[Debian-med-packaging] Bug#1075307: ncbi-tools6: ftbfs with GCC-14

[Matthias Klose]

Package: src:ncbi-tools6
Version: 6.1.20170106+dfsg2-2
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/ncbi-tools6_6.1.20170106+dfsg2-2_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

[...]
./ln-if-absent ../internal/ideogram/*.dat .
set: No match.
make[3]: [makefile:778: copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideochr*.h ../include
set: No match.
make[3]: [makefile:779: copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideoorgs.h .
make[3]: [makefile:780: copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.c .
set: No match.
make[3]: [makefile:781: copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.dat .
set: No match.
make[3]: [makefile:782: copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.h ../include
set: No match.
make[3]: [makefile:783: copy] Error 1 (ignored)
./ln-if-absent ncbidraw.c ncbidrwg.c
./ln-if-absent ncbithr.c ncbithrs.c
./ln-if-absent ../network/nsclilib/*.h ../include
./ln-if-absent ../network/blast3/client/*.h ../include
./ln-if-absent ../network/id1arch/*.h ../include
./ln-if-absent ../network/id2arch/*.h ../include
mkdir -p ../include/algo/blast/core
./ln-if-absent ../algo/blast/core/*.c .
./ln-if-absent ../algo/blast/core/*.h .
./ln-if-absent ../algo/blast/core/*.inl .
cp -fp ../algo/blast/core/*.h ../include/algo/blast/core
mkdir -p ../include/algo/blast/composition_adjustment
./ln-if-absent ../algo/blast/composition_adjustment/*.c .
cp -fp ../algo/blast/composition_adjustment/*.h \
	../include/algo/blast/composition_adjustment
mkdir -p ../include/algo/blast/api
./ln-if-absent ../algo/blast/api/*.c .
cp -fp ../algo/blast/api/*.h ../include/algo/blast/api
chmod -R ug+rw,o+r .
echo Waiting...go
Waiting...go
x86_64-linux-gnu-gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbithr.c
In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25,
                 from ../include/ncbilcl.h:150,
                 from ../include/ncbistd.h:61,
                 from ncbithr.c:289:
/usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
  196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
      |   ^~~~~~~
ncbithr.c: In function ‘s_TlsDestroyAll’:
ncbithr.c:2529:11: warning: variable ‘err_code’ set but not used [-Wunused-but-set-variable]
 2529 |       int err_code = 0;
      |           ^~~~~~~~
cp -p ncbithr.o ../lib
x86_64-linux-gnu-gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimain.c
In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25,
                 from ../include/ncbilcl.h:150,
                 from ../include/ncbi.h:57,
                 from ncbimain.c:56:
/usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
  196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
      |   ^~~~~~~
ncbimain.c:82:1: error: return type defaults to ‘int’ [-Wimplicit-int]
   82 | main(int argc, char *argv[])
      | ^~~~
make[3]: *** [makefile:513: ncbimain.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[2]: *** [debian/rules:83: override_dh_auto_build-arch] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [debian/rules:77: build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:73: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2