[Debian-med-packaging] Bug#1075544: sumalibs: ftbfs with GCC-14
Matthias Klose
doko at debian.org
Wed Jul 3 13:45:11 BST 2024
Package: src:sumalibs
Version: 1.0.36-3
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/sumalibs_1.0.36-3_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
[...]
| |
| int16_t * {aka short int *}
/<<PKGBUILDDIR>>/liblcs/../libsse/_sse.h:180:44: note: in definition of macro ‘_MM_LOADU_SI128’
180 | #define _MM_LOADU_SI128(x) _mm_loadu_si128(x)
| ^
/usr/lib/gcc/x86_64-linux-gnu/14/include/emmintrin.h:704:35: note: expected ‘const __m128i_u *’ but argument is of type ‘int16_t *’ {aka ‘short int *’}
704 | _mm_loadu_si128 (__m128i_u const *__P)
| ~~~~~~~~~~~~~~~~~^~~
/<<PKGBUILDDIR>>/liblcs/sse_banded_LCS_alignment.c:377:94: error: passing argument 1 of ‘_mm_loadu_si128’ from incompatible pointer type [-Wincompatible-pointer-types]
377 | (*(p_gap2+j)).i = _MM_LOADU_SI128(((*(p_gap1+j)).s16)+1);
| ~~~~~~~~~~~~~~~~~~~^~
| |
| int16_t * {aka short int *}
/<<PKGBUILDDIR>>/liblcs/../libsse/_sse.h:180:44: note: in definition of macro ‘_MM_LOADU_SI128’
180 | #define _MM_LOADU_SI128(x) _mm_loadu_si128(x)
| ^
/usr/lib/gcc/x86_64-linux-gnu/14/include/emmintrin.h:704:35: note: expected ‘const __m128i_u *’ but argument is of type ‘int16_t *’ {aka ‘short int *’}
704 | _mm_loadu_si128 (__m128i_u const *__P)
| ~~~~~~~~~~~~~~~~~^~~
[ 40%] Building C object CMakeFiles/suma.dir/libfasta/fasta_header_parser.c.o
/<<PKGBUILDDIR>>/liblcs/sse_banded_LCS_alignment.c: In function ‘generic_sse_banded_lcs_align’:
/usr/bin/cc -Dsuma_EXPORTS -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/libfasta -I/<<PKGBUILDDIR>>/libfile -I/<<PKGBUILDDIR>>/liblcs -I/<<PKGBUILDDIR>>/libutils -I/<<PKGBUILDDIR>>/libsse -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 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -w -g -fPIC -MD -MT CMakeFiles/suma.dir/libfasta/fasta_header_parser.c.o -MF CMakeFiles/suma.dir/libfasta/fasta_header_parser.c.o.d -o CMakeFiles/suma.dir/libfasta/fasta_header_parser.c.o -c /<<PKGBUILDDIR>>/libfasta/fasta_header_parser.c
/<<PKGBUILDDIR>>/liblcs/sse_banded_LCS_alignment.c:629:53: error: passing argument 1 of ‘reallocA16Address’ from incompatible pointer type [-Wincompatible-pointer-types]
629 | address = reallocA16Address(*address, sizeToAllocateForBand);
| ^~~~~~~~
| |
| int16_t * {aka short int *}
In file included from /<<PKGBUILDDIR>>/liblcs/sse_banded_LCS_alignment.c:13:
/<<PKGBUILDDIR>>/liblcs/../libutils/utilities.h:48:33: note: expected ‘void **’ but argument is of type ‘int16_t *’ {aka ‘short int *’}
48 | void** reallocA16Address(void** address, int size);
| ~~~~~~~^~~~~~~
/<<PKGBUILDDIR>>/liblcs/sse_banded_LCS_alignment.c:629:33: error: assignment to ‘int16_t **’ {aka ‘short int **’} from incompatible pointer type ‘void **’ [-Wincompatible-pointer-types]
629 | address = reallocA16Address(*address, sizeToAllocateForBand);
| ^
make[3]: *** [CMakeFiles/sumaa.dir/build.make:163: CMakeFiles/sumaa.dir/liblcs/sse_banded_LCS_alignment.c.o] Error 1
[ 45%] Building C object CMakeFiles/suma.dir/libfasta/fasta_seq_writer.c.o
/usr/bin/cc -Dsuma_EXPORTS -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/libfasta -I/<<PKGBUILDDIR>>/libfile -I/<<PKGBUILDDIR>>/liblcs -I/<<PKGBUILDDIR>>/libutils -I/<<PKGBUILDDIR>>/libsse -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 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -w -g -fPIC -MD -MT CMakeFiles/suma.dir/libfasta/fasta_seq_writer.c.o -MF CMakeFiles/suma.dir/libfasta/fasta_seq_writer.c.o.d -o CMakeFiles/suma.dir/libfasta/fasta_seq_writer.c.o -c /<<PKGBUILDDIR>>/libfasta/fasta_seq_writer.c
