[Debichem-devel] Bug#973027: rdkit: FTBFS in unstable with postgresql 13

[Andrius Merkys]

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