[Debichem-devel] Bug#1116968: rdkit: package new upstream release

[Andrius Merkys]

Source: rdkit
Severity: wishlist
Tags: help

Hello,

New upstream release 202503.6 is out. I have started working on 
packaging it in rdkit repository on salsa, in branch 
'package-new-upstream-release'. Build fails here:

[  7%] Building CXX object CMakeFiles/rdkit.dir/adapter.cpp.o
/usr/bin/c++ -DRDKITVER=\"007600\" -DRDK_TOOLKIT_VERSION=\"\" 
-Drdkit_EXPORTS -I/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code 
-I/usr/include/postgresql -I/usr/include/postgresql/18/server -g -O2 
-ffile-prefix-map=/home/merkys/rdkit=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security 
-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT 
CMakeFiles/rdkit.dir/adapter.cpp.o -MF 
CMakeFiles/rdkit.dir/adapter.cpp.o.d -o 
CMakeFiles/rdkit.dir/adapter.cpp.o -c 
/home/merkys/rdkit/Code/PgSQL/rdkit/adapter.cpp
In file included from 
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/ChemReactions/Reaction.h:41,
                  from /home/merkys/rdkit/Code/PgSQL/rdkit/adapter.cpp:55:
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/Substruct/SubstructMatch.h:66:27: 
error: 'span' is not a member of 'std'
    66 |                      std::span<const unsigned int> match)>
       |                           ^~~~
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/Substruct/SubstructMatch.h:66:27: 
note: 'std::span' is only available from C++20 onwards
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/Substruct/SubstructMatch.h:66:57: 
error: expression list treated as compound expression in functional cast 
[-fpermissive]
    66 |                      std::span<const unsigned int> match)>
       |                                                         ^
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/Substruct/SubstructMatch.h:66:58: 
error: template argument 1 is invalid
    66 |                      std::span<const unsigned int> match)>
       |                                                          ^
In file included from /home/merkys/rdkit/Code/PgSQL/rdkit/adapter.cpp:61:
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/GenericGroups/GenericGroups.h:607:16: 
error: 'span' in namespace 'std' does not name a template type
   607 |     const std::span<const unsigned int> &match);
       |                ^~~~
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/GenericGroups/GenericGroups.h:607:11: 
note: 'std::span' is only available from C++20 onwards
   607 |     const std::span<const unsigned int> &match);
       |           ^~~
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/GenericGroups/GenericGroups.h:607:20: 
error: expected ',' or '...' before '<' token
   607 |     const std::span<const unsigned int> &match);
       |                    ^
In file included from 
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/GeneralizedSubstruct/XQMol.h:26,
                  from /home/merkys/rdkit/Code/PgSQL/rdkit/adapter.cpp:109:
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/TautomerQuery/TautomerQuery.h:49:33: 
error: 'span' in namespace 'std' does not name a template type
    49 |                      const std::span<const unsigned int> &match,
       |                                 ^~~~
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/TautomerQuery/TautomerQuery.h:49:28: 
note: 'std::span' is only available from C++20 onwards
    49 |                      const std::span<const unsigned int> &match,
       |                            ^~~
/home/merkys/rdkit/Code/PgSQL/rdkit/../../../Code/GraphMol/TautomerQuery/TautomerQuery.h:49:37: 
error: expected ',' or '...' before '<' token
    49 |                      const std::span<const unsigned int> &match,
       |                                     ^
make[4]: *** [CMakeFiles/rdkit.dir/build.make:82: 
CMakeFiles/rdkit.dir/adapter.cpp.o] Error 1
make[4]: Leaving directory '/home/merkys/rdkit/Code/PgSQL/rdkit/build-18'
make[3]: *** [CMakeFiles/Makefile2:90: CMakeFiles/rdkit.dir/all] Error 2
make[3]: Leaving directory '/home/merkys/rdkit/Code/PgSQL/rdkit/build-18'
make[2]: *** [Makefile:139: all] Error 2
make[2]: Leaving directory '/home/merkys/rdkit/Code/PgSQL/rdkit/build-18'

I have no idea how to resolve this.

Andrius