Bug#1110701: marked as done (rdkit ftbfs with GCC 15)

Debian Bug Tracking System Tue, 07 Oct 2025 11:03:26 -0700

Your message dated Tue, 07 Oct 2025 18:00:17 +0000
with message-id <[email protected]>
and subject line Bug#1110701: fixed in rdkit 202503.6-1
has caused the Debian Bug report #1110701,
regarding rdkit ftbfs with GCC 15
to be marked as done.


This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)


-- 
1110701: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1110701
Debian Bug Tracking System
Contact [email protected] with problems

--- Begin Message ---
Package: src:rdkit
Version: 202503.1-4
Severity: important
Tags: sid forky
User: [email protected]
Usertags: ftbfs-gcc-15

rdkit ftbfs with GCC 15:

[...]
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/<<PKGBUILDDIR>>/External -I/<<PKGBUILDDIR>>/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/rdkit-202503.1-4build1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -MF CMakeFiles/hc.dir/hc.c.o.d -o CMakeFiles/hc.dir/hc.c.o -c /<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c: In function ‘hc_’:
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:29:22: warning: old-style function definition [-Wold-style-definition] 29 | /* Subroutine */ int hc_(n, len, iopt, ia, ib, crit, membr, nn, disnn, flag__,
      |                      ^~~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:93:13: error: too many arguments to function ‘ioffset_’; expected 0, have 3
   93 |       ind = ioffset_(n, &i__, &j);
      |             ^~~~~~~~ ~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:53:18: note: declared here
   53 |   extern integer ioffset_();
      |                  ^~~~~~~~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:130:10: error: too many arguments to function ‘ioffset_’; expected 0, have 3
  130 |   ind1 = ioffset_(n, &i2, &j2);
      |          ^~~~~~~~ ~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:53:18: note: declared here
   53 |   extern integer ioffset_();
      |                  ^~~~~~~~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:147:14: error: too many arguments to function ‘ioffset_’; expected 0, have 3
  147 |       ind1 = ioffset_(n, &i2, &k);
      |              ^~~~~~~~ ~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:53:18: note: declared here
   53 |   extern integer ioffset_();
      |                  ^~~~~~~~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:149:14: error: too many arguments to function ‘ioffset_’; expected 0, have 3
  149 |       ind1 = ioffset_(n, &k, &i2);
      |              ^~~~~~~~ ~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:53:18: note: declared here
   53 |   extern integer ioffset_();
      |                  ^~~~~~~~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:152:14: error: too many arguments to function ‘ioffset_’; expected 0, have 3
  152 |       ind2 = ioffset_(n, &j2, &k);
      |              ^~~~~~~~ ~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:53:18: note: declared here
   53 |   extern integer ioffset_();
      |                  ^~~~~~~~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:154:14: error: too many arguments to function ‘ioffset_’; expected 0, have 3
  154 |       ind2 = ioffset_(n, &k, &j2);
      |              ^~~~~~~~ ~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:53:18: note: declared here
   53 |   extern integer ioffset_();
      |                  ^~~~~~~~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:156:12: error: too many arguments to function ‘ioffset_’; expected 0, have 3
  156 |     ind3 = ioffset_(n, &i2, &j2);
      |            ^~~~~~~~ ~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:53:18: note: declared here
   53 |   extern integer ioffset_();
      |                  ^~~~~~~~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:244:13: error: too many arguments to function ‘ioffset_’; expected 0, have 3
  244 |       ind = ioffset_(n, &i__, &j);
      |             ^~~~~~~~ ~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:53:18: note: declared here
   53 |   extern integer ioffset_();
      |                  ^~~~~~~~
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c: In function ‘ioffset_’:
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:53:18: warning: old-style function definition [-Wold-style-definition] /<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:274:1: error: number of arguments doesn’t match prototype
  274 | {
      | ^
/<<PKGBUILDDIR>>/Code/ML/Cluster/Murtagh/hc.c:53:18: error: prototype declaration
   53 |   extern integer ioffset_();
      |                  ^~~~~~~~
make[4]: *** [Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make:82: Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:17276: Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/all] Error 2
--- End Message ---

