Your message dated Fri, 16 Aug 2024 07:34:12 +0000
with message-id <e1sertq-002n7v...@fasolo.debian.org>
and subject line Bug#1075361: fixed in parasail 2.6.2+dfsg-2
has caused the Debian Bug report #1075361,
regarding parasail: 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.
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--
1075361: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075361
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:parasail
Version: 2.6.2+dfsg-1
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/parasail_2.6.2+dfsg-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
[...]
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o tests/test_isa.o
tests/test_isa.c
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o
tests/test_matrix.o tests/test_matrix.c
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o tests/test_pssm.o
tests/test_pssm.c
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o
tests/test_query-test_query.o `test -f 'tests/test_query.c' || echo
'./'`tests/test_query.c
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o
tests/test_sw_dispatch.o tests/test_sw_dispatch.c
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o
tests/test_verify-test_verify.o `test -f 'tests/test_verify.c' || echo
'./'`tests/test_verify.c
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o
tests/test_verify_tables-test_verify_tables.o `test -f
'tests/test_verify_tables.c' || echo './'`tests/test_verify_tables.c
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o
tests/test_verify_rowcols-test_verify_rowcols.o `test -f
'tests/test_verify_rowcols.c' || echo './'`tests/test_verify_rowcols.c
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o
tests/test_verify_traces-test_verify_traces.o `test -f
'tests/test_verify_traces.c' || echo './'`tests/test_verify_traces.c
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o
tests/test_verify_cigars-test_verify_cigars.o `test -f
'tests/test_verify_cigars.c' || echo './'`tests/test_verify_cigars.c
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o tests/test_12.o
tests/test_12.c
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o tests/test_64.o
tests/test_64.c
tests/test_verify.c: In function ‘main’:
tests/test_verify.c:310:9: warning: variable ‘do_neon’ set but not used
[-Wunused-but-set-variable]
310 | int do_neon = 1;
| ^~~~~~~
tests/test_verify.c:309:9: warning: variable ‘do_altivec’ set but not used
[-Wunused-but-set-variable]
309 | int do_altivec = 1;
| ^~~~~~~~~~
tests/test_verify_tables.c: In function ‘main’:
tests/test_verify_tables.c:328:9: warning: variable ‘do_neon’ set but not used
[-Wunused-but-set-variable]
328 | int do_neon = 1;
| ^~~~~~~
tests/test_verify_tables.c:327:9: warning: variable ‘do_altivec’ set but not
used [-Wunused-but-set-variable]
327 | int do_altivec = 1;
| ^~~~~~~~~~
tests/test_verify_traces.c: In function ‘check_functions’:
tests/test_verify_traces.c:180:37: error: assignment to ‘int8_t *’ {aka ‘signed
char *’} from incompatible pointer type ‘int *’ [-Wincompatible-pointer-types]
180 | ref_trace_table =
parasail_result_get_trace_table(reference_result);
| ^
tests/test_verify_traces.c:193:69: error: passing argument 4 of ‘diff_array’
from incompatible pointer type [-Wincompatible-pointer-types]
193 | if (diff_array(size_a, size_b, ref_trace_table,
trace_table, result)) {
|
^~~~~~~~~~~
| |
| int
*
tests/test_verify_traces.c:83:17: note: expected ‘int8_t *’ {aka ‘signed char
*’} but argument is of type ‘int *’
83 | int8_t *b_,
| ~~~~~~~~^~
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o tests/test_p29.o
tests/test_p29.c
tests/test_verify_traces.c: In function ‘main’:
tests/test_verify_traces.c:239:9: warning: variable ‘do_neon’ set but not used
[-Wunused-but-set-variable]
239 | int do_neon = 1;
| ^~~~~~~
tests/test_verify_traces.c:238:9: warning: variable ‘do_altivec’ set but not
used [-Wunused-but-set-variable]
238 | int do_altivec = 1;
| ^~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I./contrib -I./contrib/sais-lite-lcp -I./src
-I/usr/include/htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -pedantic -c -o tests/test_p59.o
tests/test_p59.c
make[2]: *** [Makefile:18539: tests/test_verify_traces-test_verify_traces.o]
Error 1
make[2]: *** Waiting for unfinished jobs....
tests/test_verify_cigars.c: In function ‘main’:
tests/test_verify_cigars.c:311:9: warning: variable ‘do_neon’ set but not used
[-Wunused-but-set-variable]
311 | int do_neon = 1;
| ^~~~~~~
tests/test_verify_cigars.c:310:9: warning: variable ‘do_altivec’ set but not
used [-Wunused-but-set-variable]
310 | int do_altivec = 1;
| ^~~~~~~~~~
In file included from tests/test_p59.c:33:
tests/test_p59.h: In function ‘main’:
tests/test_p59.h:513:1: warning: string length ‘51025’ is greater than the
length ‘4095’ ISO C99 compilers are required to support [-Woverlength-strings]
513 | "GAAAGTGACAGGGAGAATGGAACCA";
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
tests/test_p59.h:1026:1: warning: string length ‘51024’ is greater than the
length ‘4095’ ISO C99 compilers are required to support [-Woverlength-strings]
1026 | "AAAGTGACAGGGAGAATGGAACCA";
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:19066: check-am] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test: error: make -j8 test "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1
returned exit code 2
make: *** [debian/rules:18: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: parasail
Source-Version: 2.6.2+dfsg-2
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
parasail, 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 parasail 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, 16 Aug 2024 09:03:57 +0200
Source: parasail
Architecture: source
Version: 2.6.2+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1075361
Changes:
parasail (2.6.2+dfsg-2) unstable; urgency=medium
.
* gcc-14.patch: new: fix incompatible pointer types. (Closes: #1075361)
* d/control: declare compliance to standards version 4.7.0.
Checksums-Sha1:
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58e974ccce8097910c314374e545479b1d2c4e44 50920
parasail_2.6.2+dfsg-2.debian.tar.xz
Checksums-Sha256:
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parasail_2.6.2+dfsg-2.dsc
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parasail_2.6.2+dfsg-2.debian.tar.xz
Files:
023a3a6d2f9425b0a5e02861224e89e0 2358 science optional
parasail_2.6.2+dfsg-2.dsc
b3af2d92a8f1908e938211d329c00c94 50920 science optional
parasail_2.6.2+dfsg-2.debian.tar.xz
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