Bug#1084629: espresso, wannier90: 'pipes' used in shared code

Control: tags -1 + patch Hello, espresso and wannier90 share an embedded library called 'testcode'. This library uses 'pipes', and this is the only deprecated module in both these source packages. I managed to successfully replace 'pipes' with 'shlex' [1] and will apply the same patch to both

Bug#1083076: python3-rdkit: SEGFAULT on import on armhf

Package: python3-rdkit Version: 202309.3-7 Severity: important Hello, python3-rdkit encounters SEGFAULT on import on armhf: $ python3 Python 3.12.6 (main, Sep 7 2024, 14:20:15) [GCC 14.2.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> from rdkit import Ch

Bug#1082878: [Debichem-devel] Bug#1082878: python3-gemmi: Please add the dist-info data's

Hello, On 2024-09-27 19:23, Picca Frédéric-Emmanuel wrote: While preparing the new version of dials, I discoverd that the gemmi dependency was not automatically generated during the packaging process. Indeed, python3-gemmi does not provide the necessary dist-info. Could you be so kind to add

Bug#1081606: debian/maven.rules help needed for cdk

Hi Emmanuel, On 2024-09-28 00:51, Emmanuel Bourg wrote: Le 27/09/2024 à 14:47, Andrius Merkys a écrit : cdk-data is an artifact of the same project, however, I cannot make maven detect it. I am almost sure the problem is due to some misconfiguration in debian/maven.rules, but I cannot find

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

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#1081606: debian/maven.rules help needed for cdk

Hello, I am trying to enable tests for cdk package on branch on salsa [1]. Build is failing with the following: [INFO] [INFO] BUILD FAILURE [INFO] ---

Bug#1082612: lintian: Argument "v0.902.0" isn't numeric in numeric lt (<) at /usr/share/lintian/lib/Lintian/Check/Debian/Upstream/Metadata.pm line 106

control: tags -1 + patch control: owner -1 ! On 2024-09-23 20:10, gregor herrmann wrote: On Mon, 23 Sep 2024 11:47:30 +0300, Andrius Merkys wrote: A simple fix would be to parse both versions using Perl version package from libversion-perl and then compare. Ack. An example can be seen at

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

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#1082612: lintian: Argument "v0.902.0" isn't numeric in numeric lt (<) at /usr/share/lintian/lib/Lintian/Check/Debian/Upstream/Metadata.pm line 106

Hi, On 2024-09-23 20:10, gregor herrmann wrote: On Mon, 23 Sep 2024 11:47:30 +0300, Andrius Merkys wrote: When running lintian on wannier90_3.1.0+ds-9.dsc which I have just uploaded, I got the following warning: Warning in processable ./wannier90_3.1.0+ds-9.dsc: Argument "v0.902.0&q

Bug#1082731: expect: unbuffer fails with "can't find package Expect"

Package: expect Version: 5.45.4-3 Severity: important Affects: src:pdb-tools Hello, When installed on clear chroot, unbuffer fails to start with: can't find package Expect while executing "package require Expect" (file "/usr/bin/unbuffer" line 6) I noticed this when building pdb-tools

Bug#1077055: [Debichem-devel] Bug#1077055: Bug#1077055: postgresql-16-rdkit: inchi support not included in rdkit build

Hi David, On 2024-09-24 17:09, David Lounsbrough wrote: I ran this inside my Docker container, it says the latest version of the package is installed: # apt-get -s install postgresql-16-rdkit Reading package lists... Done Building dependency tree... Done Reading state information... Done postg

Bug#1077055: [Debichem-devel] Bug#1077055: Bug#1077055: postgresql-16-rdkit: inchi support not included in rdkit build

Hi, On 2024-09-24 16:30, David Lounsbrough wrote: Hi, I am simply standing up a Postgres database with this package installed in it. This is the entire Dockerfile I am using: ``` FROM postgres:16 AS postgres-env RUN apt-get update && \   apt-get install -yq postgresql-16-rdkit && \   apt-ge