--- Begin Message ---

Source: rdkit
Source-Version: 202503.6-1
Done: Andrius Merkys <[email protected]>

We believe that the bug you reported is fixed in the latest version of
rdkit, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andrius Merkys <[email protected]> (supplier of updated rdkit package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Tue, 07 Oct 2025 03:44:06 -0400
Source: rdkit
Binary: librdkit-dev librdkit1t64 librdkit1t64-dbgsym postgresql-18-rdkit 
postgresql-18-rdkit-dbgsym python3-rdkit python3-rdkit-dbgsym rdkit-data 
rdkit-doc
Architecture: source amd64 all
Version: 202503.6-1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Description:
 librdkit-dev - Collection of cheminformatics and machine-learning software 
(deve
 librdkit1t64 - Collection of cheminformatics and machine-learning software 
(shar
 postgresql-18-rdkit - Cheminformatics and machine-learning software 
(PostgreSQL Cartrid
 python3-rdkit - Collection of cheminformatics and machine-learning software
 rdkit-data - Collection of cheminformatics and machine-learning software (data
 rdkit-doc  - Collection of cheminformatics and machine-learning software (docu
Closes: 1110701 1116968
Changes:
 rdkit (202503.6-1) unstable; urgency=medium
 .
   * New upstream version 202503.6 (Closes: #1110701, #1116968)
   * Make sure downloadAndCheckMD5() does not download anything.
   * Disable ChemDraw support.
   * Bump to postgresql-18.
   * Disable latexpdf due to https://github.com/rdkit/rdkit/issues/8850
   * Update debian/copyright.
Checksums-Sha1:
 6a002b7512f317c9e5ac81b8e95dcf1fd5111d69 3118 rdkit_202503.6-1.dsc
 8980fdc9e0a1aaed921ba513dcc175df8299b0b7 64217064 rdkit_202503.6.orig.tar.xz
 b559d21ad7faae4d36eff437ab8738df0e9beb89 48424 rdkit_202503.6-1.debian.tar.xz
 5088f0b61a885afcc5c9f6331e964d4eaf7158be 494292 
librdkit-dev_202503.6-1_amd64.deb
 aba955c1c12ecce0f2fba170ad263cf560bbb362 128603028 
librdkit1t64-dbgsym_202503.6-1_amd64.deb
 174dbc59cb4878c1b936c779ce2d6d155a66e765 6086180 
librdkit1t64_202503.6-1_amd64.deb
 4283e6c7a080b2ea2e891ff33f7a58cd0f5b2d04 1185972 
postgresql-18-rdkit-dbgsym_202503.6-1_amd64.deb
 3c23a4a6b571de03691a90267868a18d06e48486 260412 
postgresql-18-rdkit_202503.6-1_amd64.deb
 a0b25e23b0f5d055260dd2d41333c12005062c3d 64898476 
python3-rdkit-dbgsym_202503.6-1_amd64.deb
 86c699df748114e4896f833713bf984d79a45784 4803416 
python3-rdkit_202503.6-1_amd64.deb
 dc3496360727a95a5bf0e13a05c385e492e47e0c 13159868 rdkit-data_202503.6-1_all.deb
 002c3f5d7f2e5b1baef2f35c853c913fffc103bb 6982664 rdkit-doc_202503.6-1_all.deb
 abcb035697b7a22d30cd1dbe7ef1e6a0a33966d4 19355 rdkit_202503.6-1_amd64.buildinfo
Checksums-Sha256:
 11f5db1a23c6ddb77d03f2ac135141a8d7ffaa7a5d56010628412a3db8eddc30 3118 
rdkit_202503.6-1.dsc
