Bug#1103579: coot: autopkgtest regression: ImportError

2025-04-22 Thread Andrius Merkys
Hi, On 2025-04-19 14:09, Chris Hofstaedtler wrote: coot's autopkgtests fail with rdkit 202503.1-2: https://ci.debian.net/packages/c/coot/testing/amd64/60162582/ 76s Traceback (most recent call last): 76s File "", line 198, in _run_module_as_main 76s File "", line 88, in _run_code 7

Bug#1102784: spglib: FTBFS: scikit_build_core._vendor.pyproject_metadata.errors.ConfigurationError: "project.license-files" must not be used when "project.license" is not a SPDX license expression

2025-04-14 Thread Andrius Merkys
On 2025-04-14 20:39, Sergio Durigan Junior wrote: Apologies, this was an oversight on my end. I've just pushed the branch and the tag. Thanks, Sergio! Best wishes, Andrius

Bug#1102784: spglib: FTBFS: scikit_build_core._vendor.pyproject_metadata.errors.ConfigurationError: "project.license-files" must not be used when "project.license" is not a SPDX license expression

2025-04-13 Thread Andrius Merkys
Hi Sergio, On 2025-04-12 23:48, Sergio Durigan Junior wrote: On Saturday, April 12 2025, Santiago Vila wrote: During a rebuild of all packages in unstable, your package failed to build: Fixed and uploaded. Thanks a lot for fixing this! Please also push the changes to salsa after such uplo

Bug#1102472: python3-torch: -march=native leaks into rdeps

2025-04-09 Thread Andrius Merkys
Hi, On 2025-04-09 14:38, Santiago Vila wrote: This is my proposal to fix this bug. (to be applied with "git am"). The only problem is that salsa has a version 2.6.0+dfsg-6 which is unreleased and I don't know how that should be handled. I would suggest branching off debian/2.6.0+dfsg-5 and ap

Bug#1101533: pytorch-geometric: Failing autopkgtests

2025-04-09 Thread Andrius Merkys
Hi Santiago, On 2025-04-09 14:18, Santiago Vila wrote: Not so fast! Please take a look at https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1102472 The real solution might be in src:python3-torch, I was looking at dropping the following lines:     # https://stackoverflow.com/questi

Bug#1101533: pytorch-geometric: Failing autopkgtests

2025-04-09 Thread Andrius Merkys
Hi Santiago, On 2025-04-09 12:37, Santiago Vila wrote: Hi. We are an architecture away (riscv64) from passing the autopkgtests. I'm making this official and visible by reopening again. https://qa.debian.org/excuses.php?package=pytorch-geometric The problem is that the package is arch:all and i

Bug#1101533: Processed: Re: Bug#1101533: pytorch-geometric: Failing autopkgtests

2025-04-05 Thread Andrius Merkys
Hi Santiago, Apologies for not replying earlier. I was busy taking care of openstructure and its reverse dependencies. I use it in my dayjob, hence the priority. On 2025-04-01 13:52, Santiago Vila wrote: Note: I think autopkgtest is very smart and it would be possible to skip tests condition

Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

2025-04-05 Thread Andrius Merkys
Control: tags -1 + patch pending On Wed, 2 Apr 2025 10:05:52 +0300 Andrius Merkys wrote: I finally managed to isolate the difference in cdhit output which causes segfaults in provean. It seems that cdhit >= 4.8.1-4 replaced full FASTA headers in its output with partial IDs: diff -r /h

Bug#1101533: Processed: Re: Bug#1101533: pytorch-geometric: Failing autopkgtests

2025-04-02 Thread Andrius Merkys
Hi, On 2025-04-02 13:28, Santiago Vila wrote: Well, it still didn't work. Do we need a dependency somewhere on the current version in unstable? (the failing tests say "testing"). I'd like to understand this but I entered the autopkgtests world recently... I find it strange that autopkgtests

Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

2025-04-02 Thread Andrius Merkys
A note for posterity: I solved this bug by comparing the outputs of each tool used in provean (cdhit and blastdbcmd) between last known working environment (Ubuntu Xenial) and Ubuntu Focal (where it is broken). After preparing a patch, I checked it on Debian Sid as well. Correct output with

Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

2025-04-02 Thread Andrius Merkys
Hello, I finally managed to isolate the difference in cdhit output which causes segfaults in provean. It seems that cdhit >= 4.8.1-4 replaced full FASTA headers in its output with partial IDs: diff -r /home/andrius/provean/good/cdhit.cluster /home/andrius/provean/bad/cdhit.cluster 1c1 < >gi

Bug#1101533: pytorch-geometric: Failing autopkgtests

2025-03-31 Thread Andrius Merkys
Hi Santiago, On 2025-03-29 01:30, Santiago Vila wrote: The autopkgtests for this package are failing, and I guess that they need to pass before the package can propagate to testing. In 2.6.1-3, I've disabled the tests which can't even run because the dependencies may not be installed, but the

Bug#1101467: redmine-plugin-redhopper: Should be removed from Debian

2025-03-28 Thread Andrius Merkys
Hi, On 2025-03-28 02:09, Soren Stoutner wrote: redmine-plugin-redhopper is abandoned upstream: https://www.redmine.org/plugins/redhopper It also depends on a package that is no longer in Debian: ruby-acts-as-list And it is unlikely to work with Redmine 6.x. Considering the above, it is prob

Bug#1100238: lintian: FTBFS: make[1]: *** No rule to make target '/usr/share/cdbs/1/rules/simple-patchsys.mk'. Stop.

