Your message dated Sat, 14 Dec 2024 09:08:00 +0000
with message-id <e1tmo80-007h57...@fasolo.debian.org>
and subject line Bug#1075544: fixed in sumalibs 1.0.36-4
has caused the Debian Bug report #1075544,
regarding sumalibs: 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.)
--
1075544: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075544
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:sumalibs
Version: 1.0.36-3
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/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
--- End Message ---
--- Begin Message ---
Source: sumalibs
Source-Version: 1.0.36-4
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
sumalibs, 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.
Andreas Tille <ti...@debian.org> (supplier of updated sumalibs 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: SHA256
Format: 1.8
Date: Sat, 14 Dec 2024 09:25:27 +0100
Source: sumalibs
Architecture: source
Version: 1.0.36-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1075544
Changes:
sumalibs (1.0.36-4) unstable; urgency=medium
.
* DEB_CFLAGS_MAINT_APPEND -Wno-incompatible-pointer-types
Closes: #1075544
* Standards-Version: 4.7.0 (routine-update)
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