 88fa533178ab825e336ad22a6d0b8f1d392f038a99dec8787f25ad27d4a5544a 64217064 
rdkit_202503.6.orig.tar.xz
 253074af5e385b0afff106ef54598a971e9f8d43db38f46e808e9363da2aea97 48424 
rdkit_202503.6-1.debian.tar.xz
 30caa1b0d6232d59fa9a9b2904bfc60068a54f4ac8cef83fd5f14c64e4ccfb36 494292 
librdkit-dev_202503.6-1_amd64.deb
 df17c4aa6138b368a1b9d621ac5a9ee08ac32a48c3da075701373390fd7609ee 128603028 
librdkit1t64-dbgsym_202503.6-1_amd64.deb
 bbc6397d2d7d60e1f1714cb3269eebbc994d86b177bb6fd756b213d04271b9e3 6086180 
librdkit1t64_202503.6-1_amd64.deb
 9a4a9b941d365e9b93e397c55165ea03e7ded37925bc135e60b29b379d1fcac8 1185972 
postgresql-18-rdkit-dbgsym_202503.6-1_amd64.deb
 343c351d3e2ded8bdd4463557d5ab79ccaffbb4632a18020950571fe07b3d7df 260412 
postgresql-18-rdkit_202503.6-1_amd64.deb
 0e8132f4423342d1db841fc80d906d9e0f4922d217641a78e7d4d495a847cba4 64898476 
python3-rdkit-dbgsym_202503.6-1_amd64.deb
 92581afd3d69741334a5e941a325d07e80c0eb4515b7048fa40093b2b8e92840 4803416 
python3-rdkit_202503.6-1_amd64.deb
 7eba0c961ffc7413257f9ea3d729e159d4c7fa34091f1d28a9c66e75797da684 13159868 
rdkit-data_202503.6-1_all.deb
 dfb768169a6702b63df4aba0378b1c5a10298c9166ae835622c80ef0444c7435 6982664 
rdkit-doc_202503.6-1_all.deb
 aa67fd2944d95306241594f840aec2c4b098eca0636a5c6f3386eb4137ff139e 19355 
rdkit_202503.6-1_amd64.buildinfo
Files:
 92715d1c93f51ef4f33988ef6a3588ae 3118 science optional rdkit_202503.6-1.dsc
 93941122f9c12328a05e5489ed103015 64217064 science optional 
rdkit_202503.6.orig.tar.xz
 d92660bf1117dae60c65279ff3d88b26 48424 science optional 
rdkit_202503.6-1.debian.tar.xz
 54fb5873de8cd50d460eeda486564a76 494292 libdevel optional 
librdkit-dev_202503.6-1_amd64.deb
 70d21b55ae9d7d48ec141faa31a57c55 128603028 debug optional 
librdkit1t64-dbgsym_202503.6-1_amd64.deb
 4124856c5a2f6de7a956e96ded1dc2ed 6086180 libs optional 
librdkit1t64_202503.6-1_amd64.deb
 8a7292719d507e443d923278aa3f70c3 1185972 debug optional 
postgresql-18-rdkit-dbgsym_202503.6-1_amd64.deb
 530e5e2cc9266bae4297186b44a2521f 260412 database optional 
postgresql-18-rdkit_202503.6-1_amd64.deb
 b7df798dd55975e59269e1559575cca9 64898476 debug optional 
python3-rdkit-dbgsym_202503.6-1_amd64.deb
 c4f2e1f4c9b899b6f06b9cf5d4d03196 4803416 python optional 
python3-rdkit_202503.6-1_amd64.deb
 ad96387a27cbf23f18ea57ce9c248f20 13159868 science optional 
rdkit-data_202503.6-1_all.deb
 27a752e0bb283e328ab808c05c56fbd3 6982664 doc optional 
rdkit-doc_202503.6-1_all.deb
 aac717d7bc91af0108c586803b1fc938 19355 science optional 
rdkit_202503.6-1_amd64.buildinfo

-----BEGIN PGP SIGNATURE-----
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=V5kc
-----END PGP SIGNATURE-----

pgp7WmrTGy7rM.pgp
Description: PGP signature

--- End Message ---

Bug#1110701: marked as done (rdkit ftbfs with GCC 15)

Reply via email to