[ 50%] Building C object CMakeFiles/suma.dir/libfasta/header_mem_handler.c.o
/usr/bin/cc -Dsuma_EXPORTS -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/libfasta -I/<<PKGBUILDDIR>>/libfile -I/<<PKGBUILDDIR>>/liblcs -I/<<PKGBUILDDIR>>/libutils -I/<<PKGBUILDDIR>>/libsse -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 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -w -g -fPIC -MD -MT CMakeFiles/suma.dir/libfasta/header_mem_handler.c.o -MF CMakeFiles/suma.dir/libfasta/header_mem_handler.c.o.d -o CMakeFiles/suma.dir/libfasta/header_mem_handler.c.o -c /<<PKGBUILDDIR>>/libfasta/header_mem_handler.c
fasta_header_parser.l: In function ‘header_parser’:
fasta_header_parser.l:85:44: error: passing argument 2 of ‘store_in_header_table’ from incompatible pointer type [-Wincompatible-pointer-types]
In file included from fasta_header_parser.l:13:
/<<PKGBUILDDIR>>/libfasta/header_mem_handler.h:16:36: note: expected ‘char **’ but argument is of type ‘void **’
16 | char* store_in_header_table(char*, char**, int*, int*);
| ^~~~~~
fasta_header_parser.l:103:43: error: passing argument 2 of ‘store_in_header_table’ from incompatible pointer type [-Wincompatible-pointer-types]
/<<PKGBUILDDIR>>/libfasta/header_mem_handler.h:16:36: note: expected ‘char **’ but argument is of type ‘void **’
16 | char* store_in_header_table(char*, char**, int*, int*);
| ^~~~~~
fasta_header_parser.l:114:43: error: passing argument 2 of ‘store_in_header_table’ from incompatible pointer type [-Wincompatible-pointer-types]
/<<PKGBUILDDIR>>/libfasta/header_mem_handler.h:16:36: note: expected ‘char **’ but argument is of type ‘void **’
16 | char* store_in_header_table(char*, char**, int*, int*);
| ^~~~~~
[ 54%] Building C object CMakeFiles/suma.dir/libfile/fileHandling.c.o
/usr/bin/cc -Dsuma_EXPORTS -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/libfasta -I/<<PKGBUILDDIR>>/libfile -I/<<PKGBUILDDIR>>/liblcs -I/<<PKGBUILDDIR>>/libutils -I/<<PKGBUILDDIR>>/libsse -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 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -w -g -fPIC -MD -MT CMakeFiles/suma.dir/libfile/fileHandling.c.o -MF CMakeFiles/suma.dir/libfile/fileHandling.c.o.d -o CMakeFiles/suma.dir/libfile/fileHandling.c.o -c /<<PKGBUILDDIR>>/libfile/fileHandling.c
[ 59%] Building C object CMakeFiles/suma.dir/libfasta/sequence.c.o
/usr/bin/cc -Dsuma_EXPORTS -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/libfasta -I/<<PKGBUILDDIR>>/libfile -I/<<PKGBUILDDIR>>/liblcs -I/<<PKGBUILDDIR>>/libutils -I/<<PKGBUILDDIR>>/libsse -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 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -w -g -fPIC -MD -MT CMakeFiles/suma.dir/libfasta/sequence.c.o -MF CMakeFiles/suma.dir/libfasta/sequence.c.o.d -o CMakeFiles/suma.dir/libfasta/sequence.c.o -c /<<PKGBUILDDIR>>/libfasta/sequence.c
make[3]: *** [CMakeFiles/suma.dir/build.make:93: CMakeFiles/suma.dir/libfasta/fasta_header_parser.c.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:114: CMakeFiles/sumaa.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:88: CMakeFiles/suma.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:19: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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