control: block -1 by 1071523 The problem is connected to the removal of r-cran-spatstat.core from testing/unstable. Since r-cran-sf (Test-)Depends r-cran-spatstat.geom fixing bug #1071523 should be sufficient to let r-cran-sf migrate. Kind regards Andreas.

Bug#1064135: bigmemory: fails to migrate to testing for too long: autopkgtest fails on arm*, ppc64el and s390x

2024-06-27 Thread Andreas Tille
Hi Michael, I've opened issue #115 on Github four months ago but there is no activity so far. Could you please confirm that you are watching the issue tracker on Github or are you possibly using some other development platform? Just asking since the tags lagging behind the versioned tarballs at

Bug#1071860: not fixed in 7.0-005-2 (was: Bug#1071860 closed by Debian FTP Masters (reply to Andreas Tille ) (Bug#1071860: fixed in fis-gtm 7.0-005-

2024-06-23 Thread Andreas Tille
Control: tags -1 help Hi Andreas, strange, it has build for me. Am Sun, Jun 23, 2024 at 08:03:30AM +0200 schrieb Andreas Metzler: > Control: reopen 1071860 > ... > CMake Error at CMakeLists.txt:529 (message): > FATAL: libgcrypt-config not found (LIBGCRYPT_CONFIG_SCRIPT-NOTFOUND) > [...] I

Bug#1072109: marked as pending in python-awkward

2024-06-06 Thread Andreas Tille
Control: tag -1 pending Hello, Bug #1072109 in python-awkward reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at:

Bug#1071358: r-cran-rgeos: FTBFS: geos.c:102:13: error: format not a string literal and no format arguments

2024-05-18 Thread Andreas Tille
Control: block -1 by 1071375 thanks Hi Santiago, Am Fri, May 17, 2024 at 10:41:36PM +0200 schrieb Santiago Vila: > Package: src:r-cran-rgeos > Version: 0.6-4-2 > Severity: serious > Tags: ftbfs thanks a lot for your QA effort. It turns out that the package is not maintained at CRAN any more.

Bug#1070839: r-cran-data.table: autopkgtest regression on i386

2024-05-11 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/Rdatatable/data.table/issues/6133

Bug#1070839: [Help] Re: Bug#1070839: r-cran-data.table: autopkgtest regression on i386

2024-05-10 Thread Andreas Tille
Control: tags -1 help Hi Graham, Am Fri, May 10, 2024 at 10:44:48AM + schrieb Graham Inggs: > Source: r-cran-data.table > Version: 1.15.4+dfsg-1 > Severity: serious > User: debian...@lists.debian.org > Usertags: regression > > r-cran-data.table's autopkgtest has regressed on i386 [1]. I've

Bug#1070515: dipy: FTBFS with nocheck profile

2024-05-07 Thread Andreas Tille
Control: tags -1 help thanks Hi Grahamm Am Mon, May 06, 2024 at 02:08:25PM + schrieb Graham Inggs: > Source: dipy > Version: 1.8.0-2 > Severity: serious > Tags: ftbfs patch thanks a lot for the patch which looks perfectly sensible. Unfortunatly the build runs into a different error as you

Bug#1069370: shasta: FTBFS: dpkg-shlibdeps: error: cannot continue due to the error above

2024-05-07 Thread Andreas Tille
Control: tags -1 help Hi, I pushed some potential fix to Git but this does not help[1]. :-( Any idea is welcome Andreas. [1] https://salsa.debian.org/med-team/shasta/-/jobs/5695708 -- https://fam-tille.de

Bug#1070459: Tagging help

2024-05-07 Thread Andreas Tille
Control: tags -1 help thanks

Bug#1070459: psortb: FTBFS: binding.c:52:13: error: implicit declaration of function ‘free’

2024-05-06 Thread Andreas Tille
Hi, I've fixed the original error in Git but Salsa CI shows another one[1] which is more tricky since it involves a header file for a perl module and I have no idea how to fix this. Any help from the team is welcome. Kind regards Andreas. [1]

Bug#1069876: libsbml: autopkgtest regression

2024-04-26 Thread Andreas Tille
Hi, Am Fri, Apr 26, 2024 at 09:27:55AM +0200 schrieb Sebastian Ramacher: > 95s autopkgtest [21:29:51]: test autodep8-python3: [--- > 95s Testing with python3.12: Short note: If I understood upstream correctly they currently support Python3.11 only. In any case they