Bug#1075155: libccp4: ftbfs with GCC-14

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#1082109: [Debichem-devel] Bug#1082109: Bug#1082109: inchi: support for .sdf (v3000 dialect) is not functional

control: reassign -1 src:inchi control: owner -1 ! control: tags -1 + confirmed Dear Norwid, I managed to get inchi-1 executable to build and ensured that it passes the test with pyridine.sdf which you have described. Will upload the fixed package soon. Best, Andrius

Bug#1077055: [Debichem-devel] Bug#1077055: postgresql-16-rdkit: inchi support not included in rdkit build

Control: tags -1 + moreinfo Hi David, On Thu, 25 Jul 2024 12:05:55 -0500 David Lounsbrough wrote: To reproduce, I simply ran this Dockerfile: FROM postgres:16 AS postgres-env RUN apt-get update && \ apt-get install -yq postgresql-16-rdkit && \ apt-get clean Then when I try to build a

Bug#1082109: [Debichem-devel] Bug#1082109: Bug#1082109: inchi: support for .sdf (v3000 dialect) is not functional

Dear Norwid, On 2024-09-23 12:29, Norwid Behrnd via Debichem-devel wrote: In the more general case of a .mol/.sdf file about models with multiple atoms and at least one explicit bond, the reference executable of InChI 1.07.1 is able to process data in the v3000 dialect. Their executable publish

Bug#1082612: lintian: Argument "v0.902.0" isn't numeric in numeric lt (<) at /usr/share/lintian/lib/Lintian/Check/Debian/Upstream/Metadata.pm line 106

Package: lintian Version: 2.118.2 Hello, When running lintian on wannier90_3.1.0+ds-9.dsc which I have just uploaded, I got the following warning: Warning in processable ./wannier90_3.1.0+ds-9.dsc: Argument "v0.902.0" isn't numeric in numeric lt (<) at /usr/share/lintian/lib/Lintian/Check/D

Bug#1082109: [Debichem-devel] Bug#1082109: inchi: support for .sdf (v3000 dialect) is not functional

Hi Norwid, On 2024-09-18 16:13, Norwid Behrnd via Debichem-devel wrote: The compiled reference executable of InChI 1.07.1[1] for Linux 64bit assigns InChI for .sdf in either v2000, or v3000 dialect. While replying to an issue report,[2] I noticed `inchi_main` as packaged by DebiChem currently s

Bug#1078202: restfuldb: diff for NMU version 0.16.0+dfsg-1.1

Hi, On 2024-09-17 00:55, gregor herrmann wrote: I've prepared an NMU for restfuldb (versioned as 0.16.0+dfsg-1.1) and uploaded it to DELAYED/5. Please feel free to tell me if I should delay it longer. Thanks a lot for taking care of this issue. DELAYED/5 is fine with me. Andrius

Bug#1078097: cod-tools: diff for NMU version 3.10.0+dfsg-1.1

Hi, On 2024-09-17 00:48, gregor herrmann wrote: I've prepared an NMU for cod-tools (versioned as 3.10.0+dfsg-1.1) and uploaded it to DELAYED/5. Please feel free to tell me if I should delay it longer. Thanks a lot for taking care of this issue. DELAYED/5 is fine with me. Andrius

Bug#1081843: libstar-parser-perl: homepage defunct

Control: tags -1 + patch Hi, On 2024-09-15 16:51, Ben Tris wrote: The current homepage seems not to exist. http://pdb.sdsc.edu/STAR/ No alternative found. This has one nice simple page. https://www.iucr.org/resources/cif/software/starparser I agree that iucr.org webpage for starparser would

Bug#1081606: cdk: run upstream tests during build

Source: cdk Severity: wishlist Forwarded: https://salsa.debian.org/java-team/cdk/-/tree/with-tests Tags: help Hello, cdk includes an extensive testsuite. To ensure the built package's integrity, it would be nice to run the testsuite during build. According to git log, there were several unsucc

