[Debian-med-packaging] Bug#1075205: libslow5lib: ftbfs with GCC-14

Matthias Klose doko at debian.org
Wed Jul 3 13:34:22 BST 2024 

Package: src:libslow5lib
Version: 0.7.0+dfsg-2.1
Severity: important
Tags: sid trixie
User: debian-gcc at 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/libslow5lib_0.7.0+dfsg-2.1_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

[...]
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make  -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 20%] Building C object CMakeFiles/slow5.dir/src/slow5_misc.c.o
[ 20%] Building C object CMakeFiles/slow5_static.dir/src/slow5_idx.c.o
[ 40%] Building C object CMakeFiles/slow5_static.dir/src/slow5_press.c.o
[ 40%] Building C object CMakeFiles/slow5_static.dir/src/slow5_misc.c.o
/usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5_misc.c.o -MF CMakeFiles/slow5_static.dir/src/slow5_misc.c.o.d -o CMakeFiles/slow5_static.dir/src/slow5_misc.c.o -c /<<PKGBUILDDIR>>/src/slow5_misc.c
/usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5_press.c.o -MF CMakeFiles/slow5_static.dir/src/slow5_press.c.o.d -o CMakeFiles/slow5_static.dir/src/slow5_press.c.o -c /<<PKGBUILDDIR>>/src/slow5_press.c
[ 50%] Building C object CMakeFiles/slow5.dir/src/slow5.c.o
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/usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5.c.o -MF CMakeFiles/slow5_static.dir/src/slow5.c.o.d -o CMakeFiles/slow5_static.dir/src/slow5.c.o -c /<<PKGBUILDDIR>>/src/slow5.c
/usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5.c.o -MF CMakeFiles/slow5.dir/src/slow5.c.o.d -o CMakeFiles/slow5.dir/src/slow5.c.o -c /<<PKGBUILDDIR>>/src/slow5.c
[ 70%] Building C object CMakeFiles/slow5.dir/src/slow5_idx.c.o
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/usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5_idx.c.o -MF CMakeFiles/slow5_static.dir/src/slow5_idx.c.o.d -o CMakeFiles/slow5_static.dir/src/slow5_idx.c.o -c /<<PKGBUILDDIR>>/src/slow5_idx.c
/usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5_press.c.o -MF CMakeFiles/slow5.dir/src/slow5_press.c.o.d -o CMakeFiles/slow5.dir/src/slow5_press.c.o -c /<<PKGBUILDDIR>>/src/slow5_press.c
/usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5_idx.c.o -MF CMakeFiles/slow5.dir/src/slow5_idx.c.o.d -o CMakeFiles/slow5.dir/src/slow5_idx.c.o -c /<<PKGBUILDDIR>>/src/slow5_idx.c
/usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -std=c99 -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5_misc.c.o -MF CMakeFiles/slow5.dir/src/slow5_misc.c.o.d -o CMakeFiles/slow5.dir/src/slow5_misc.c.o -c /<<PKGBUILDDIR>>/src/slow5_misc.c
/<<PKGBUILDDIR>>/src/slow5_press.c: In function ‘ptr_depress_svb_zd’:
/<<PKGBUILDDIR>>/src/slow5_press.c:1125:31: error: passing argument 2 of ‘zigzag_delta_decode’ from incompatible pointer type [-Wincompatible-pointer-types]
 1125 |     zigzag_delta_decode(diff, orig, length, 0);
      |                               ^~~~
      |                               |
      |                               int16_t * {aka short int *}
In file included from /<<PKGBUILDDIR>>/src/slow5_press.c:12:
/usr/include/streamvbyte_zigzag.h:36:57: note: expected ‘int32_t *’ {aka ‘int *’} but argument is of type ‘int16_t *’ {aka ‘short int *’}
   36 | void zigzag_delta_decode(const uint32_t * in, int32_t * out, size_t N, int32_t prev);
      |                                               ~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/src/slow5_press.c: In function ‘ptr_depress_svb_zd’:
/<<PKGBUILDDIR>>/src/slow5_press.c:1125:31: error: passing argument 2 of ‘zigzag_delta_decode’ from incompatible pointer type [-Wincompatible-pointer-types]
 1125 |     zigzag_delta_decode(diff, orig, length, 0);
      |                               ^~~~
      |                               |
      |                               int16_t * {aka short int *}
In file included from /<<PKGBUILDDIR>>/src/slow5_press.c:12:
/usr/include/streamvbyte_zigzag.h:36:57: note: expected ‘int32_t *’ {aka ‘int *’} but argument is of type ‘int16_t *’ {aka ‘short int *’}
   36 | void zigzag_delta_decode(const uint32_t * in, int32_t * out, size_t N, int32_t prev);
      |                                               ~~~~~~~~~~^~~
make[4]: *** [CMakeFiles/slow5_static.dir/build.make:121: CMakeFiles/slow5_static.dir/src/slow5_press.c.o] Error 1
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make[4]: *** [CMakeFiles/slow5.dir/build.make:121: CMakeFiles/slow5.dir/src/slow5_press.c.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:114: CMakeFiles/slow5.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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make[2]: *** [Makefile:139: all] Error 2
make[2]: 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[1]: *** [debian/rules:23: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:15: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

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