Your message dated Sat, 31 Oct 2020 14:10:36 +0000 with message-id <[email protected]> and subject line Bug#973027: fixed in rdkit 202003.4-3 has caused the Debian Bug report #973027, regarding rdkit: FTBFS in unstable with postgresql 13 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.) -- 973027: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=973027 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Source: rdkit Version: 202003.4-2 Severity: serious Tags: ftbfs sid Hello, rdkit FTBFS in unstable with postgresql 13. From [1]: dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean pg_buildext checkcontrol --- debian/control 2020-09-22 08:32:21.000000000 -1200 +++ debian/control.cexQZ6 2021-11-25 14:26:59.459300200 -1200 @@ -159,10 +159,10 @@ . This package contains the header files. -Package: postgresql-12-rdkit +Package: postgresql-13-rdkit Architecture: any Section: database -Depends: ${misc:Depends}, ${shlibs:Depends}, postgresql-12 +Depends: ${misc:Depends}, ${shlibs:Depends}, postgresql-13 Suggests: Description: Cheminformatics and machine-learning software (PostgreSQL Cartridge) RDKit is a Python/C++ based cheminformatics and machine-learning software Error: debian/control needs updating from debian/control.in. Run 'pg_buildext updatecontrol'. If you are seeing this message in a buildd log, a sourceful upload is required. make: *** [/usr/share/postgresql-common/pgxs_debian_control.mk:9: debian/control] Error 1 However, replacing s/postgresql-12/postgresql-13/ does not fix the issue as rdkit seemingly uses no longer present postgresql header file: gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -W format-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -W format -Werror=format-security -fno-omit-frame-pointer -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/<<PKGBUILDDIR>>/Code -DRDKITVER='"007300"' -I. -I/<<PKGBUILDDIR>>/Code/PgSQL/rdkit -I/usr/incl ude/postgresql/13/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o rdkit_gist.o /< <PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c /<<PKGBUILDDIR>>/Code/PgSQL/rdkit/rdkit_gist.c:35:10: fatal error: access/tuptoaster.h: No such file or directory 35 | #include <access/tuptoaster.h> | ^~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[2]: *** [/<<PKGBUILDDIR>>/Code/PgSQL/rdkit/Makefile:109: rdkit_gist.o] Error 1 Andrius [1] https://tests.reproducible-builds.org/debian/rbuild/unstable/amd64/rdkit_202003.4-2.rbuild.log.gz
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--- Begin Message ---Source: rdkit Source-Version: 202003.4-3 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: Wed, 28 Oct 2020 09:10:34 -0400 Source: rdkit Binary: librdkit-dev librdkit1 librdkit1-dbgsym postgresql-13-rdkit postgresql-13-rdkit-dbgsym python3-rdkit python3-rdkit-dbgsym rdkit-data rdkit-doc Architecture: source amd64 all Version: 202003.4-3 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 librdkit1 - Collection of cheminformatics and machine-learning software (shar postgresql-13-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: 973027 Changes: rdkit (202003.4-3) unstable; urgency=medium . * Team upload. * Updating postgresql version (Closes: #973027). 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