Bug#1024889: Pending

2024-04-25 Thread Andreas Tille
Control: tags -1 pending Control: block -1 by 1064596 thanks Pplacer needs to be build against the old version of MCL which is featuring some OCAML patch. This old version was just uploaded to new. Kind regards Andreas. -- https://fam-tille.de

Bug#1069509: r-cran-metamix: FTBFS on armhf: tests fail

2024-04-25 Thread Andreas Tille
Hi Lucas, thanks a lot for all your work on rebuilding the archive on different architectures. That's really appreciated. In this specific case I wonder whether your build host has simply trouble initialising MPI given I find strings like MPI_ERRORS_ARE_FATAL Kind regards Andreas. Am

Bug#1055847: Please check python-sparse issue at Github

2024-04-24 Thread Andreas Tille
Hi Diane and Ghislain, you are listed as Uploaders of python-sparse. Since I now have other tasks than maintaining team maintained packages I would be really happy if you could subscribe upstream issue https://github.com/pydata/sparse/issues/628 and continue what I have started. Thanks a

Bug#1012893: Status of the t64 transition

2024-04-19 Thread Andreas Tille
Hi Sebastian, thank you for your work on t64 transition. Am Thu, Apr 18, 2024 at 09:22:02PM +0200 schrieb Sebastian Ramacher: I've spotted these Debian Med packages. > gentle > jellyfish > quorum > sbmltoolbox No idea how we can help here. Please let us know if we can do something. > anfo

Bug#1066334: Redefinition of _Int (Was: acedb: FTBFS: acein.c:2045:15: error: implicit declaration of function ‘add_history’ [-Werror=implicit-function-declaration])

2024-04-14 Thread Andreas Tille
H again, Am Sun, Apr 14, 2024 at 07:17:41AM +0200 schrieb Andreas Tille: > Am Sat, Apr 13, 2024 at 10:46:17PM +0100 schrieb Jeremy Sowden: > > > > The one after this looks like a GTK problem, and that's the point at > > which I bow out. I was able to fix some more missi

Bug#1066334: cython/bison issue (Was: acedb: FTBFS: acein.c:2045:15: error: implicit declaration of function ‘add_history’ [-Werror=implicit-function-declaration])

2024-04-13 Thread Andreas Tille
Hi Jeremy, Am Sat, Apr 13, 2024 at 10:46:17PM +0100 schrieb Jeremy Sowden: > > The one after this looks like a GTK problem, and that's the point at > which I bow out. Thanks a lot for your help so far. Your patches are pushed to Git. Kind regards Andreas. -- https://fam-tille.de

Bug#1066334: cython/bison issue (Was: acedb: FTBFS: acein.c:2045:15: error: implicit declaration of function ‘add_history’ [-Werror=implicit-function-declaration])

2024-04-13 Thread Andreas Tille
Control: tags -1 help thanks Hi, while I was able to fix the origininal cause of the failure I'm now blocked by some issue that cython seems to miss adding some #include but I have no idea how to accomplish this. The Salsa CI build log[1] says: ... y.tab.c: In function 'yyparse':

Bug#1067957: [[maude-bugs]] [EXTERNAL] Re: Maude fails to build on armhf

2024-04-10 Thread Andreas Tille
Hi, Am Wed, Apr 10, 2024 at 03:33:53PM -0700 schrieb Steven Eker: > I like that solution since I believe there are 64-bit platforms where long > is 32-bits. I've updated my development version thus: > >   // >   //    timeValue.tv_sec is 64-bit since Linux kernel 5.6 but GMP doesn't > yet have

Bug#1067957: [[maude-bugs]] [EXTERNAL] Re: Maude fails to build on armhf

2024-04-10 Thread Andreas Tille
Hi, I'd suggest to set Build-Depends: architecture-is-64-bit, architecture-is-little-endian and remove 32bit architectures of maude. Kind regards Andreas. -- https://fam-tille.de

Bug#1068401: Pending uplad (Was: Bug#1068401: ltrsift dependencies unsatisfiable on 32-bit non-i386 architectures.)

2024-04-04 Thread Andreas Tille
Hi Sascha, Am Thu, Apr 04, 2024 at 10:33:16PM +0200 schrieb Sascha Steinbiss: > Interesting to see that there is no ltrsift-examples package indeed. But > I must have had my reasons back then... > > Anyway, to be honest I don't see much long-term future for LTRsift. I am > actually surprised to

Bug#1065339: src:r-cran-rstanarm: FTBFS on mips64el and risc64

2024-04-04 Thread Andreas Tille
Control: retitle -1 src:r-cran-rstanarm: FTBFS on mips64el and risc64 Control: reopen -1 Control: tags -1 upstream Control: forwarded -1 https://github.com/stan-dev/rstanarm/issues/619 thanks As per autobuilders log[1] the package fails to build on mips64el and risc64 with ... g++ -std=gnu++17

Bug#1068401: Pending uplad (Was: Bug#1068401: ltrsift dependencies unsatisfiable on 32-bit non-i386 architectures.)

