Your message dated Sun, 05 Oct 2025 21:35:49 +0000
with message-id <[email protected]>
and subject line Bug#1097910: fixed in sortmerna 4.3.7-3
has caused the Debian Bug report #1097910,
regarding sortmerna: ftbfs with GCC-15
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 [email protected]
immediately.)
--
1097910: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097910
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:sortmerna
Version: 4.3.7-2
Severity: important
Tags: sid forky
User: [email protected]
Usertags: ftbfs-gcc-15
[This bug is NOT 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-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.
The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/sortmerna_4.3.7-2_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.
To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other 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-15/porting_to.html
[...]
| ^~~~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:43:1: note: in
expansion of macro ‘KSEQ_INIT’
43 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
[ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o
cd
/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna
&& /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2
-ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W
-Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT
src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o -MF
CMakeFiles/smr_objs.dir/read.cpp.o.d -o CMakeFiles/smr_objs.dir/read.cpp.o -c
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp
[ 76%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o
cd
/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna
&& /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2
-ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W
-Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT
src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o -MF
CMakeFiles/smr_objs.dir/readfeed.cpp.o.d -o
CMakeFiles/smr_objs.dir/readfeed.cpp.o -c
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp
[ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o
cd
/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna
&& /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2
-ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W
-Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT
src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o -MF
CMakeFiles/smr_objs.dir/readstats.cpp.o.d -o
CMakeFiles/smr_objs.dir/readstats.cpp.o -c
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readstats.cpp
[ 78%] Building CXX object
src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o
cd
/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna
&& /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2
-ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W
-Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT
src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o -MF
CMakeFiles/smr_objs.dir/references.cpp.o.d -o
CMakeFiles/smr_objs.dir/references.cpp.o -c
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/references.cpp
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In member
function ‘void Readfeed::init(std::vector<std::__cxx11::basic_string<char> >&,
const int&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:105:69:
warning: unused parameter ‘dbg’ [-Wunused-parameter]
105 | void Readfeed::init(std::vector<std::string>& readfiles, const int& dbg)
| ~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static
member function ‘static bool Readfeed::loadReadByIdx(Read&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:187:37:
warning: unused parameter ‘read’ [-Wunused-parameter]
187 | bool Readfeed::loadReadByIdx(Read & read)
| ~~~~~~~^~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static
member function ‘static bool Readfeed::loadReadById(Read&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:271:35:
warning: unused parameter ‘read’ [-Wunused-parameter]
271 | bool Readfeed::loadReadById(Read& read)
| ~~~~~~^~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static
member function ‘static bool Readfeed::hasnext(std::ifstream&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:553:39:
warning: unused parameter ‘ifs’ [-Wunused-parameter]
553 | bool Readfeed::hasnext(std::ifstream& ifs)
| ~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In member
function ‘bool Readfeed::define_format(const int&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:857:36:
warning: comparison is always false due to limited range of data type
[-Wtype-limits]
857 | if (str[i] > 127 || str[i] < 0) {
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp: In member
function ‘void Read::unmarshallJson(KeyValueDatabase&)’:
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp:540:46:
warning: unused parameter ‘kvdb’ [-Wunused-parameter]
540 | void Read::unmarshallJson(KeyValueDatabase & kvdb)
| ~~~~~~~~~~~~~~~~~~~^~~~
[ 80%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o
cd
/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna
&& /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2
-ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W
-Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT
src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o -MF
CMakeFiles/smr_objs.dir/refstats.cpp.o.d -o
CMakeFiles/smr_objs.dir/refstats.cpp.o -c
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/refstats.cpp
In file included from
/build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:40,
from
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readstats.cpp:52:
/build/reproducible-path/sortmerna-4.3.7/include/kseq.h:171:20: warning: ‘int
kseq_read(kseq_t*)’ defined but not used [-Wunused-function]
171 | static int kseq_read(kseq_t *seq)
\
| ^~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/include/kseq.h:221:9: note: in
expansion of macro ‘__KSEQ_READ’
221 | __KSEQ_READ
| ^~~~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:43:1: note: in
expansion of macro ‘KSEQ_INIT’
43 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
[ 81%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o
cd
/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna
&& /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/include
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph
-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT
src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o -MF
CMakeFiles/smr_objs.dir/ssw.c.o.d -o CMakeFiles/smr_objs.dir/ssw.c.o -c
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/ssw.c
In file included from
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/ssw.c:52:
/build/reproducible-path/sortmerna-4.3.7/include/ssw.h:38:23: error: ‘bool’
cannot be defined via ‘typedef’
38 | typedef unsigned char bool;
| ^~~~
/build/reproducible-path/sortmerna-4.3.7/include/ssw.h:38:23: note: ‘bool’ is a
keyword with ‘-std=c23’ onwards
/build/reproducible-path/sortmerna-4.3.7/include/ssw.h:38:1: warning: useless
type name in empty declaration
38 | typedef unsigned char bool;
| ^~~~~~~
make[3]: *** [src/sortmerna/CMakeFiles/smr_objs.dir/build.make:334:
src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory
'/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make[2]: *** [CMakeFiles/Makefile2:257:
src/sortmerna/CMakeFiles/smr_objs.dir/all] Error 2
make[2]: Leaving directory
'/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make[1]: *** [Makefile:159: all] Error 2
make[1]: Leaving directory
'/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
dh_auto_build: error: cd .pybuild/cpython3_3.13/build && make -j8
"INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
E: pybuild pybuild:389: build: plugin cmake failed with: exit code=25:
dh_auto_build --buildsystem=cmake
--builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build
--
dh_auto_build: error: pybuild --build -i python{version} -p "3.12 3.13"
returned exit code 13
make: *** [debian/rules:19: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: sortmerna
Source-Version: 4.3.7-3
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
sortmerna, 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.
Étienne Mollier <[email protected]> (supplier of updated sortmerna 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: Sun, 05 Oct 2025 23:01:51 +0200
Source: sortmerna
Architecture: source
Version: 4.3.7-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1097910
Changes:
sortmerna (4.3.7-3) unstable; urgency=medium
.
* c23.patch: new: fix build failure with bool redefinition. (Closes:
#1097910)
* d/watch: port to v5 Github template.
* d/control: declare compliance to standards version 4.7.2.
* d/control: drop redundant Rules-Requires-Root: no.
* concurrentqueue.h.patch: normalize Last-Update.
* d/copyright: point to the versioned LGPL-3.
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Files:
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