2025-03-13 Thread Andrius Merkys
On 2025-03-12 18:31, Santiago Vila wrote: debian/rules:4: /usr/share/cdbs/1/rules/simple-patchsys.mk: No such file or directory make[1]: *** No rule to make target '/usr/share/cdbs/1/rules/simple-patchsys.mk'. Stop. This is closely related to autopkgtest failure for lintian which emits the

Bug#1093086: [Debichem-devel] Bug#1093086: Bug#1093086: rdkit: FTBFS on big-endian architectures

2025-03-06 Thread Andrius Merkys
Hi Michael, On 2025-03-04 02:40, Michael Banck wrote: On Mon, Mar 03, 2025 at 12:22:17PM +0200, Andrius Merkys wrote: I think this is high time to proceed with architecture limiting. Are you planning to update rdkit to 202409.5, or are you fine with me performing the architecture limiting ASAP

Bug#1093086: [Debichem-devel] Bug#1093086: Bug#1093086: rdkit: FTBFS on big-endian architectures

2025-03-03 Thread Andrius Merkys
Hi Michael, On 2025-01-16 09:45, Michael Banck wrote: On Thu, Jan 16, 2025 at 09:39:08AM +0200, Andrius Merkys wrote: However, the issue with FTBFS on big-endian architectures persists. Yeah :-/ We may have to drop the support for big-endians as well. I opened an upstream issue yesterday

Bug#1093354: pytorch-geometric: FTBFS: Error: Python 3.13+ not yet supported for torch.compile

2025-02-24 Thread Andrius Merkys
Hi, On 2025-02-22 13:40, Santiago Vila wrote: Please note that the autopkgtests for the fixed version https://tracker.debian.org/pkg/pytorch-geometric do not pass. [ Not sure if this deserves a new bug, or reopening this one, as the way it fails is very similar ]. These are because python3-

Bug#1071132: ovito accesses the internet during the build

2025-02-20 Thread Andrius Merkys
Dear Maintainer, On Tue, 14 May 2024 23:49:11 +0300 Adrian Bunk wrote: Running Sphinx v7.2.6 loading intersphinx inventory from https://ovito.org/docs/current/python/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv... Warning, treated as error: f

Bug#1071807: prody: FTBFS: ModuleNotFoundError: No module named 'numpy.testing.decorators'

2025-02-13 Thread Andrius Merkys
Hello, The upstream has said they are not considering fixing this a priority, thus unless someone from Debian side is willing to work on a patch, prody will not make it to trixie. Andrius

Bug#1094821: spglib: autopkgtest failure on 32 bits blocking ruby3.3 transition

2025-02-13 Thread Andrius Merkys
Hi, On 2025-02-06 23:39, Lucas Nussbaum wrote: Digging a bit further, Thanks for investigating this issue. 1/ I confirmed that it has nothing to do with ruby (pybuild-autopkgtest fails the same way with no ruby packages installed) Good. 2/ It seems that the bottom line is: spglib built a

Bug#1093488: php-text-figlet: Useless in Debian

2025-02-05 Thread Andrius Merkys
Hi David, On Sun, 19 Jan 2025 10:19:54 +0100 David =?iso-8859-1?Q?Pr=E9vot?= wrote: This package hasn’t seen an upstream activity for more than twelve years, and has no dependencies (besides php-text-captcha, but the same can probably be said about it) in Debian. Given how PHP has changed in t

Bug#1093501: [pkg-php-pear] Bug#1093501: php-text-password: Useless in Debian

2025-02-05 Thread Andrius Merkys
Hi David, Sorry for not replying faster. On 2025-01-21 00:12, David Prévot wrote: On 20/01/2025 08:25, Andrius Merkys wrote: On 2025-01-19 12:16, David Prévot wrote: This package hasn’t seen any upstream activity for a few years, and has no dependencies (besides php-text-captcha, but the

Bug#1094821: spglib: autopkgtest failure on 32 bits blocking ruby3.3 transition

2025-01-31 Thread Andrius Merkys
Hi, On 2025-01-31 15:54, Lucas Kanashiro wrote: spglib autopkgtest is failing on 32 bits architectures due to some issues with the python test suite: https://ci.debian.net/packages/s/spglib/testing/armel/57276728 https://ci.debian.net/packages/s/spglib/testing/armhf/57232534/ https://ci.debian

Bug#1094697: [Debichem-devel] Bug#1094697: gemmi: FTBFS with numpy 2.x

2025-01-30 Thread Andrius Merkys
On 2025-01-30 12:30, Andrey Rakhmatullin wrote: Can be seen on https://ci.debian.net/packages/g/gemmi/testing/amd64/57218911/ but also fails during package build. FAILED tests/test_hkl.py::TestMtz::test_f_phi_grid - AssertionError: False is... FAILED tests/test_hkl.py::TestSfMmcif::test_reading