2024-04-04 Thread Andreas Tille
Control: tags -1 pending thanks Hi Sascha, after routine-update dh_missing failed due to compat level 13 which defaults to fail if some files are not installed. This made me aware that upstream in principle installs a test suite we could use for an autopkgtest. I also realised that you once

Bug#1067959: sambamba: FTBFS on armhf (supported compiler issue)

2024-03-29 Thread Andreas Tille
Hi, Am Fri, Mar 29, 2024 at 10:32:25PM +0900 schrieb Kentaro HAYASHI: > sambamba fails to build on armhf. Thanks a lot for this bug report. I'd recommend to drop 32bit architectures for this package. Kind regards Andreas. > FYI: > >

Bug#1060104: dcmtk: FTBFS on armel: Error: bad immediate value for offset (4100)

2024-03-19 Thread Andreas Tille
Hi Emanuele. Am Tue, Mar 19, 2024 at 12:16:16PM +0100 schrieb Emanuele Rocca: > I've uploaded a NMU to DELAYED/2: https://bugs.debian.org/1067147 Thanks a lot for your attempt to help. In principle we have a team wide low threshold NMU - so undelayed NMUs are fine. The kind of race condition

Bug#1060104: dcmtk: FTBFS on armel: Error: bad immediate value for offset (4100)

2024-03-19 Thread Andreas Tille
Hi again, sorry, I did not checked the situation. Am Tue, Mar 19, 2024 at 10:34:13AM +0100 schrieb Andreas Tille: > Testing removals are happening automatically if some RC bug exists > for a certain time without pinging. Just writing some additional > information to the bug in quest

Bug#1063980: Mark affected test xfail and reduce bug severity + report upstream

2024-03-18 Thread Andreas Tille
Control: tags -1 important Control: tags -1 upstream Control: forwarded -1 https://github.com/jnothman/UpSetPlot/issues/273 thanks Hi, I've checked the new upstream version of python-upsetplot which shows the same problem. Thus I marked the one affected test xfail and reported the problem

Bug#1066409: Reassign nodejs and merge bug (Was: Linker fails to find libraries in unstable but succeeds in testing)

2024-03-15 Thread Andreas Tille
Control: reassign -1 nodejs Control: forcemerge 1066399 -1 thanks Hi Jochen, Am Fri, Mar 15, 2024 at 08:46:11AM +0100 schrieb Jochen Sprickerhof: > > I guess that's the same as #1066399. > > libnode-dev: > libv8.so -> libnode.so > libnode.so -> libnode.so.108t64 > > But libnode.so.108t64

Bug#1066409: Linker fails to find libraries in unstable but succeeds in testing

2024-03-15 Thread Andreas Tille
Hi, thanks to the next round of Lucas' FTBFS QA rebuilds (at least) one package of the R pkg team is affected by some strange linker issue #1066409 r-cran-v8: FTBFS: ld: cannot find -lv8: No such file or directory which boils down to[1] g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o

Bug#1066409: [Help] Re: Bug#1066409: r-cran-v8: FTBFS: ld: cannot find -lv8: No such file or directory

2024-03-15 Thread Andreas Tille
"Action needed for R-pkg Uploaders"-mail I would be happy if you would pronounce whether you are up for maintaining this package actively or not. You are mentioned as only Uploader but the changelog says: $ grep '^ --' debian/changelog -- Andreas Tille Fri, 22 Dec 2023 10:19:13 +0100 -- A

Bug#1065759: Retitle libbio-samtools-perl: FTBFS on arm{el,hf}: lib/Bio/DB/Sam.xs:324:4: error: implicit declaration of function ‘bam_sort_core’; did you mean ‘bam_format1_core’? [-Werror=implicit-fun

2024-03-12 Thread Andreas Tille
Control: retitle -1 libbio-samtools-perl: FTBFS: lib/Bio/DB/Sam.xs:324:4: error: implicit declaration of function ‘bam_sort_core’; did you mean ‘bam_format1_core’? [-Werror=implicit-function-declaration] Control: tags -1 help thanks I can confirm that this bug also occures on amd64 thus

