[Debian-med-packaging] Bug#1075361: parasail: ftbfs with GCC-14
Matthias Klose
doko at debian.org
Wed Jul 3 13:39:25 BST 2024
Package: src:parasail
Version: 2.6.2+dfsg-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/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
More information about the Debian-med-packaging
mailing list