[Debian-med-packaging] Bug#1096578: emboss: ftbfs with GCC-15

Mon Feb 17 17:11:40 GMT 2025

Package: src:emboss
Version: 6.6.0+dfsg-15
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-15

[This bug is NOT 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-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.

The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/emboss_6.6.0+dfsg-15_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.

To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other 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-15/porting_to.html

[...]
 3831 |     AjBool bool = ajFalse;
      |                 ^
ajsql.c:3849:10: error: expected identifier or '(' before '=' token
 3849 |     bool = ajSqlcolumnNumberToStr(sqlr, column, &str);
      |          ^
ajsql.c:3851:12: error: expected identifier or '(' before ')' token
 3851 |     if(bool)
      |            ^
ajsql.c:3851:8: error: declaration in the controlling expression must have an initializer
 3851 |     if(bool)
      |        ^~~~
ajsql.c:3856:12: error: expected expression before 'bool'
 3856 |     return bool;
      |            ^~~~
ajsql.c: In function 'ajSqlcolumnNumberToUint':
ajsql.c:3880:12: error: two or more data types in declaration specifiers
 3880 |     AjBool bool = ajFalse;
      |            ^~~~
ajsql.c:3880:17: error: expected identifier or '(' before '=' token
 3880 |     AjBool bool = ajFalse;
      |                 ^
ajsql.c:3895:10: error: expected identifier or '(' before '=' token
 3895 |     bool = ajSqlcolumnNumberToStr(sqlr, column, &str);
      |          ^
ajsql.c:3897:12: error: expected identifier or '(' before ')' token
 3897 |     if(bool)
      |            ^
ajsql.c:3897:8: error: declaration in the controlling expression must have an initializer
 3897 |     if(bool)
      |        ^~~~
ajsql.c:3902:12: error: expected expression before 'bool'
 3902 |     return bool;
      |            ^~~~
ajsql.c: In function 'ajSqlcolumnNumberToUlong':
ajsql.c:3926:12: error: two or more data types in declaration specifiers
 3926 |     AjBool bool = ajFalse;
      |            ^~~~
ajsql.c:3926:17: error: expected identifier or '(' before '=' token
 3926 |     AjBool bool = ajFalse;
      |                 ^
ajsql.c:3941:10: error: expected identifier or '(' before '=' token
 3941 |     bool = ajSqlcolumnNumberToStr(sqlr, column, &str);
      |          ^
ajsql.c:3943:12: error: expected identifier or '(' before ')' token
 3943 |     if(bool)
      |            ^
ajsql.c:3943:8: error: declaration in the controlling expression must have an initializer
 3943 |     if(bool)
      |        ^~~~
ajsql.c:3948:12: error: expected expression before 'bool'
 3948 |     return bool;
      |            ^~~~
make[5]: *** [Makefile:1326: libajax_la-ajsql.lo] Error 1
make[5]: *** Waiting for unfinished jobs....
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../plplot -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -DNO_AUTH -DDEBIAN -I/usr/include/mariadb -I/usr/include/mariadb/mysql -I/usr/include/postgresql -DAJAX_FIXED_ROOT=\"/usr/share/EMBOSS\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/emboss-6.6.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ajseq.c -o libajax_la-ajseq.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../plplot -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -DNO_AUTH -DDEBIAN -I/usr/include/mariadb -I/usr/include/mariadb/mysql -I/usr/include/postgresql -DAJAX_FIXED_ROOT=\"/usr/share/EMBOSS\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/emboss-6.6.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ajseqwrite.c -o libajax_la-ajseqwrite.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../plplot -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -DNO_AUTH -DDEBIAN -I/usr/include/mariadb -I/usr/include/mariadb/mysql -I/usr/include/postgresql -DAJAX_FIXED_ROOT=\"/usr/share/EMBOSS\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/emboss-6.6.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ajindex.c -o libajax_la-ajindex.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../plplot -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -DNO_AUTH -DDEBIAN -I/usr/include/mariadb -I/usr/include/mariadb/mysql -I/usr/include/postgresql -DAJAX_FIXED_ROOT=\"/usr/share/EMBOSS\" -DAJAX_SYSTEM=\"Linux\" -DPREFIX=\"/usr\" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/emboss-6.6.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ajseqread.c -o libajax_la-ajseqread.o >/dev/null 2>&1
make[5]: Leaving directory '/build/reproducible-path/emboss-6.6.0+dfsg/ajax/core'
make[4]: *** [Makefile:712: all] Error 2
make[4]: Leaving directory '/build/reproducible-path/emboss-6.6.0+dfsg/ajax/core'
make[3]: *** [Makefile:409: all-recursive] Error 1
make[3]: Leaving directory '/build/reproducible-path/emboss-6.6.0+dfsg/ajax'
make[2]: *** [Makefile:458: all-recursive] Error 1
make[2]: Leaving directory '/build/reproducible-path/emboss-6.6.0+dfsg'
dh_auto_build: error: make -j8 AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\" "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/emboss-6.6.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" "LDFLAGS=-lexpat -L/usr/lib/x86_64-linux-gnu/ -lmariadb -lpq -Wl,-z,relro -Wl,-z,now" returned exit code 2
make[1]: *** [debian/rules:54: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/emboss-6.6.0+dfsg'
make: *** [debian/rules:13: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2