Bug#1094717: [Debichem-devel] Bug#1094717: rdkit: FTBFS with numpy 2.x

2025-01-30 Thread Andrius Merkys
On 2025-01-30 13:37, Bas Couwenberg wrote: Dear Maintainer, Your package FTBFS during the numpy2 transition: https://buildd.debian.org/status/fetch.php?pkg=rdkit&arch=amd64&ver=202409.4-1%2Bb1&stamp=1738065005&raw=0 It is interesting to see the following error in the build logs: A module

Bug#1093582: libautomaton-java: inconsistent JAR and POM placement

2025-01-24 Thread Andrius Merkys
Hi, On Fri, 24 Jan 2025 15:30:50 +1300 Vladimir Petko wrote: The patch updated groupId from 'dk.brics.automaton' to 'dk.brics'. This means that reverse-dependencies need to be updated. This is a separate issue in src:android-platform-tools-base. src:automaton was broken and fixed in 1.12-4+

Bug#1093354: pytorch-geometric: FTBFS: Error: Python 3.13+ not yet supported for torch.compile

2025-01-22 Thread Andrius Merkys
Hello, On 2025-01-17 20:54, Santiago Vila wrote: === short test summary info  FAILED test/data/test_feature_store.py::test_feature_store - RuntimeError: Boolean value of Tensor with more than one value is ambiguous

Bug#1093501: [pkg-php-pear] Bug#1093501: php-text-password: Useless in Debian

2025-01-19 Thread Andrius Merkys
Hi David, On 2025-01-19 12:16, David Prévot wrote: This package hasn’t seen any upstream activity for a few years, and has no dependencies (besides php-text-captcha, but the same can probably be said about it) in Debian. Given how PHP has changed in the mean time, I doubt it’s even still working

Bug#1093086: [Debichem-devel] Bug#1093086: Bug#1093086: rdkit: FTBFS on big-endian architectures

2025-01-16 Thread Andrius Merkys
Hi, On 2025-01-16 09:45, Michael Banck wrote: I opened an upstream issue yesterday evening and somebody mentioned interest in looking at it, so maybe let's wait a day or two whether they get a fix/PR, but yeah, otherwise we should drop big-endian at least temporarily. Thanks for forwarding the

Bug#1093086: [Debichem-devel] Bug#1093086: Bug#1093086: Bug#1093086: Bug#1093086: rdkit: FTBFS on big-endian architectures

2025-01-15 Thread Andrius Merkys
Control: found -1 202409.4-1 Hi Michael, On 2025-01-15 19:44, Michael Banck wrote: I did not have a problem building it, so I uploaded 202409.4-1, let's see how that one goes on the autobuilders. Thanks a lot for uploading 202409.4-1. Interestingly, the problem with 'convert' does not resurf

Bug#1093086: [Debichem-devel] Bug#1093086: rdkit: FTBFS on big-endian architectures

2025-01-15 Thread Andrius Merkys
Hello, On 2025-01-15 09:54, Andrius Merkys wrote: From a quick glance it seems that a lot of problems are related to Python pickle reading. Upstream has made some fixes related to endianness in version 202409.4 [1], thus packaging the newer upstream version might mitigate the problem. [1

Bug#1093086: rdkit: FTBFS on big-endian architectures

2025-01-14 Thread Andrius Merkys
Source: rdkit Version: 202409.2-3 Severity: serious Tags: ftbfs Hello, rdkit FTBFS in sid on s390x and ppc64. This manifests in the failure of many tests: The following tests FAILED: 8 - testDataStructs (Subprocess aborted) 9 - testFPB (Subprocess aborted) 10 - te

Bug#1083076: marked as pending in rdkit

2025-01-13 Thread Andrius Merkys
Control: tag -1 pending Hello, Bug #1083076 in rdkit 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: https://salsa.debian.org/debichem-team/rdkit/-/commit/e8a99524ffc5416293e85f3f22aac0

Bug#1083076: [Debichem-devel] Bug#1083076: Bug#1083076: Bug#1083076: 1083076 affects armel too

2025-01-13 Thread Andrius Merkys
Hi Michael, On 2025-01-11 22:01, Michael Banck wrote: On Mon, Dec 23, 2024 at 01:27:35PM +0200, Andrius Merkys wrote: Since the freeze is drawing near, and rdkit is blocking a lot of packages, I would suggest considering shipping rdkit without 32bit support in trixie. This would cause all its

Bug#1091570: simbody: FTBFS on i386: tests fail

2025-01-02 Thread Andrius Merkys
Control: tags -1 + confirmed Hello, On 2024-12-28 18:37, Lucas Nussbaum wrote: The following tests FAILED: 5 - RandomTest (Failed) I can confirm this test fails. I tried building with DEB_BUILD_OPTIONS=noopt, but got the same result, so this is unrelated to optimization. The cod

Bug#1083076: [Debichem-devel] Bug#1083076: 1083076 affects armel too

2024-12-23 Thread Andrius Merkys
Hi, On Thu, 28 Nov 2024 18:40:07 +0100 Michael Banck wrote: On Thu, Nov 28, 2024 at 09:40:01AM +0200, Andrius Merkys wrote: > The same issue persists on armel too. I think we should add autopkgtest to > possibly identify other architectures having this issue. Looks like to be a general