Bug#1075155: libccp4: ftbfs with GCC-14

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#1079981: transition: inchi

Hi Sebastian, On 2024-09-08 22:10, Sebastian Ramacher wrote: On 2024-09-08 14:21:57 +0300, Andrius Merkys wrote: inchi has migrated to testing and all its binary reverse dependencies seem to have switched from libinchi1 to libinchi1.07. However, transition tracker [1] shows the reverse

Bug#585905: cassandra: ITP -> RFP

retitle 585905 RFP: cassandra -- highly scalable distributed datastore noowner 585905 thanks Hello, I am giving up my efforts to package cassandra. My latest packaging attempt (year 2019) can be found at salsa [1]. In short, I managed to collect all the dependencies, but I failed to get cassan

Bug#1009673: RM: swagger-core -- RoM; not needed

severity 1009673 normal retitle 1009673 RM: swagger-core -- RoM; not needed reassign 1009673 ftp.debian.org affects 1009673 + src:swagger-core thanks Hello, Two years ago I offered src:swagger-core for adoption. Since no one was interested, and it has no reverse dependencies, I am asking for it

Bug#1079981: transition: inchi

Hi, inchi has migrated to testing and all its binary reverse dependencies seem to have switched from libinchi1 to libinchi1.07. However, transition tracker [1] shows the reverse dependencies as partially migrated - what could be the issue with them? Andrius [1] https://release.debian.org/tr

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

Hi, An upload of -8 has failed somewhy, I will retry ASAP. Andrius

Bug#1080050: Should mbdyn be removed from unstable?

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#1080035: ITP: jna-inchi -- wrapper to access InChI from Java

Package: wnpp Owner: Andrius Merkys Severity: wishlist Control: block -1 by 1079981 * Package name: jna-inchi Version : 1.2.1 Upstream Author : Daniel Lowe * URL : https://github.com/dan2097/jna-inchi * License : LGPL-2.1+ Programming Lang: Java

Bug#964773: 964773: inchi to become free software again

control: tags -1 - wontfix control: owner -1 ! On Fri, 15 Mar 2024 13:12:14 +0200 Andrius Merkys wrote:> An update: the upcoming inchi release is going to be licensed under Expat [1]. Thus an opportunity may appear to build rdkit with inchi support. rdkit builds successfully with libin

Bug#1079981: transition: inchi

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition Hello, I would like to request a transition slot for inchi (experimental -> unstable) due to soname bump. Current ben tracker [1] is OK. Rebuild results for reverse dependencies: * jni

Bug#1079894: rust-abnf-core: seemingly incorrect homepage

Source: rust-abnf-core Version: 0.6.0-3 Hello, Homepage field in debian/control seems off: it points to https://github.com/duesee/imap-codec while debian/watch points to https://github.com/duesee/abnf-core. Andrius

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

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

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#1079794: tahoe-lafs: package new upstream release 1.19.0

Source: tahoe-lafs Severity: wishlist Control: block -1 by 1068692 Hello, New upstream release 1.19.0 is out. This bug is to track the process of updating tahoe-lafs to it. Andrius

Bug#1075155: libccp4: ftbfs with GCC-14

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#1076519: #1076519: inchi packaging status

control: owner -1 ! control: forwarded -1 https://salsa.debian.org/debichem-team/inchi/-/tree/package/1.07 Hello, I started working on packaging inchi 1.07.1 in a branch on salsa.debian.org. Right now I am working on refreshing patches. Andrius

Bug#1077055: [Debichem-devel] Bug#1077055: postgresql-16-rdkit: inchi support not included in rdkit build

Hi David, On 7/25/24 18:51, David Lounsbrough via Debichem-devel wrote: I wanted to ask if there's a reason that `inchi` support is not enabled for this package. You can read more about the attempts to enable InChI support in rdkit in [1]. In short, inchi package in Debian seems incompatible

