Your message dated Fri, 06 Sep 2024 20:53:55 +0000
with message-id <e1smfxr-000oz8...@fasolo.debian.org>
and subject line Bug#1075273: fixed in mindthegap 2.3.0-4
has caused the Debian Bug report #1075273,
regarding mindthegap: ftbfs with GCC-14
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.)
--
1075273: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075273
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:mindthegap
Version: 2.3.0-3
Severity: important
Tags: sid trixie
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-14
[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-14/g++-14, but succeeds to build with gcc-13/g++-13. 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/2024/07/01/mindthegap_2.3.0-3_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 14, either set CC=gcc-14 CXX=g++-14 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-14/porting_to.html
[...]
695 | position + 1, //switch to 1-based
| ~~~~~~~~~~~~
| |
| uint64_t {aka long unsigned int}
/<<PKGBUILDDIR>>/src/FindBreakpoints.hpp: In instantiation of ‘void
FindBreakpoints<span>::writeBreakpoint(int, std::string&, uint64_t,
std::string&, std::string&, int, std::string, bool, bool) [with long unsigned
int span = 32; std::string = std::__cxx11::basic_string<char>; uint64_t = long
unsigned int]’:
/<<PKGBUILDDIR>>/src/FindHeteroInsertion.hpp:145:57: required from ‘bool
FindHeteroInsertion<span>::update() [with long unsigned int span = 32]’
145 |
this->_find->writeBreakpoint(this->_find->breakpoint_id(),
this->_find->chrom_name(), this->_find->position() - 1 + i, kmer_begin_str,
kmer_end_str, i, STR_HET_TYPE,
this->_find->het_kmer_history(this->_find->het_kmer_begin_index() +
i).is_repeated, this->_find->kmer_end_is_repeated());
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/FindHeteroInsertion.hpp:48:6: required from here
48 | bool FindHeteroInsertion<span>::update()
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/FindBreakpoints.hpp:642:63: warning: format ‘%lli’ expects
argument of type ‘long long int’, but argument 5 has type ‘uint64_t’ {aka ‘long
unsigned int’} [-Wformat=]
642 |
fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s
left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n",
| ~~~^
| |
| long long
int
| %li
......
645 | position+1, //switch to 1-based
| ~~~~~~~~~~
| |
| uint64_t {aka long unsigned int}
/<<PKGBUILDDIR>>/src/FindBreakpoints.hpp:642:113: warning: format ‘%lli’
expects argument of type ‘long long int’, but argument 12 has type ‘uint64_t’
{aka ‘long unsigned int’} [-Wformat=]
642 |
fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s
left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n",
|
~~~^
|
|
|
long long int
|
%li
......
652 | position+1, //switch to 1-based
| ~~~~~~~~~~
| |
| uint64_t {aka long unsigned int}
/<<PKGBUILDDIR>>/src/FindBreakpoints.hpp: In instantiation of ‘void
FindBreakpoints<span>::writeVcfVariant(int, std::string&, uint64_t, char*,
char*, int, std::string) [with long unsigned int span = 32; std::string =
std::__cxx11::basic_string<char>; uint64_t = long unsigned int]’:
/<<PKGBUILDDIR>>/src/FindDeletion.hpp:158:30: required from ‘bool
FindDeletion<span>::update() [with long unsigned int span = 32]’
158 | this->_find->writeVcfVariant(this->_find->breakpoint_id(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
159 |
this->_find->chrom_name(),
|
~~~~~~~~~~~~~~~~~~~~~~~~~~
160 |
del_start_pos, del_sequence, alt_char, repeat_size, STR_DEL_TYPE);
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/FindDeletion.hpp:62:6: required from here
62 | bool FindDeletion<span>::update()
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/FindBreakpoints.hpp:668:49: warning: format ‘%lli’ expects
argument of type ‘long long int’, but argument 4 has type ‘uint64_t’ {aka ‘long
unsigned int’} [-Wformat=]
668 |
fprintf(this->finder->_vcf_file,"%s\t%lli\tbkpt%i\t%s\t%s\t.\tPASS\tTYPE=%s;LEN=%i;FUZZY=%i\tGT\t1/1\n",
| ~~~^
| |
| long long int
| %li
669 | chrom_name.c_str(),
670 | position+1, //switch to 1-based
| ~~~~~~~~~~
| |
| uint64_t {aka long unsigned int}
[ 90%] Linking CXX executable bin/nwalign
/usr/bin/cmake -E cmake_link_script CMakeFiles/nwalign.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-Wl,-z,relro -Wl,-z,now -rdynamic
CMakeFiles/nwalign.dir/src/nwAlign/nwalign.cpp.o -o bin/nwalign
-L/usr/lib/x86_64-linux-gnu/hdf5/serial
-Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial -lgatbcore -lhdf5
make[3]: *** [CMakeFiles/MindTheGap.dir/build.make:107:
CMakeFiles/MindTheGap.dir/src/Finder.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 90%] Built target nwalign
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:88: CMakeFiles/MindTheGap.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:159: 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:9: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: mindthegap
Source-Version: 2.3.0-4
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
mindthegap, 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 1075...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated mindthegap 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: Fri, 06 Sep 2024 21:01:08 +0200
Source: mindthegap
Architecture: source
Version: 2.3.0-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1075273
Changes:
mindthegap (2.3.0-4) unstable; urgency=medium
.
* fix-use-as-function.patch: new: fix build failure with gcc-14.
(Closes: #1075273)
* d/control: declare compliance to standards version 4.7.0.
* d/control: add myself to uploaders.
* d/salsa-ci.yml: do not test build on i386 due to missing dependency.
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Files:
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