Bug#1089231: dials: autopkgtest regression in testing

2024-12-09 Thread Andrius Merkys
Hello, On 2024-12-07 15:56, Graham Inggs wrote: 219s from .pinkindexer import PinkIndexer 219s /usr/lib/python3/dist-packages/dials/algorithms/indexing/lattice_search/pinkindexer.py:5: in 219s import gemmi 219s E ModuleNotFoundError: No module named 'gemmi' dials autopkgtest apparently does

Bug#1088896: [Debichem-devel] Bug#1088896: smiles-scripts: FTBFS: scripts/smi_isomorphism: -(1) XXXXXXX: different number of moieties [...], 1 vs. 2

2024-12-02 Thread Andrius Merkys
Control: tags -1 + confirmed Control: owner -1 ! Hello, On 2024-12-02 18:48, Santiago Vila wrote: Package: src:smiles-scripts Version: 0.2.0+dfsg1-6 Severity: serious Tags: ftbfs Dear maintainer: During a rebuild of all packages in unstable, your package failed to build This happens due to

Bug#1083076: 1083076 affects armel too

2024-11-27 Thread Andrius Merkys
control: retitle -1 python3-rdkit: SEGFAULT on import on armhf and armel Hello, The same issue persists on armel too. I think we should add autopkgtest to possibly identify other architectures having this issue. Andrius

Bug#1083076: found in rdkit/202409.2-2 as well

2024-11-27 Thread Andrius Merkys
control: found -1 202409.2-2 Hello, The issue with segmentation fault on armhf persists in rdkit/202409.2-2 as well. Andrius

Bug#1085136: python3-mongomock: It no longer seems to work with the current pymongo

2024-11-20 Thread Andrius Merkys
Hi, On Tue, 15 Oct 2024 11:39:58 +0200 "Salvo \"LtWorf\" Tomaselli" wrote: Dear Maintainer, unfortunately pymongo changed API This python code no longer works from mongomock import gridfs gridfs.enable_gridfs_integration() I am not familiar with the package. There seems to be a new upstrea

Bug#1086353: apache-opennlp: FTBFS: autobuilder hangs

2024-11-06 Thread Andrius Merkys
Control: tags -1 + confirmed On 10/30/24 13:15, Santiago Vila wrote: [INFO] --- [INFO]  T E S T S [INFO] --- E: Build killed with signal TERM after 60 minutes of inactivity ---

Bug#1082747: cod-tools: FTBFS (only) on riscv64

2024-09-29 Thread Andrius Merkys
Hello, I am one of the upstream developers of cod-tools. Thanks a lot everyone for tracking down the issue and coming up with a patch. On 2024-09-29 22:52, Santiago Vila wrote: El 29/9/24 a las 20:21, Aurelien Jarno escribió: 1) Defining the rule with an absolute path: I would have gone wi

Bug#1082747: cod-tools: FTBFS (only) on riscv64

2024-09-26 Thread Andrius Merkys
Hi, On 2024-09-25 18:30, gregor herrmann wrote: I noticed that cod-tools 3.10.0+dfsg-1.1 fails to build but only on riscv64: https://buildd.debian.org/status/package.php?p=cod-tools https://buildd.debian.org/status/logs.php?pkg=cod-tools I care about this issue because 1) I uploaded the -1.1 N

Bug#1075155: libccp4: ftbfs with GCC-14

2024-09-24 Thread Andrius Merkys
control: severity -1 important Hello, I have added -Wno-incompatible-pointer-types to CFLAGS for now, avoiding FTBFS in order to let all reverse dependencies migrate before the freeze. The upstream is informed about the issue, -Wno-incompatible-pointer-types should be removed as soon as prope

Bug#1075155: libccp4: ftbfs with GCC-14

2024-09-10 Thread Andrius Merkys
control: forwarded -1 c...@dl.ac.uk Hello, I re-forwarded the issue to ccp4@ and got reply that the upstream has recorded the bug in their internal issue tracker. Andrius

Bug#1080517: [Debichem-devel] Bug#1080517: jni-inchi: FTBFS with inchi 1.07.1

2024-09-05 Thread Andrius Merkys
Hi, An upload of -8 has failed somewhy, I will retry ASAP. Andrius

Bug#1080050: Should mbdyn be removed from unstable?

2024-08-29 Thread Andrius Merkys
Control: severity -1 normal Control: retitle -1 RM: mbdyn -- RoM; rc-buggy Control: reassign -1 ftp.debian.org Control: affects -1 + src:mbdyn Hello, On 2024-08-30 07:32, Helmut Grohne wrote: I suggest removing mbdyn from Debian for the following reasons: * It accumulated one RC-bug: + #9

Bug#1079604: epics-base:FTBFS:build failure (not support riscv64)

2024-08-28 Thread Andrius Merkys
Hi Yue, On 2024-08-25 08:24, Yue Gui wrote: Dear epics-base Maintainer, The package epics-base build failed on arch riscv64.The crucial buildd log below: [snip] My solution to this issue: Add riscv64 support for this package. I have completed the development of the patch for supporting the

Bug#1073390: marked as pending in python-docxcompose

2024-08-28 Thread Andrius Merkys
Control: tag -1 pending Hello, Bug #1073390 in python-docxcompose 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: https://salsa.debian.org/python-team/packages/python-docxcompose/-/comm