Bug#1076519: [Debichem-devel] Bug#1076519: libinchi1: new version 1.07 of InChI (now MIT license scheme)

provides the software equivalent to version 1.03/June 15, 2010. While Andrius Merkys thankfully packaged this version in 2019, there already was the request to provide the community a package corresponding to a more recent version of InChI. However, starting with version 1.04 (September 2011

Bug#1074897: cura-engine: ftbfs with GCC-14

Control: retitle -1 rapidjson: causes FTBFS with GCC-14 Control: block 1075335 by -1 Control: block 1075439 by -1 Hello, When building other packages with rapidjson-dev with GCC-14, the following failure occurs: /usr/include/rapidjson/document.h: In member function ‘rapidjson::GenericStringR

Bug#1075834: [Debichem-devel] Bug#1075834: Bug#1075834: python3-ase: new upstream release available

Hi, On 7/8/24 21:11, Graham Inggs wrote: On Sat, 6 Jul 2024 at 02:45, Drew Parsons wrote: debian/watch is broken. gitlab access to the tarballs is confusing, and I wasn't able to find a simple fix for debian/watch Apparently, this changed in gitlab in March, 2024 [1]. version=4 opts="searchm

Bug#1056457: spglib 2.2.0-3 builds for all supported Python versions

Hello, Since 2.2.0-3 spglib builds for all supported Python versions. Thus the autopkgtest for all supported Python versions can be turned back on. Andrius

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

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#1073494: ITP: openapi-schema-validator -- Validate schema against the OpenAPI Schema Specifications

On 2024-06-27 23:20, Julian Gilbey wrote: It's the other way round, but I'll add you anyway. Thanks! Best, Andrius

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

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

Bug#1073494: ITP: openapi-schema-validator -- Validate schema against the OpenAPI Schema Specifications

Hi Julian, On 2024-06-17 19:34, Julian Gilbey wrote: Super, thanks! I'll add you now. Would you also like to be added to python-openapi-spec-validator? I gather python-openapi-spec-validator is a dependency of python-openapi-schema-validator, right? If so, you can add me. It will be team

Bug#1073494: ITP: openapi-schema-validator -- Validate schema against the OpenAPI Schema Specifications

On 2024-06-16 17:43, Julian Gilbey wrote: * Package name: openapi-schema-validator Version : 0.6.2 Upstream Author : Artur Maciag * URL : https://github.com/python-openapi/openapi-schema-validator * License : BSD-3-clause Programming Lang: Python Descr

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

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]

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#1006482: lintian: non-standard-dir-in-var var/db/

Hi, On 2024-06-17 15:09, Maytham Alsudany wrote: Control: tags -1 + moreinfo On Sat, 26 Feb 2022 10:07:32 +0200 Martin-Éric Racine wrote: Lintian incorrectly reports /var/db/ as non-standard-dir-in-var. /var/db Data bank

Bug#1072576: coot: save its states in HOME.

On 2024-06-11 07:54, Paul Emsley wrote: I have been a bit sloppy with my file names and you should not be. Let's call the "refmac-dictionary" the "ccp4-monomer-library" OK, I will rename it to 'ccp4-monomer-library'. This is where it lives: https://github.com/MonomerLibrary/monomers Looki

Bug#1072576: coot: save its states in HOME.

Hi, On 2024-06-11 07:50, Paul Emsley wrote: OK, so 1.1.09 should now read and save the state and config files in an XDG Base Directory compliant manner. Thanks. I will update the Debian package ASAP. I have cleaned up some of the terminal output (it is verbose because doing so helps me diagn

Bug#1057556: elpa: FTBFS: not enough slots available

Control: owner -1 ! On Fri, 31 May 2024 14:46:28 +0200 Santiago Vila wrote:> Instead of patch-2.txt and patch-3.txt, the following more simple patch would also fix the issue (I've tested it on single-cpu systems and also on m6a.large instances from AWS, which have 1 core and two threads). (S

Bug#1072576: coot: save its states in HOME.

