Your message dated Thu, 20 Jul 2023 09:19:17 +0000
with message-id <[email protected]>
and subject line Bug#1037780: fixed in molmodel 3.1.0-4
has caused the Debian Bug report #1037780,
regarding molmodel: ftbfs with GCC-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
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--
1037780: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037780
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:molmodel
Version: 3.1.0-2
Severity: normal
Tags: sid trixie
User: [email protected]
Usertags: ftbfs-gcc-13
[This bug is targeted to the upcoming trixie release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.
The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/molmodel_3.1.0-2_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 13, either set CC=gcc-13 CXX=g++-13 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-13/porting_to.html
[...]
/<<PKGBUILDDIR>>/src/Representation.cpp:129:5: note: in expansion of macro
‘MK_RESIDUE_SPECIFIER’
129 | MK_RESIDUE_SPECIFIER("deoxythymidine", "dt", 'T', UNKNOWN,
DEOXYTHYMINE);
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Representation.cpp:19:55: error: ‘ResidueType’ is not a
class, namespace, or enumeration
19 |
static_assert(std::underlying_type_t<ResidueType>(ResidueType::type) <
NUM_RESIDUE_TYPES, "Residue type out of range, check NUM_RESIDUE_TYPES"); \
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Representation.cpp:132:5: note: in expansion of macro
‘MK_RESIDUE_SPECIFIER’
132 | MK_RESIDUE_SPECIFIER("disulphidebridgedcysteine", "cyx", 'x',
HYDROPHOBIC, DISULPHIDEBRIDGEDCYSTEINE);
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Representation.cpp:20:48: error: ‘ResidueType’ is not a
class, namespace, or enumeration
20 | arr.at(std::underlying_type_t<ResidueType>(ResidueType::type)) =
ResidueSpecifier{longName, abbrevName, shortName, ResidueProp::prop,
ResidueType::type}; \
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Representation.cpp:132:5: note: in expansion of macro
‘MK_RESIDUE_SPECIFIER’
132 | MK_RESIDUE_SPECIFIER("disulphidebridgedcysteine", "cyx", 'x',
HYDROPHOBIC, DISULPHIDEBRIDGEDCYSTEINE);
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Representation.cpp:20:120: error: too many initializers
for ‘Repr::ResidueSpecifier’
20 | arr.at(std::underlying_type_t<ResidueType>(ResidueType::type)) =
ResidueSpecifier{longName, abbrevName, shortName, ResidueProp::prop,
ResidueType::type}; \
|
^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Representation.cpp:132:5: note: in expansion of macro
‘MK_RESIDUE_SPECIFIER’
132 | MK_RESIDUE_SPECIFIER("disulphidebridgedcysteine", "cyx", 'x',
HYDROPHOBIC, DISULPHIDEBRIDGEDCYSTEINE);
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Representation.cpp:20:86: error: expected
primary-expression before ‘{’ token
20 | arr.at(std::underlying_type_t<ResidueType>(ResidueType::type)) =
ResidueSpecifier{longName, abbrevName, shortName, ResidueProp::prop,
ResidueType::type}; \
|
^
/<<PKGBUILDDIR>>/src/Representation.cpp:132:5: note: in expansion of macro
‘MK_RESIDUE_SPECIFIER’
132 | MK_RESIDUE_SPECIFIER("disulphidebridgedcysteine", "cyx", 'x',
HYDROPHOBIC, DISULPHIDEBRIDGEDCYSTEINE);
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Representation.cpp: In constructor
‘Repr::AtomName::AtomName(const std::string&)’:
/<<PKGBUILDDIR>>/src/Representation.cpp:139:5: error: class ‘Repr::AtomName’
does not have any field named ‘type’
139 | type{getAtomType(name)}
| ^~~~
/<<PKGBUILDDIR>>/src/Representation.cpp:139:10: error: ‘getAtomType’ was not
declared in this scope
139 | type{getAtomType(name)}
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Representation.cpp: At global scope:
/<<PKGBUILDDIR>>/src/Representation.cpp:144:1: error: ‘AtomType’ does not name
a type
144 | AtomType getAtomType(const std::string &name) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/Representation.cpp:176:1: error: ‘ResidueProp’ does not
name a type; did you mean ‘Residue’?
176 | ResidueProp getResidueProp(const ResidueType type) {
| ^~~~~~~~~~~
| Residue
/<<PKGBUILDDIR>>/src/Representation.cpp:180:52: error: ‘ResidueType’ does not
name a type; did you mean ‘Residue’?
180 | const ResidueSpecifier & getResidueSpecifier(const ResidueType type) {
| ^~~~~~~~~~~
| Residue
In file included from /usr/include/c++/13/bits/move.h:37,
from /usr/include/c++/13/bits/exception_ptr.h:41,
from /usr/include/c++/13/exception:164,
from /usr/include/c++/13/stdexcept:38,
from /<<PKGBUILDDIR>>/src/Representation.h:6:
/usr/include/c++/13/type_traits: In substitution of ‘template<class _Tp> using
std::underlying_type_t = typename std::underlying_type::type [with _Tp = const
int]’:
/<<PKGBUILDDIR>>/src/Representation.cpp:181:68: required from here
/usr/include/c++/13/type_traits:2622:11: error: no type named ‘type’ in ‘struct
std::underlying_type<const int>’
2622 | using underlying_type_t = typename underlying_type<_Tp>::type;
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Representation.cpp:184:1: error: ‘ResidueType’ does not
name a type; did you mean ‘Residue’?
184 | ResidueType getResidueType(const std::string &name) {
| ^~~~~~~~~~~
| Residue
make[3]: *** [CMakeFiles/SimTKmolmodel.dir/build.make:261:
CMakeFiles/SimTKmolmodel.dir/src/Representation.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:104: CMakeFiles/SimTKmolmodel.dir/all] Error
2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:139: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install
--strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: molmodel
Source-Version: 3.1.0-4
Done: Andrius Merkys <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <[email protected]> (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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 20 Jul 2023 04:50:25 -0400
Source: molmodel
Architecture: source
Version: 3.1.0-4
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1037780
Changes:
molmodel (3.1.0-4) unstable; urgency=medium
.
* Fix FTBFS with GCC-13 (Closes: #1037780)
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