Bug#1064024: juce: FTBFS on mips64el: Failed to build juceaide

2024-08-28 Thread Andrius Merkys
Hello, It seems that the global offset table gets exceeded for mips64el even with -mxgot. As the trixie freeze is drawing near I would suggest RMing juce binaries (and their reverse dependencies) for mips64el for the time being. Andrius

Bug#1075155: libccp4: ftbfs with GCC-14

2024-08-27 Thread Andrius Merkys
control: forwarded -1 ccp4-...@dl.ac.uk Hello, The actual log excerpt reporting build failure is the following: fortran/cmtzlib_f.c: In function 'lrhist_': fortran/cmtzlib_f.c:279:43: error: passing argument 2 of 'ccp4_lrhist' from incompatible pointer type [-Wincompatible-pointer-types] 27

Bug#1073561: [Debichem-devel] Bug#1073561: openbabel: FTBFS: failing tests test_tautomer_2[27]

2024-06-30 Thread Andrius Merkys
control: tags -1 + unreproducible control: severity -1 normal On 2024-06-30 18:53, Michael Banck wrote: Hi, On Sat, Jun 29, 2024 at 10:21:02PM +0300, Adrian Bunk wrote: On Mon, Jun 17, 2024 at 04:58:46PM +0300, Andrius Merkys wrote: Source: openbabel Version: 3.1.1+dfsg-9 Severity: serious

Bug#1073455: [Debichem-devel] Bug#1073455: openstructure: FTBFS: TypeError: unsupported operand type(s) for -: 'NoneType' and 'float'

2024-06-25 Thread Andrius Merkys
control: forwarded -1 openstructure-us...@maillist.unibas.ch On 2024-06-16 16:08, Lucas Nussbaum wrote: == ERROR: testSpearmanCorrel (__main__.TestTable.testSpearmanCorrel) ---

Bug#1073561: openbabel: FTBFS: failing tests test_tautomer_2[27]

2024-06-17 Thread Andrius Merkys
Source: openbabel Version: 3.1.1+dfsg-9 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs Hi, openbabel FTBFS both in unstable (if a fix for #1073327 is applied) and testing with the following: 99% tests passed, 2 tests failed out of 229 Total Test time (real) = 317.34 sec The f

Bug#1073327: [Debichem-devel] Bug#1073327: openbabel: FTBFS: xml.cpp:245:39: error: invalid conversion from ‘const xmlError*’ {aka ‘const _xmlError*’} to ‘xmlError*’ {aka ‘_xmlError*’} [-fpermissive]

2024-06-17 Thread Andrius Merkys
Hello, On 2024-06-16 15:48, Lucas Nussbaum wrote: /<>/src/formats/xml/xml.cpp:245:39: error: invalid conversion from ‘const xmlError*’ {aka ‘const _xmlError*’} to ‘xmlError*’ {aka ‘_xmlError*’} [-fpermissive] 245 | xmlError* perr = xmlGetLastError(); |

Bug#1069873: rdkit: FTBFS convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb).

2024-05-27 Thread Andrius Merkys
Control: severity -1 important On Fri, 26 Apr 2024 09:25:06 +0300 Andrius Merkys wrote: Since I need to upload rdkit to experimental to deal with time_t64 transition, I am going to disable latexpdf documentation building for the time being and deal with this issue later. I have disabled

Bug#1071655: pytorch: FTBFS on ppc64el

2024-05-22 Thread Andrius Merkys
/home/merkys/pytorch-2.1.2+dfsg/build/aten/src -I/home/merkys/pytorch-2.1.2+dfsg/aten/src -I/home/merkys/pytorch-2.1.2+dfsg/build -I/home/merkys/pytorch-2.1.2+dfsg -I/home/merkys/pytorch-2.1.2+dfsg/cmake/../third_party/benchmark/include -I/usr/lib/llvm-16/include -I/home/merkys/pytorch-2.1.2

Bug#1035833: cpptraj: autopkgtest failure everywhere except on amd64

2024-05-17 Thread Andrius Merkys
Control: severity -1 important Control: retitle -1 cpptraj: FTBFS on \!amd64 On Wed, 10 May 2023 02:29:08 +0530 Kiran S Kunjumon wrote: You package cpptraj has an autopkgtest, great. However, it fails everywhere except on amd64. Can you please investigate the situation and fix it? I have ex

Bug#1035833: cpptraj: autopkgtest failure everywhere except on amd64

2024-05-13 Thread Andrius Merkys
On Wed, 10 May 2023 02:29:08 +0530 Kiran S Kunjumon wrote: === FAILURES === TEST: /tmp/autopkgtest-lxc.kz5vbtvg/downtmp/build.qgE/src/test/Test_SPAM CPPTRAJ: SPAM Test ../MasterTest.sh: line 495: 3218 Killed $c

Bug#1064311: rdkit: NMU diff for 64-bit time_t transition

2024-04-29 Thread Andrius Merkys
Hi, On Wed, 24 Apr 2024 23:57:17 +0200 Chris Hofstaedtler wrote:> An upload with t64 binaries is required as soon as possible. Given the packages have to go to binary-NEW, you must upload with binaries, and then probably follow up with a source-only upload once they are ACCEPTed. t64 binarie