Bug#1064921: src:r-cran-estimatr: fails to migrate to testing for too long: autopkgtest regression on i386

2024-03-11 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/DeclareDesign/estimatr/issues/407 Control: reopen -1 thanks I have forwarded this problem upstream. I've also reopened this bug to make sure it will show up on our sentinel Kind regards Andreas. -- http://fam-tille.de

Bug#1064922: src:r-cran-gbm: fails to migrate to testing for too long: autopkgtest regression

2024-03-11 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/gbm-developers/gbm/issues/78 Control: reopen -1 thanks I have forwarded this bug upstream. I've also re-opened the bug to make sure it appears on our list of bugs. -- http://fam-tille.de

Bug#1064135: src:r-cran-bigmemory: fails to migrate to testing for too long: autopkgtest fails on arm*, ppc64el and s390x

2024-02-29 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/kaneplusplus/bigmemory/issues/115 Control: reopen -1 Thanks Bug was forwarded upstream with no response so far. Re-opening to stay aware that this bug exists. -- http://fam-tille.de

Bug#1026587: cerealizer: TypeError: __dict__ must be set to a dictionary, not a 'NoneType'

2024-02-28 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 j...@lesfleursdunormal.fr Hi Jean-Baptiste, the Debian packaged version of cerealizer recieved a bug report about a build failure TypeError: __dict__ must be set to a dictionary, not a 'NoneType' You can read the relevant part of the build

Bug#1054736: Do we need versiontools in Debian any more?

2024-02-26 Thread Andreas Tille
Hi Benjamin, as far as I can see no other package is using versiontools and it seems orphaned upstream. Do you think we need this package in Debian or should we rather ask ftpmaster for removal? I personally have no specific interest in this package and was just hunting some Python3.12 related

Bug#1064160: pngcrush FTBFS with libpng 1.6.42

2024-02-25 Thread Andreas Tille
Control: tags -1 patch Control: tags -1 pending Hi Marga, I've pushed the patch used in ArchLinux to Git[1]. I could do another NMU but I would prefer to move the package to Debian Phototools team and I'd volunteer to do that move. Kind regards Andreas. [1]

Bug#1061765: Help needed to fix python-coverage-test-runner

2024-02-23 Thread Andreas Tille
HI Andrius, Am Fri, Feb 23, 2024 at 09:29:27AM +0200 schrieb Andrius Merkys: > > ModuleNotFoundError: No module named 'imp' > > I had a similar problem. I worked it around by depending on > python3-zombie-imp, the original code did not require any modifications. Nice hint - implemented. Thanks

Bug#1061765: Help needed to fix python-coverage-test-runner

2024-02-22 Thread Andreas Tille
Control: tags -1 help Hi, I've attempted to fix python-coverage-test-runner in Git since this package is finally responsible for the failure of vmdb2: File "/usr/lib/python3/dist-packages/CoverageTestRunner.py", line 22, in import imp ModuleNotFoundError: No module named 'imp' In the

Bug#1058895: Status of sqlalchemy

2024-02-22 Thread Andreas Tille
Hi, we have quite some Python3.12 related bugs caused by sqlalchemy which seem to be fixed in experimental (which is lagging behind upstream 2.0.27 as well as version 1.4 in unstable where upstream just released 1.4.51). It seems the issue that leads to bug #1058265 > File

Bug#1056503: Bug#1052619: ITP: pydantic-core -- Rust implementation of pydantic core functionality

2024-02-22 Thread Andreas Tille
Hi Timo, thanks for the quick update. Am Thu, Feb 22, 2024 at 09:08:19AM +0100 schrieb Timo Röhling: > * Andreas Tille [2024-02-22 08:49]: > > any progress with pydantic-core? I've checked Salsa for the string > > "pydantic" but did not found pydantic-core there. It

Bug#1056503: ITP: pydantic-core -- Rust implementation of pydantic core functionality

2024-02-21 Thread Andreas Tille
Hi Timo, any progress with pydantic-core? I've checked Salsa for the string "pydantic" but did not found pydantic-core there. It would be really great to have pydantic 2.x (I stumbled upon python-semantic-release which also needs it to easily fix #1056503 by upgrading to latest upstream which

Bug#1055728: Segyio is lagging behind upstream (Was: segyio ftbfs with Python 3.12)

2024-02-21 Thread Andreas Tille
't import the symbols to the std:: > namespace. In general, the headers Standard C++ imports from Standard C > snips the .h and prefixes c, so stdint.h -> cstdint, stdio.h -> cstdio, etc. > > -- Tino Didriksen > > > On Wed, 21 Feb 2024 at 11:16, Andreas Tille wrote: >