On 2024-06-05 10:13, Andrius Merkys wrote: The REFMAC dictionary packaged in Debian as refmac-dictionary needs some adjustment to make usable by coot and make the messages above go away. I have the fix for refmac-dictionary at hand, by the way. I will upload it soon. Andrius

Bug#1072576: coot: save its states in HOME.

Control: tags -1 + confirmed Hi, On 2024-06-04 17:31, Picca Frédéric-Emmanuel wrote: While using coot I found that it save it's states in these files DEBUG:: saving state to filename 0-coot.state.py State file 0-coot.state.py written. State file 0-coot-history.py written. State file 0-coot-his

Bug#1072618: coot: layla fails to start unless LD_LIBRARY_PATH is specified

Package: coot Version: 1.1.08+dfsg-3 Severity: important Forwarded: https://github.com/pemsley/coot/issues/120 layla executable fails to start unless LD_LIBRARY_PATH is given for it to locate the coot private libraries, e.g.: $ LD_LIBRARY_PATH=/usr/lib/ layla A thin wrapper is needed to set t

Bug#1072564: nmu: cctbx_2023.12+ds2+~3.17.0+ds1-4 clipper_ 2.1.20201109-2 libpdb-redo_3.0.5-2 ssm_1.4.0-2

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: binnmu Hello, I want to request binNMU on packages which are affected by libccp4 soname change due to time_t64 transition: nmu cctbx_2023.12+ds2+~3.17.0+ds1-4 . ANY . unstable . -m "Rebuild

Bug#1072515: general: Repeating cracking sound in headphones when nothing is playing.

Hi Christian, On 2024-06-03 11:38, Christian Böck wrote: when using headphones with my laptop (Thinkpad W550s) I get a repeating cracking (~1sec intervalls) when nothing is playing. I have a similar issue on a workstation with Ubuntu 22.04. What is your operating system version? I believe the

Bug#1070770: lintian: check for testing presence of "nodocs" in DEB_BUILD_OPTIONS

On 2024-06-02 19:49, Louis-Philippe Véronneau wrote:> Sounds like a plan. I made the changed you proposed and also made sure the tag will output the problematic BUILD_OPTION. That way, when/if someone wants to make it more generic, it'll be possible to pass other invalid BUILD_OPTION. The tag

Bug#1072383: lintian: flag packages bloated by auxiliary tests/docs/examples

Hi Aaron, On 2024-06-02 05:41, Aaron M. Ucko wrote: A number of binary packages accompany their primary content by tests, examples, and/or other documentation that appreciably increase their size, in some cases by more than an order of magnitude, and as such would be very reasonable to split out

Bug#998820: lintian: overly generic python modules /usr/lib/python3/dist-packages/benchmarks/*.py

On 2024-06-03 08:51, Andreas Beckmann wrote: Followup-For: Bug #998820 Then we also have /usr/lib/python3/dist-packages/build/lib/doc/conf.py ^^^ e.g. nxtomo 1.2.3-2 usr/lib/python3/dist-packages/build/lib/docs/conf.py

Bug#1072195: valgrind: add support for loong64

Package: valgrind Version: 1:3.20.0-2.1 Severity: wishlist Control: block 1072148 by -1 X-Debbugs-CC: wuruil...@loongson.cn Hello, In #1072148 a patch to support loong64 has been proposed in epics-base. The proposed patch modifies valgrind header (valgrind/valgrind.h) embedded in epics-base so

Bug#1072148: epics-base: please add support for loong64

On 2024-05-30 05:17, wuruilong wrote: I checked valgrind debian package is not supported loongarch architecture. Thanks for checking. I would like to remove the embedded valgrind/valgrind.h and use the header from valgrind package. Thus I would suggest implementing loongarch support in valgri