Bug#1065660: antlr4-maven-plugin: please provide debian-versioned maven coordinates

2024-04-26 Thread Andrius Merkys
Control: severity -1 important Control: tags -1 - ftbfs Hi, On 2024-04-25 19:12, Santiago Vila wrote: I noticed that chemicaltagger currently FTBFS and I believe it is because of this problem, so to avoid duplicate reports, I'm raising this one to serious. A build log for chemicaltagger is a

Bug#1065660: antlr4-maven-plugin: please provide debian-versioned maven coordinates

2024-04-25 Thread Andrius Merkys
Hi, On 2024-04-25 19:12, Santiago Vila wrote: I noticed that chemicaltagger currently FTBFS and I believe it is because of this problem, so to avoid duplicate reports, I'm raising this one to serious. A build log for chemicaltagger is available here: https://tests.reproducible-builds.org/deb

Bug#1069873: rdkit: FTBFS convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb).

2024-04-25 Thread Andrius Merkys
Source: rdkit Version: 202309.3-3 Severity: serious Tags: ftbfs sid Hello, rdkit FTBFS with the following error in latexpdf documentation build: Extension error: convert exited with error: [stderr] b'convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb).\n' [stdout] b'' m

Bug#1064311: rdkit: NMU diff for 64-bit time_t transition

2024-04-25 Thread Andrius Merkys
Hi Chris, On 2024-04-25 00:57, Chris Hofstaedtler wrote: t64 is already in unstable and making its way to testing. So you are a bit late with getting rdkit fixed for t64. An upload with t64 binaries is required as soon as possible. Given the packages have to go to binary-NEW, you must upload wi

Bug#1063124: libccp4: NMU diff for 64-bit time_t transition

2024-04-24 Thread Andrius Merkys
Hi, On Mon, 05 Feb 2024 07:52:37 + Steve Langasek wrote: If you have any concerns about this patch, please reach out ASAP. Although this package will be uploaded to experimental immediately, there will be a period of several days before we begin uploads to unstable; so if information becom

Bug#1064311: rdkit: NMU diff for 64-bit time_t transition

2024-04-23 Thread Andrius Merkys
Hi, On Mon, 19 Feb 2024 21:35:16 + Steve Langasek wrote:> Since turning on 64-bit time_t is being handled centrally through a change to the default dpkg-buildflags (https://bugs.debian.org/1037136), it is important that libraries affected by this ABI change all be uploaded close together

Bug#1068942: unblock 1068942 by 1069098

2024-04-18 Thread Andrius Merkys
control: unblock 1068942 by 1069098 Hello, emboss no longer builds on s390x and its binaries have been RMed from s390x, unblocking emboss migration to testing. This in principle should resolve the current bug. Andrius

Bug#1069226: tomogui: FTBFS: RuntimeError: Sphinx is required to build or test the documentation

2024-04-17 Thread Andrius Merkys
Source: tomogui Version: 0.3.1-2 Severity: serious Tags: ftbfs Hello, tomogui FTBFS in sid on amd64: running build_doc Traceback (most recent call last): File "/home/merkys/tomogui-0.3.1/setup.py", line 804, in setup_package() File "/home/merkys/tomogui-0.3.1/setup.py

Bug#1069225: freesas: FTBFS: fatal error: numpy/arrayobject.h: No such file or directory

2024-04-17 Thread Andrius Merkys
-protection -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/home/merkys/freesas-0.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -g -DNDEBUG "-DPyMODINIT_FUNC=__attribute__((visib

Bug#1069224: nabu: FTBFS: AssertionError: OpenclUnsharpMask: max error is too high with method

2024-04-17 Thread Andrius Merkys
Source: nabu Version: 2023.1.1-3 Severity: serious Tags: ftbfs Hello, nabu FTBFS in sid on amd64: FAILURES =

Bug#1066450: opensearch: FTBFS with lucene9/9.10.0+dfsg

2024-04-02 Thread Andrius Merkys
control: retitle -1 opensearch: FTBFS with lucene9/9.10.0+dfsg I have recently updated lucene9. Current FTBFS is caused by missing lucene9 classes. Thus it seems that lucene9 API has changed breaking backwards compatibility. Andrius

Bug#1066296: RE: Bug#1066296: xli: FTBFS: dither.c:77:36: error: implicit declaration of function ‘strlen’ [-Werror=implicit-function-declaration]

2024-03-26 Thread Andrius Merkys
Hi Nilson, On Wed, 13 Mar 2024 17:34:15 + Nilson Silva wrote: Relevant part (hopefully): > cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -DSYSPATHFILE=\"/usr

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

2024-02-22 Thread Andrius Merkys
Hi Andreas, On 2024-02-23 09:15, Andreas Tille wrote: 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

Bug#1041027: rapidjson FTBFS with googletest 1.13.0

2024-02-08 Thread Andrius Merkys
On Thu, 8 Feb 2024 10:22:10 +0200 Andrius Merkys wrote: I attach a patch which fixes the issue by setting -std=c++14 (as needed by googletest) and commenting out a code line in include/rapidjson/document.h which is gone in the newest upstream commit [1]. [1] https://github.com/Tencent

Bug#1041027: rapidjson FTBFS with googletest 1.13.0

2024-02-08 Thread Andrius Merkys
control: tags -1 + patch On Fri, 14 Jul 2023 11:03:55 +0300 Adrian Bunk wrote: Source: rapidjson Version: 1.1.0+dfsg2-7.1 Severity: serious Tags: ftbfs trixie sid https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/rapidjson.html ... In file included from /usr/src/gtest/include

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

2024-02-01 Thread Andrius Merkys
Hi Andreas, On 2024-01-31 13:08, Andreas Tille wrote: 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 fo

Bug#1058127: python-mpiplus: FTBFS: AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?