Bug#1055728: Segyio is lagging behind upstream (Was: segyio ftbfs with Python 3.12)

2024-02-21 Thread Andreas Tille
Hi, I've found in the set of patches for segyio other cherry-picked patches to adapt to certain Python3.x versions[1]. The patch kindly suggested by s3v to fix this bug[2] would simply be another cherry-pick from upstream who has meanwhile released a couple of new versions incorporating all

Bug#1064223: imbalanced-learn: fails tests with sklearn 1.4: needs new versions

2024-02-20 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/scikit-learn-contrib/imbalanced-learn/issues/1062 Hi, thanks a lot for the hint about the new version of imbalanced-learn. Unfortunately it is not sufficient to simply upgrade to latest upstream as you can see in Salsa CI[1].

Bug#1044054: dyda: test failure with pandas 2.0

2024-02-18 Thread Andreas Tille
Control: tags -1 help Hi, I've pushed the packaging to Debian Science team on Salsa which created a persistent autopkgtest log in Salsa CI[1] where the said bug can be reproduced. Any help to fix TypeError: Could not convert string 'classification' to numeric The above exception was the direct

Bug#1044060: More qiime related issues affecting q2-quality-control (Was: Help needed to port qiime to Python3.12)

2024-02-18 Thread Andreas Tille
Hi again, Am Sun, Feb 18, 2024 at 12:25:49PM +0100 schrieb Andreas Tille: > I just realised that a new qiime version is out. I will upgrade > to latest upstream and see how this might affect this issue The new qiime upstream version does not change anything. After I switched q2-* pa

Bug#1044060: More qiime related issues affecting q2-quality-control (Was: Help needed to port qiime to Python3.12)

2024-02-18 Thread Andreas Tille
Hi, I just realised that a new qiime version is out. I will upgrade to latest upstream and see how this might affect this issue Kind regards Andreas. Am Sun, Feb 18, 2024 at 12:11:04PM +0100 schrieb Andreas Tille: > Control: tags -1 help > > Hi again, > > I hope to ap

Bug#1044060: More qiime related issues affecting q2-quality-control (Was: Help needed to port qiime to Python3.12)

2024-02-18 Thread Andreas Tille
no attribute '_str' This all goes back to the qiime package but I admit I have no idea how to fix this. Kind regards Andreas. [3] https://salsa.debian.org/med-team/q2-quality-control/-/jobs/5320775#L700 Am Sat, Feb 17, 2024 at 11:36:41AM +0100 schrieb Andreas Tille: > Hi, > > as

Bug#1044064: Help needed fpr last Pandas issue in pyrange (Was: q2-taxa: test failure with pandas 2.1)

2024-02-18 Thread Andreas Tille
Control: tags -1 help Hi again, Am Sat, Feb 17, 2024 at 07:31:48PM +0100 schrieb s3v: > More immediate fix is attached but I guess there is a more elegant > way by changing the code in _ids_to_keep_from_taxonomy() function. thanks a lot for all your fixes you provided for Debian Med packages.

Bug#1053943: [Help] q2-taxa: test failure with pandas 2.1 (Was: q2-types: test failure with pandas 2.1)

2024-02-17 Thread Andreas Tille
Control: tags -1 help Am Sat, Feb 17, 2024 at 06:35:41AM +0100 schrieb s3v: > Attached patch makes autopkg tests pass in unstable on a basis of > your work/references and [1] (iteritems() was deprecated since version > 1.5.0 in favor of items()). Cool. This is uploaded (but not yet in incoming

Bug#1053944: q2-types: test failure with pandas 2.1 (Was: Bug#1044068: q2templates: FTBFS with pandas 2.0)

2024-02-16 Thread Andreas Tille
Control: tags -1 help Hi again, thanks again for your great help. I admit I need some help for q2-types as well. While log in the bug report vanished you will easily find things like TypeError: read_csv() got an unexpected keyword argument 'squeeze' when trying to build the package. I've

Bug#1044068: q2templates: FTBFS with pandas 2.0

2024-02-16 Thread Andreas Tille
Hi, thanks a lot for all your help! I've just uploaded q2templates. If you have more hints to pandas2 related bugs these are very welcome. Kind regards Andreas. Am Fri, Feb 16, 2024 at 02:29:15PM +0100 schrieb s3v: > Hi, > > sorry for writing again but, after removing override for