Bug#1072148: epics-base: please add support for loong64

On 2024-05-29 11:32, wuruilong wrote: Modify the valgrind header file because valgrind's code has gone too long without loongarch support. Does the valgrind Debian package support loong64? If so, the embedded valgrind/valgrind.h can be replaced with the header from Debian package. Andrius

Bug#1072148: epics-base: please add support for loong64

Control: forwarded -1 https://github.com/epics-base/epics-base/pull/329 Hi, On 2024-05-29 10:31, wuruilong wrote: Compile error on loongarch, reference upstream code to provide patch. Link to upstream code:https://github.com/epics-base/epics-base/pull/329 Why does this patch modify the embedd

Bug#1039087: removing embeded version of yajl

Hi, On 2024-05-28 18:35, PICCA Frederic-Emmanuel wrote: Here the diff between the epics version (debian patch unapplyed) and the current 2.1.0 version of yajl (debian patch unapplyed). It seems EPICS authors have forked yajl and implemented JSON5 support there. As a result, the code diverged

Bug#1072115: ERROR:: Failure to read or parse /usr/share/coot/ui/coot-gtk4.ui

Control: severity -1 serious Control: owner -1 ! Hi, On 2024-05-28 23:07, Picca Frédéric-Emmanuel wrote: while trying to start coot, I get this error message. $ coot INFO:: built with GTK 4.12.5 pdd /usr/share/coot WARNING:: Coot REFMAC dictionary override COOT_REFMAC_LIB_DIR /usr/share/coot/

Bug#1039087: removing embeded version of yajl

Hi, On 2024-05-28 17:49, PICCA Frederic-Emmanuel wrote: following a different path..., I added this in the rules file -export POSIX_CFLAGS+=$(CFLAGS) +export POSIX_CFLAGS+=$(CFLAGS) $(shell pkgconf --cflags yajl) export POSIX_CFLAGS+=$(CPPFLAGS) export POSIX_CPPFLAGS+=$(CPPFLAGS) -export POSIX

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

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#1071573: Status of libnet-ssl-expiredate-perl

Hi Mason, On 2024-05-27 13:11, Mason James wrote: sorry for my late reply and no objections from me! Now worries, I finished the package and uploaded today. Best, Andrius

Bug#1059706: epics-base.pc is still broken

Hi, On Sat, 4 May 2024 22:53:36 +0900 Kentaro HAYASHI wrote: I've attached PoC patches which are based on https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1059706#33 Before: $ pkg-config --cflags epics-base -I/build/reproducible-path/epics-base-7.0.8+dfsg1/include -I/build/reproducible-pat

Bug#1071573: Status of libnet-ssl-expiredate-perl

Control: owner -1 ! Hello, It is quite important to me to get libnet-ssl-expiredate-perl done ASAP. Thus if you do not have any objections, I am going to finalize it. Andrius

Bug#1071655: pytorch: FTBFS on ppc64el

/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#1071573: ITP: libnet-ssl-expiredate-perl -- obtain expiration date of certificate

Package: wnpp Owner: Mason James Severity: wishlist Control: block 1036769 by -1 X-Debbugs-CC: m...@kohaaloha.com * Package name: libnet-ssl-expiredate-perl Version : 1.24 Upstream Author : Hirose Masaaki * URL : https://metacpan.org/release/Net-SSL-ExpireDate * Licen

Bug#1070770: lintian: check for testing presence of "nodocs" in DEB_BUILD_OPTIONS

On 2024-05-19 15:48, Julian Gilbey wrote: But here I'd suggest doing the opposite: checking for valid build options (and note: this is a check for DEB_BUILD_OPTIONS, not for DEB_BUILD_PROFILES). There is a very short list of standard build options: those listed in dpkg-buildpackage(1) (parallel=

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

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#1071207: ITP: r-cran-calculus -- High Dimensional Numerical and Symbolic Calculus