2024-01-16 Thread Andrius Merkys
Hi Yogeswaran, On 2024-01-16 03:43, Yogeswaran Umasankar wrote: I have removed the hard-coded version number from setup.py. I found that the issue was due to changes in PEP440 version naming convention in versioneer. For this package no need python3-versioneer, upstream has its own versioneer.py

Bug#1058127: python-mpiplus: FTBFS: AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?

2024-01-15 Thread Andrius Merkys
Hi Yogeswaran, On 2024-01-14 18:46, Yogeswaran Umasankar wrote: I created a patch for fixing AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. In the process I have updated it to the latest upstream too. I’ve attached the debdiff for you to check out. I noticed you hav

Bug#1054974: behave: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13

2024-01-15 Thread Andrius Merkys
Hi, On 2024-01-15 17:34, Christoph Berg wrote: Re: Andrius Merkys The patch proposed in #1042610 does not fix test failure. Interestingly, the failure seems to be nondeterministic: after patching #1042610 some builds succeed. However, I did not manage to find the root cause. The difference

Bug#1054974: behave: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13

2024-01-04 Thread Andrius Merkys
Hi, On Tue, 12 Dec 2023 19:35:09 +0100 s3v wrote: please see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1042610 for a proposed patch. The patch proposed in #1042610 does not fix test failure. Interestingly, the failure seems to be nondeterministic: after patching #1042610 some builds

Bug#1042610: #1042610: patch works

2024-01-04 Thread Andrius Merkys
Control: tags -1 + patch Hello, I can confirm that the provided patch (+B-D on python3-doc) fixes the bug. However, #1054974 is not fixed, thus behave still FTBFS. Andrius

Bug#1059175: dials: FTBFS: Imported target "DXTBX::DXTBX" includes non-existent path

2023-12-20 Thread Andrius Merkys
Control: tags -1 + patch pending Hi, On 2023-12-21 00:42, Sebastian Ramacher wrote: Source: dials Version: 3.12.1+dfsg3-5 Severity: serious Tags: ftbfs Justification: fails to build from source (but built successfully in the past) X-Debbugs-Cc: sramac...@debian.org https://buildd.debian.org/st

Bug#1056457: [Debichem-devel] Bug#1056457: python-ase's autopkg tests fail with Python 3.12

2023-12-20 Thread Andrius Merkys
Control: tags -1 + patch Hi, On 2023-12-20 20:23, s3v wrote: After applying [1][2][3] from upstream and adding "-p no:warnings":   addopts = -p no:cacheprovider -p no:warnings in ase/test/pytest.ini (DeprecationWarnings from various packages make tests fail), I was able to build your pack

Bug#1058690: liblatex-tounicode-perl: trying to overwrite .../ltx2unitxt.1.gz, which is also in package texlive-bibtex-extra 2023.20231207-1

2023-12-14 Thread Andrius Merkys
Control: tags -1 + patch Hello, On 2023-12-14 16:07, Vincent Lefevre wrote: Package: liblatex-tounicode-perl Version: 0.54-1 Severity: serious As a consequence of the upgrade of texlive-bibtex-extra to 2023.20231207-3: [...] Selecting previously unselected package liblatex-tounicode-perl. (Re

Bug#1058454: [Debichem-devel] Bug#1058454: prody: autopkgtest regression on i386

2023-12-12 Thread Andrius Merkys
Hi, On 2023-12-12 13:48, Graham Inggs wrote: Source: prody Version: 2.3.1+dfsg-3 Severity: serious Tags: sid trixie User: debian...@lists.debian.org Usertags: regression Hi Maintainer The autopkgtest of prody 2.3.1+dfsg-3 is failing when tested with numpy 1:1.24.2-2 [1]. I've copied what I ho

Bug#1057951: [Debichem-devel] Bug#1057951: promod3: FTBFS: No such file or directory: 'model.pdb'

2023-12-11 Thread Andrius Merkys
Control: owner -1 ! Hi, On 2023-12-11 14:04, Santiago Vila wrote: # Also happens in bookworm found 1057951 3.2.1+ds-6 thanks El 11/12/23 a las 12:06, Andrius Merkys escribió: I can reproduce this in clean chroot on barriere.d.o. Interestingly, FTBFS happens only when building on two threads

Bug#1057951: [Debichem-devel] Bug#1057951: promod3: FTBFS: No such file or directory: 'model.pdb'

2023-12-11 Thread Andrius Merkys
Control: tags -1 + confirmed Hi, On 2023-12-10 22:51, Santiago Vila wrote: Package: src:promod3 Version: 3.3.1+ds-1 Severity: serious Tags: ftbfs Dear maintainer: During a rebuild of all packages in unstable, your package failed to build: -

Bug#1055896: cod-tools: FTBFS: source.c:33:5: error: ‘SPGCONST’ undeclared (first use in this function); did you mean ‘OP_CONST’?