Bug#1044079: augur: FTBFS with pandas 2.0

2024-02-15 Thread Andreas Tille
Control: tags -1 pending Hi, thanks a lot for this hint. Am Wed, Feb 14, 2024 at 10:36:05AM +0100 schrieb s3v: > I don't know if renaming is a drop-in replacement Me neither but I simply trust that its passing its test suite. Kind regards Andreas. -- http://fam-tille.de

Bug#1056419: Spinx help needed

2024-02-14 Thread Andreas Tille
Control: tags -1 pending Hi, I pushed fixes for #1056419 and #1058311 to Git and I think should be fixed as well. The only remaining build problem is new and caused by sphinx[1]: dh_sphinxdoc -i -O--buildsystem=pybuild dh_sphinxdoc: error:

Bug#1063599: More info (Was: mathgl: FTBFS on amd64: tests seg fault)

2024-02-14 Thread Andreas Tille
Control: tags -1 moreinfo Control: severity -1 important Hi Sebastian, the package builds nicely in my local pbuilder, in Salsa CI as well as in the autobuilders. Thus I'm tagging the bug moreinfo and set severity to important. Kind regards Andreas. -- http://fam-tille.de

Bug#1056419: Can we also move uncertainties to DPT (Was: python-hug: autopkgtest failure with Python 3.12)

2024-02-14 Thread Andreas Tille
Hi, thanks for Federico confirming, thus I will move the package to not need to ask again in a possible future attempt. Am Wed, Feb 14, 2024 at 12:24:03PM +0100 schrieb Alexandre Detiste: > Hi Andreas, > > I think usage of "past" has been neutered since: > > if sys.version_info < (3,): >

Bug#1056419: Can we also move uncertainties to DPT (Was: python-hug: autopkgtest failure with Python 3.12)

2024-02-14 Thread Andreas Tille
Hi again Federico, > Am Thu, Feb 08, 2024 at 07:02:09PM +0100 schrieb Federico Ceratto: > > Sure, go ahead, and thank you for taking care of the bug! After you accepted python-hug I wonder whether we can also move python-uncertainties to DPT. I think the usage of past in uncertainties is

Bug#1063800: Should we restrict libtread-pool to 64bit only

2024-02-12 Thread Andreas Tille
Am Mon, Feb 12, 2024 at 10:09:43PM -0500 schrieb Aaron M. Ucko: > Andreas Tille writes: > > >Build-Depends libthread-pool 4.0.0 which does not build > >for 32bit architectures[1] > > I see a fix in experimental: > > https://buildd.debian.org/statu

Bug#1063800: Should we restrict libtread-pool to 64bit only (Was: Bug#1063800: src:pinfish: fails to migrate to testing for too long: not installable on armel, armhf and i386)

2024-02-12 Thread Andreas Tille
Hi, the chain of dependencies for pinfish which creates the problem is pinfish depends racon which in turn can't install its Build-Depends libthread-pool 4.0.0 which does not build for 32bit architectures[1] My suggestion to solve the issue is to explicitly set Architecture:

Bug#1059385: r-cran-ggally: autopkgtest regression

2024-02-12 Thread Andreas Tille
Control: block -1 by 1063785 Control: tags -1 pending Hi, as per upstream the test fails due to the missing Test-Depends r-cran-intergraph. This is uploaded to new (WNPP #1063785) and will be uploaded as soon as it has cleared new. Kind regards Andreas. -- http://fam-tille.de

Bug#1058997: Patch is not sufficient (Was: flask-autoindex is incompatible with Py3.12)

2024-02-09 Thread Andreas Tille
Control: tags -1 - patch Hi Alexandre, I've applied your patch in Git but as you can see in Salsa CI[1] it is not sufficient to fix the build issue. Kind regards and thanks for your help anyway Andreas. [1] https://salsa.debian.org/python-team/packages/flask-autoindex/-/jobs/5272253 --

Bug#1059666: python-hug: autopkgtest failure with Python 3.12

2024-02-09 Thread Andreas Tille
Hi Federico, Am Thu, Feb 08, 2024 at 07:02:09PM +0100 schrieb Federico Ceratto: > Sure, go ahead, and thank you for taking care of the bug! Done.[1] Please note: I activated build-time testing and non-trivial autopkgtest. This involved some fixes for Python3.11, Python3.12 as well as numpy. I

Bug#1056227: Fixed Python3.12 issue but astropy issue is pending (Was: aplpy's autopkg tests fail with Python 3.12)