Package: wnpp Owner: Andrius Merkys Severity: wishlist * Package name: r-cran-calculus Version : 1.0.1 Upstream Author : Emanuele Guidotti * URL : https://cran.r-project.org/package=calculus * License : GPL-3 Programming Lang: GNU R Description

Bug#1071176: ITP: python-htmltools -- Tools for creating, manipulating, and writing HTML

Package: wnpp Owner: Andrius Merkys Severity: wishlist * Package name: python-htmltools Version : 0.5.1 Upstream Author : Posit Software, PBC * URL : https://github.com/rstudio/py-htmltools * License : Expat Programming Lang: Python Description

Bug#1071089: RM: cpptraj [arm64 armel armhf i386 mips64el ppc64el riscv64 s390x] -- ROM; FTBFS on non-amd64 archs

Package: ftp.debian.org Severity: normal Hello, Please remove cpptraj binaries for the following architectures: arm64 armel armhf i386 mips64el ppc64el riscv64 s390x It FTBFS on non-amd64 architectures as noticed in #1035833. Andrius

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

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#1036769: lintian: Check for certificates .pem/.crt/.pkcs12 with expiry set

Control: owner -1 ! Hi, On Thu, 25 May 2023 17:27:48 +0200 Florian Lohoff wrote: i am in the middle of a stretch rebuild for mipsel (Upgrade path from jessie as stretch dropped 75% of supported systems with mips32) A big issue are certificates, mostly for build tests which have an expire date

Bug#1070275: RM: macromoleculebuilder [armhf] -- ROM; unsupported on 32bit archs

Package: ftp.debian.org Severity: normal Hello, Please remove macromoleculebuilder binaries for armhf. The upstream has confirmed the package is no longer supported on 32bit architectures. Andrius

Bug#1068925: 1068925: macromoleculebuilder should be limited to 64bit

Control: owner -1 ! Hello, Upstream has confirmed that macromoleculebuilder should be limited to 64bit. I am going to limit the architectures and file for RM on armhf soon. Andrius

Bug#956194: streamlit status

Hello, Is anybody still interested in streamlit? Some time ago I packaged its dependency node-xxhashjs and ended up maintaining it. I do not use node-xxhashjs myself and would like to pass its maintenance to people interested in streamlit. Andrius

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

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

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

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).

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

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

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

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#1068578: RFH: singularity-container -- container platform focused on supporting "Mobility of Compute"

Hi Nilesh, On 2024-04-10 19:53, Nilesh Patra wrote: On Mon, Apr 08, 2024 at 08:59:26AM +0300, Andrius Merkys wrote: On 2024-04-07 15:28, Nilesh Patra wrote: Assistance required with maintaining the singularity-container package. I am not offering help with singularity-container, but do you

Bug#1068942: unblock 1068942 by 1069098

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

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

-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

Source: nabu Version: 2023.1.1-3 Severity: serious Tags: ftbfs Hello, nabu FTBFS in sid on amd64: FAILURES =

Bug#1069170: RM: emboss [s390x] -- ROM; FTBFS

control: tags -1 - moreinfo On Wed, 17 Apr 2024 14:03:10 +0300 Andrius Merkys wrote:> Please remove emboss binaries for s390x because of #1069098. I have not yet filed RM requests for all the reverse dependencies, therefore I tag this with moreinfo, to be removed once I am done. RM b

Bug#1069174: RM: embassy-domsearch [s390x] -- ROM; Build-Depends missing on s390x

Package: ftp.debian.org Severity: normal Control: block 1069170 by -1 Hello, Please remove embassy-domsearch binaries for s390x, as emboss-lib is no longer built there due to #1069098. Andrius

Bug#1069173: RM: embassy-domalign [s390x] -- ROM; Build-Depends missing on s390x

Package: ftp.debian.org Severity: normal Control: block 1069170 by -1 Hello, Please remove embassy-domalign binaries for s390x, as emboss-lib is no longer built there due to #1069098. Andrius

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