Your message dated Thu, 08 Sep 2022 12:56:16 +0000
with message-id <e1owh4q-008dxg...@fasolo.debian.org>
and subject line Bug#1016227: fixed in openbabel 3.1.1+dfsg-7
has caused the Debian Bug report #1016227,
regarding openbabel: FTBFS: obutil.h:65:14: error: ‘clock’ was not declared in
this scope
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 ow...@bugs.debian.org
immediately.)
--
1016227: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1016227
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: openbabel
Version: 3.1.1+dfsg-6
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20220728 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
> -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
> -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
> -D__WXGTK__ -Dasciiformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
> -I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
> -I/usr/include/cairo -I/usr/include/libxml2 -isystem
> /usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.0 -isystem
> /usr/include/wx-3.0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98
> -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread
> -fopenmp -fPIC -std=gnu++11 -MD -MT
> src/formats/CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o -MF
> CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o.d -o
> CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o -c
> /<<PKGBUILDDIR>>/src/depict/asciipainter.cpp
> In file included from /<<PKGBUILDDIR>>/src/depict/asciipainter.cpp:18:
> /<<PKGBUILDDIR>>/include/openbabel/obutil.h: In member function ‘void
> OpenBabel::OBStopwatch::Start()’:
> /<<PKGBUILDDIR>>/include/openbabel/obutil.h:65:14: error: ‘clock’ was not
> declared in this scope
> 65 | start= clock();
> | ^~~~~
> /<<PKGBUILDDIR>>/include/openbabel/obutil.h:40:1: note: ‘clock’ is defined in
> header ‘<ctime>’; did you forget to ‘#include <ctime>’?
> 39 | #include <math.h>
> +++ |+#include <ctime>
> 40 |
> /<<PKGBUILDDIR>>/include/openbabel/obutil.h: In member function ‘double
> OpenBabel::OBStopwatch::Lap()’:
> /<<PKGBUILDDIR>>/include/openbabel/obutil.h:70:13: error: ‘clock’ was not
> declared in this scope
> 70 | stop= clock();
> | ^~~~~
> /<<PKGBUILDDIR>>/include/openbabel/obutil.h:70:13: note: ‘clock’ is defined
> in header ‘<ctime>’; did you forget to ‘#include <ctime>’?
> /<<PKGBUILDDIR>>/include/openbabel/obutil.h:71:40: error: ‘CLOCKS_PER_SEC’
> was not declared in this scope
> 71 | return((stop - start) / (double) CLOCKS_PER_SEC);
> | ^~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/include/openbabel/obutil.h:71:40: note: the macro
> ‘CLOCKS_PER_SEC’ had not yet been defined
> In file included from /usr/include/time.h:33,
> from /usr/include/pthread.h:23,
> from
> /usr/include/x86_64-linux-gnu/c++/12/bits/gthr-default.h:35,
> from /usr/include/x86_64-linux-gnu/c++/12/bits/gthr.h:148,
> from /usr/include/c++/12/ext/atomicity.h:35,
> from /usr/include/c++/12/bits/ios_base.h:39,
> from /usr/include/c++/12/ios:42,
> from /usr/include/c++/12/istream:38,
> from /usr/include/c++/12/sstream:38,
> from /<<PKGBUILDDIR>>/include/openbabel/depict/painter.h:25,
> from
> /<<PKGBUILDDIR>>/include/openbabel/depict/asciipainter.h:21,
> from /<<PKGBUILDDIR>>/src/depict/asciipainter.cpp:19:
> /usr/include/x86_64-linux-gnu/bits/time.h:34: note: it was later defined here
> 34 | #define CLOCKS_PER_SEC ((__clock_t) 1000000)
> |
> In file included from /<<PKGBUILDDIR>>/include/openbabel/op.h:25,
> from /<<PKGBUILDDIR>>/src/ops/gen2D.cpp:22:
> /<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: ‘template<class
> _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated
> [-Wdeprecated-declarations]
> 41 | struct OBERROR CharPtrLess : public std::binary_function<const
> char*,const char*, bool>
> | ^~~~~~~~~~~~~~~
> In file included from /usr/include/c++/12/string:48,
> from /usr/include/c++/12/bits/locale_classes.h:40,
> from /usr/include/c++/12/bits/ios_base.h:41,
> from /usr/include/c++/12/ios:42,
> from /usr/include/c++/12/ostream:38,
> from /usr/include/c++/12/iostream:39,
> from /<<PKGBUILDDIR>>/src/ops/gen2D.cpp:21:
> /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
> 131 | struct binary_function
> | ^~~~~~~~~~~~~~~
> In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
> from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
> from /<<PKGBUILDDIR>>/include/openbabel/obmolecformat.h:36,
> from /<<PKGBUILDDIR>>/src/formats/MNAformat.cpp:31:
> /<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: ‘template<class
> _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated
> [-Wdeprecated-declarations]
> 41 | struct OBERROR CharPtrLess : public std::binary_function<const
> char*,const char*, bool>
> | ^~~~~~~~~~~~~~~
> In file included from /usr/include/c++/12/string:48,
> from /usr/include/c++/12/bits/locale_classes.h:40,
> from /usr/include/c++/12/bits/ios_base.h:41,
> from /usr/include/c++/12/ios:42,
> from /usr/include/c++/12/ostream:38,
> from /usr/include/c++/12/iostream:39,
> from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:24:
> /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
> 131 | struct binary_function
> | ^~~~~~~~~~~~~~~
> make[4]: *** [src/formats/CMakeFiles/asciiformat.dir/build.make:93:
> src/formats/CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2022/07/28/openbabel_3.1.1+dfsg-6_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220728;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220728&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: openbabel
Source-Version: 3.1.1+dfsg-7
Done: Andrius Merkys <mer...@debian.org>
We believe that the bug you reported is fixed in the latest version of
openbabel, 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 1016...@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 openbabel 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: Thu, 08 Sep 2022 08:29:09 -0400
Source: openbabel
Architecture: source
Version: 3.1.1+dfsg-7
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Andrius Merkys <mer...@debian.org>
Closes: 1016227
Changes:
openbabel (3.1.1+dfsg-7) unstable; urgency=medium
.
* Include <ctime> in obutil.h (Closes: #1016227)
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