[Debian-med-packaging] Bug#1074930: ecopcr: ftbfs with GCC-14

Wed Jul 3 13:25:43 BST 2024

Package: src:ecopcr
Version: 1.0.1+dfsg-4
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/ecopcr_1.0.1+dfsg-4_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

[...]
   dh_autoreconf_clean -O--sourcedirectory=src
   dh_clean -O--sourcedirectory=src
 debian/rules binary
dh binary --sourcedirectory=src --with python3
   dh_update_autotools_config -O--sourcedirectory=src
   dh_autoreconf -O--sourcedirectory=src
   dh_auto_configure -O--sourcedirectory=src
   dh_auto_build -O--sourcedirectory=src
	cd src && make -j8 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecoisundertaxon.d ecoisundertaxon.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecofind.d ecofind.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecopcr.d ecopcr.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecopcr.o ecopcr.c
make -C libapat
make -C libecoPCR
make -C libthermo
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecofind.o ecofind.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecogrep.o ecogrep.c
make[2]: Entering directory '/<<PKGBUILDDIR>>/src/libapat'
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o libstki.d libstki.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecoisundertaxon.o ecoisundertaxon.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o apat_search.d apat_search.c
make[2]: Entering directory '/<<PKGBUILDDIR>>/src/libthermo'
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o nnparams.d nnparams.c
make[2]: Entering directory '/<<PKGBUILDDIR>>/src/libecoPCR'
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o econame.d econame.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o apat_parse.d apat_parse.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecofilter.d ecofilter.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecotax.d ecotax.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o nnparams.o nnparams.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecoseq.d ecoseq.c
ecogrep.c: In function ‘main’:
ecogrep.c:317:29: error: implicit declaration of function ‘isatty’ [-Wimplicit-function-declaration]
  317 |                         if (isatty(fileno(stdin)) == 0)
      |                             ^~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apat_parse.o apat_parse.c
make[1]: *** [global.mk:11: ecogrep.o] Error 1
make[1]: *** Waiting for unfinished jobs....
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecorank.d ecorank.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecoMalloc.d ecoMalloc.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecoIOUtils.d ecoIOUtils.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecoError.d ecoError.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apat_search.o apat_search.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecodna.d ecodna.c
gcc -M -Wdate-time -D_FORTIFY_SOURCE=2 -o ecoapat.d ecoapat.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o libstki.o libstki.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecoapat.o ecoapat.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecodna.o ecodna.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecoError.o ecoError.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecoIOUtils.o ecoIOUtils.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecoMalloc.o ecoMalloc.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecorank.o ecorank.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecoseq.o ecoseq.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecotax.o ecotax.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ecofilter.o ecofilter.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -w -O3 -w -Wdate-time -D_FORTIFY_SOURCE=2 -c -o econame.o econame.c
ar -cr libapat.a apat_parse.o apat_search.o libstki.o
ranlib libapat.a
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src/libapat'
ar -cr libecoPCR.a ecoapat.o ecodna.o ecoError.o ecoIOUtils.o ecoMalloc.o ecorank.o ecoseq.o ecotax.o ecofilter.o econame.o
ranlib libecoPCR.a
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src/libecoPCR'
ar -cr libthermo.a nnparams.o
ranlib libthermo.a
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src/libthermo'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: error: cd src && make -j8 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2