Your message dated Wed, 21 Jun 2023 11:53:25 +0000
with message-id <e1qbwor-009i4x...@fasolo.debian.org>
and subject line Bug#1037472: fixed in molmodel 3.1.0-3
has caused the Debian Bug report #1037472,
regarding molmodel: FTBFS with gemmi 0.6.2+ds-1
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
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--
1037472: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037472
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: molmodel
Severity: serious
Version: 3.1.0-2
Hello,
molmodel FTBFS after recent update of gemmi to 0.6.2+ds-1:
/home/merkys/molmodel-3.1.0/src/PDBReader.cpp: In function
'gemmi::Structure getStructureFromFile(const std::string&)':
/home/merkys/molmodel-3.1.0/src/PDBReader.cpp:98:29: error:
'make_structure_from_block' is not a member of 'gemmi::impl'; did you
mean 'gemmi::make_structure_from_block'?
98 | return gemmi::impl::make_structure_from_block (
gemmiDoc.blocks.at(0) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/gemmi/mmread.hpp:13,
from
/home/merkys/molmodel-3.1.0/./include/molmodel/internal/Compound.h:48,
from
/home/merkys/molmodel-3.1.0/./include/molmodel/internal/CompoundSystem.h:6,
from
/home/merkys/molmodel-3.1.0/./include/molmodel/internal/PDBReader.h:36,
from /home/merkys/molmodel-3.1.0/src/PDBReader.cpp:33:
/usr/include/gemmi/mmcif.hpp:15:21: note:
'gemmi::make_structure_from_block' declared here
15 | GEMMI_DLL Structure make_structure_from_block(const cif::Block&
block);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: *** [CMakeFiles/SimTKmolmodel.dir/build.make:219:
CMakeFiles/SimTKmolmodel.dir/src/PDBReader.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
/home/merkys/molmodel-3.1.0/src/Pdb.cpp: In function 'gemmi::Structure
gemmiStructFromDoc(const gemmi::cif::Document&)':
/home/merkys/molmodel-3.1.0/src/Pdb.cpp:39:25: error:
'make_structure_from_block' is not a member of 'gemmi::impl'; did you
mean 'gemmi::make_structure_from_block'?
39 | return
gemmi::impl::make_structure_from_block(doc.blocks.front());
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/gemmi/mmread.hpp:13,
from
/home/merkys/molmodel-3.1.0/./include/molmodel/internal/Compound.h:48,
from
/home/merkys/molmodel-3.1.0/./include/molmodel/internal/Pdb.h:6,
from /home/merkys/molmodel-3.1.0/src/Pdb.cpp:4:
/usr/include/gemmi/mmcif.hpp:15:21: note:
'gemmi::make_structure_from_block' declared here
15 | GEMMI_DLL Structure make_structure_from_block(const cif::Block&
block);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
The issue is better fixed upstream, I will forward the report. In the
meantime it is OK to remove molmodel from testing to not obstruct the
upcoming openmm transition.
Andrius
--- End Message ---
--- Begin Message ---
Source: molmodel
Source-Version: 3.1.0-3
Done: Andrius Merkys <mer...@debian.org>
We believe that the bug you reported is fixed in the latest version of
molmodel, 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 1037...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <mer...@debian.org> (supplier of updated molmodel 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 21 Jun 2023 07:13:00 -0400
Source: molmodel
Architecture: source
Version: 3.1.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Andrius Merkys <mer...@debian.org>
Closes: 1037472
Changes:
molmodel (3.1.0-3) unstable; urgency=medium
.
* Adapt upstream fix to restore compatibility with gemmi (Closes: #1037472)
* Set upstream metadata fields: Repository-Browse.
* Update standards version to 4.6.2, no changes needed.
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