2023-11-14 Thread Andrius Merkys
Control: owner -1 ! Hi, On 2023-11-14 14:27, Gianfranco Costamagna wrote: https://github.com/cod-developers/cod-tools/commit/2e9c0aaa367366883105fa9a7ba3d965495700f8 Just removing SPGCONST from the source.c file is enough, trivial patch attached: Sadly I opened an upstream PR before upstrea

Bug#1055447: htsjdk: FTBFS: 35741 tests completed, 9 failed, 10 skipped

2023-11-08 Thread Andrius Merkys
Hi Pierre, On 2023-11-08 12:14, Pierre Gruet wrote: Thanks for the bug report. It was not easy to reproduce this one! Interesting, I ran rebuild two times and both times it failed :) I spotted this issue during ratt-rebuild of a bunch of other packages, did not really give a decent look. I

Bug#1055237: does not conform to the standards for library packaging

2023-11-07 Thread Andrius Merkys
Hello, On Thu, 02 Nov 2023 18:10:19 +0100 Pierre Gruet wrote: Recently catch2/3.4.0-1 was uploaded to Debian, great. Yet the binary packages do not follow the layout for libraries that is described in Policy Section 8. For instance I think we should provide a shared library and if there are eno

Bug#1055153: skeema: FTBFS on mips64el

2023-11-06 Thread Andrius Merkys
Hello, On Wed, 1 Nov 2023 11:49:20 +0100 Sebastian Ramacher wrote: Source: skeema Version: 1.11.0+ds-1 Severity: serious Tags: ftbfs Justification: fails to build from source (but built successfully in the past) I am unable to reproduce this on eller. Most likely the test timeout is due to

Bug#1055447: htsjdk: FTBFS: 35741 tests completed, 9 failed, 10 skipped

2023-11-06 Thread Andrius Merkys
Finished generating test XML results (0.354 secs) into: /home/merkys/htsjdk-3.0.5+dfsg/build/test-results/testWithDefaultReference Generating HTML test report... Finished generating test html results (0.42 secs) into: /home/merkys/htsjdk-3.0.5+dfsg/build/reports/tests/testWithDefaultReference

Bug#1052877: redmine: FTBFS: make[1]: *** [debian/rules:20: override_dh_auto_configure] Error 7

2023-10-24 Thread Andrius Merkys
s this particular build issue, but one test case fails: Failure: IssueTest#test_issue_overdue_should_respect_user_timezone [/home/merkys/redmine-5.0.4/test/unit/issue_test.rb:3381]: Expected false to be truthy. rails test test/unit/issue_test.rb:3359 Maybe it is worth to replace all '~>'

Bug#1054433: node-puppeteer: website is build with Docusaurus not packaged for debian

2023-10-23 Thread Andrius Merkys
Hi, On 2023-10-23 22:06, Bastien Roucariès wrote: Source: fasttext Source package names in Subject and Source do not match. Please retitle if this is not intentional. Best, Andrius

Bug#1054432: [Pkg-javascript-devel] Bug#1054432: node-puppeteer: website is build with Docusaurus not packaged for debian

2023-10-23 Thread Andrius Merkys
Hi, On 2023-10-23 22:04, Bastien Roucariès wrote: Source: node-katex Source package names in Subject and Source do not match. Please retitle if this is not intentional. Best, Andrius

Bug#1053865: prody: incompatible with python3-biopython > 1.79

2023-10-12 Thread Andrius Merkys
Source: prody Version: 2.3.1+dfsg-3 Severity: serious Justification: FTBFS Tags: sid ftbfs Forwarded: https://github.com/prody/ProDy/issues/1723 Hello, prody FTBFS with python3-biopython > 1.79: == FAIL: testBuildMSAlocal (pro

Bug#1052888: epics-base: FTBFS: make[2]: *** [configure/RULES_TOP:62: runtests] Error 1

2023-10-09 Thread Andrius Merkys
Control: tags -1 + unreproducible On Tue, 26 Sep 2023 15:34:01 +0200 Lucas Nussbaum wrote: Source: epics-base Version: 7.0.7+dfsg1-5 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu...@debian.org Usertags: ftbfs-20230925 ftbfs-trixie Hi, During a rebuild of all packages

Bug#1049872: armel and armhf excluded from asmjit architectures

2023-09-30 Thread Andrius Merkys
control: severity -1 normal Hello, In 0.0~git20230914.917f19d-1 I have excluded armel and armhf architectures from the list of architectures asmjit is built upon. Thus I think the severity should be normal now. Andrius

Bug#1049872: FTBFS on multiple release architectures

2023-09-12 Thread Andrius Merkys
Hi Emanuele, On 2023-09-11 12:07, Emanuele Rocca wrote: On 2023-09-09 08:38, Andrius Merkys wrote: This is news to me. Could you please point out where in Debian Policy I can read more about such requirement? I thought I saw packages dropping support for one or another release architecture

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