2024-02-09 Thread Andreas Tille
Control: tags -1 pending Hi Ole, I've fixed the distutils issue of Python3.12 in Git but there is an issue pending which you probably can solve way more easier than I: from astropy.config.configuration import ( E ImportError: cannot import name 'update_default_config' from

Bug#1059666: python-hug: autopkgtest failure with Python 3.12

2024-02-08 Thread Andreas Tille
Hi Federico, I'd volunteer to fix this bug but my personal policy is to work on team maintained packages only. Would you mind if I move the package to Debian Python Team? Kind regards Andreas. -- http://fam-tille.de

Bug#1059642: [AmanoTeam/duckpy] Example stopped working (Issue #15)

2024-02-08 Thread Andreas Tille
Hi Alisson, Am Thu, Feb 08, 2024 at 07:12:35AM -0800 schrieb Alisson L.: > Hello, and thanks for reaching out. An empty results list usually means that > DuckDuckGo has blocked your IP. I have just tried here with my home IP, and > it worked fine: Argh, what might be the reason for blocking on

Bug#1059642: python-duckpy: autopkgtest failure with Python 3.12

2024-02-08 Thread Andreas Tille
Control: retitle -1 python-duckpy: autopkgtest failure Control: tags -1 upstream Control: forwarded -1 https://github.com/AmanoTeam/duckpy/issues/15 Hi, the problem does not only exists for Python3.12. Thus I changed the bug title and reported the issue upstream. Kind regards Andreas. --

Bug#1058336: Team-maintenance of visidata in Debian Science team (Was: visidata: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13)

2024-02-08 Thread Andreas Tille
Hi Anja, when analysing Python3.12 bugs like this I stumbled upon visidata. While I have no idea for a fix my first attempt would be to update to the latest upstream version and see whether the bug might be fixed. I would love to help out (with such an upgrade or sponsoring the package.)

Bug#1063431: src:r-cran-future.apply: fails to migrate to testing for too long: autopkgtest failure

2024-02-08 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/HenrikBengtsson/future.apply/issues/120 Hi Paul, thanks a lot for all your work. I have forwarded the problem upstream. Kind regards Andreas. -- http://fam-tille.de

Bug#1058364: python-etcd: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13

2024-02-08 Thread Andreas Tille
Control: tags -1 pending Hi, I've fixed the issue reported in the bug in Git. However, Salsa CI shows another issue[1]: if _is_instance_mock(spec): > raise InvalidSpecError(f'Cannot spec a Mock object. > [object={spec!r}]') E mock.mock.InvalidSpecError: Cannot spec

Bug#1056442: What about upgrading to latest upstream (Was: pyrlp's autopkg tests fail with Python 3.12)

2024-02-08 Thread Andreas Tille
Hi Ben, I'd volunteer to upgrade pyrlp to its latest upstream version (4.0.0) if the package can be moved to DPT. Please note: I have not yet checked the latest upstream version - I'm just hunting for "any" Python3.12 related bug and see what I can do if packages are team maintained. Kind

Bug#1044079: [Help] augur: FTBFS with pandas 2.0

2024-02-07 Thread Andreas Tille
Control: tags -1 help Hi Rebecca, Étienne has forwarded the issue long ago but it seems upstream does not want to move to Pandas 2.x[1] and simply closed the issue. Since I do not see any good reason that we maintain two versions of Pandas I need to ask for some help in this issue. Kind

Bug#1062427: ghmm: NMU diff for 64-bit time_t transition

2024-02-07 Thread Andreas Tille
Hi Lukas, Am Thu, Feb 01, 2024 at 11:27:43AM +0100 schrieb Lukas Märdian: > please note that ghmm seems to FTBFS for a reason unrelated to this NMU: > > dh_install > dh_install: warning: Cannot find (any matches for) > "usr/lib/python3*/site-packages/*" (tried in ., debian/tmp) > > dh_install:

Bug#1044055: Reopen

2024-02-06 Thread Andreas Tille
Control: reopen -1 The issue is not closed by latest upload -- http://fam-tille.de

Bug#1044068: q2templates: FTBFS with pandas 2.0

2024-02-04 Thread Andreas Tille
Hi Rebecca, I've checked several Debian Med packages for your assumption that replacing pandas.util.testing might help but non of the candidates I've checked was caused by this. I'm rather seeing quite strange errors like in the case of q2templates here in Salsa CI

Bug#1044073: Sorry Re: python-altair and pandas 2.0

2024-02-04 Thread Andreas Tille
Am Sat, Feb 03, 2024 at 10:51:05PM + schrieb Rebecca N. Palmer: > > I think we should strive for latest upstream in > > general > > Agreed, assuming that doing so doesn't break things. I picked an upstream version which is compatible with pandas 2.x but does not need any not yet packaged

Bug#1044071: Bug#1043240: transition: pandas 1.5 -> 2.1 - please upload fixes

2024-02-03 Thread Andreas Tille
Hi again, Am Fri, Feb 02, 2024 at 09:56:14PM +0100 schrieb Andreas Tille: > Hi Rebecca, > > Am Tue, Jan 30, 2024 at 08:05:35AM + schrieb Rebecca N. Palmer: > > I intend to upload pandas 2.x to unstable soon. These packages have a patch > > in their bug - please upl

Bug#1044073: python-altair and pandas 2.0

2024-02-03 Thread Andreas Tille
Hi Rebecca, Am Sat, Feb 03, 2024 at 09:32:32PM + schrieb Rebecca N. Palmer: > Please don't skip/xfail tests - my suggestion above is an actual fix: > > https://salsa.debian.org/rnpalmer-guest/python-altair/-/tree/fix1044073?ref_type=heads > > (In a fork because, despite its description,

Bug#1044076: influxdb-python and pandas 2.1

2024-02-03 Thread Andreas Tille
Hi Rebecca, Am Sat, Feb 03, 2024 at 12:32:07PM + schrieb Rebecca N. Palmer: > My fixes are pushed to Salsa, but they're in a fork because this isn't a > debian-science package: > https://salsa.debian.org/rnpalmer-guest/influxdb-python Argh, I missed that link inside the bug report and

Bug#1044073: python-altair: FTBFS with pandas 2.0

2024-02-03 Thread Andreas Tille
Short notice while traveling. I tried @pytest.skip which failed since it seems even from altair.jupyter.jupyter_chart import ( IntervalSelection, IndexSelection, PointSelection, ) is a problem. WHen uncommenting this even more errors arrise. Sorry for my brevity Andreas. Am

Bug#1044073: python-altair: FTBFS with pandas 2.0

2024-02-02 Thread Andreas Tille
Hi, I tried to upgrade python-altair in Git to the latest upstream version which should work with Pandas 2.0. Unfortunately it has a new dependency[1] which is not packaged yet. I had no luck to skip the according test which fails in build time test[2]. Kind regards Andreas. [1]

Bug#1044076: influxdb-python: FTBFS with pandas 2.0

2024-02-02 Thread Andreas Tille
Hi Rebecca, I followed your hint "replacing all 3 instances of pandas.util.testing with pandas.testing" [1] but as you can see in Salsa CI there are remaining issues[2]. The Python3.12 issues should be fixed meanwhile in version 5.3.1-5. Any further hints / patches (preferably pushed to Salsa)

Bug#1061344: User input needed: Stop supporting 32 bit architectures with emboss (Was: emboss-lib: identified for time_t transition but no ABI in shlibs)

2024-02-01 Thread Andreas Tille
Hi again, I've filed bug #1062371 RM: emboss [armel armhf i386 hppa m68k powerpc sh4] -- ROM; No support of 32 bit architectures any more Kind regards Andreas. Am Wed, Jan 31, 2024 at 07:53:26AM +0100 schrieb Andreas Tille: > Hi again, > > besides my suggested solution to

Bug#1058454: Do we really need to support 32bit in abinit and prody (maybe others)

2024-01-31 Thread Andreas Tille
Hi, in connection with the time_t transition in Debian Med we are discussing[1] whether we really need 32 bit support for some of our tools or whether we should realistically drop this support to concentrate on problems which are more relevant for our users. I wonder whether we could also

Bug#1061344: User input needed: Stop supporting 32 bit architectures with emboss (Was: emboss-lib: identified for time_t transition but no ABI in shlibs)

2024-01-30 Thread Andreas Tille
/ReleaseGoals/64bit-time Am Fri, Jan 26, 2024 at 10:44:09AM +0100 schrieb Andreas Tille: > Hi Charles, > > I wonder how we can properly solve this bug. In the early stage of > Emboss packaging obviously the packages > >libajax6, >libajax6-dev, >

Bug#1060965: q2cli: AttributeError: module 'bibtexparser' has no attribute 'bparser'

2024-01-30 Thread Andreas Tille
Control: tags -1 - upstream Control: tags -1 pending The issue was resolved by downgrading bibtexparser to the latest stable upstream release (the formerly uploaded beta caused the problem). Unfortunately there is a new issue in the new version of q2cli which fails to build due to test suite

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