[Debian-med-packaging] Bug#957681: phylip: ftbfs with GCC-10

[Matthias Klose]

Package: src:phylip
Version: 1:3.697+dfsg-1
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

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-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/phylip_3.697+dfsg-1_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 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-10/porting_to.html

[...]
dh build --with javahelper --no-parallel
   dh_update_autotools_config -O--no-parallel
   dh_autoreconf -O--no-parallel
   dh_auto_configure -O--no-parallel
   jh_linkjars -O--no-parallel
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx all
	cd src && make -j1 "INSTALL=install --strip-program=true" -f Makefile.unx all
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
Building PHYLIP version 3.696
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DUNX -fomit-frame-pointer -Wdate-time -D_FORTIFY_SOURCE=2  -c -o clique.o clique.c
clique.c: In function ‘getoptions’:
clique.c:219:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  219 |     scanf("%c%*[^\n]", &ch);
      |     ^~~~~~~~~~~~~~~~~~~~~~~
clique.c:249:15: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  249 |               scanf("%ld%*[^\n]", &Cliqmin);
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
clique.c:273:15: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  273 |               scanf("%c%*[^\n]", &ch2);
      |               ^~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DUNX -fomit-frame-pointer -Wdate-time -D_FORTIFY_SOURCE=2  -c -o disc.o disc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DUNX -fomit-frame-pointer -Wdate-time -D_FORTIFY_SOURCE=2  -c -o phylip.o phylip.c
In file included from /usr/include/stdio.h:867,
                 from phylip.c:32:
In function ‘fgets’,
    inlined from ‘getstryng’ at phylip.c:234:11,
    inlined from ‘readlong’ at phylip.c:464:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  263 |  return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘fgets’,
    inlined from ‘getstryng’ at phylip.c:234:11,
    inlined from ‘initcategs’ at phylip.c:600:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  263 |  return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘fgets’,
    inlined from ‘getstryng’ at phylip.c:234:11,
    inlined from ‘initprobcat’ at phylip.c:631:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  263 |  return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘fgets’,
    inlined from ‘getstryng’ at phylip.c:234:11,
    inlined from ‘initfreqs’ at phylip.c:1018:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  263 |  return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘fgets’,
    inlined from ‘getstryng’ at phylip.c:234:11,
    inlined from ‘readlong’ at phylip.c:464:5,
    inlined from ‘initnumlines’ at phylip.c:1123:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  263 |  return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DUNX -fomit-frame-pointer clique.o disc.o phylip.o -lm -Wl,-z,relro -Wl,-z,now -o clique
/usr/bin/ld: disc.o:./src/phylip.h:354: multiple definition of `firstplotblock'; clique.o:./src/phylip.h:354: first defined here
/usr/bin/ld: disc.o:./src/phylip.h:334: multiple definition of `javarun'; clique.o:./src/phylip.h:334: first defined here
/usr/bin/ld: phylip.o:./src/phylip.h:334: multiple definition of `javarun'; clique.o:./src/phylip.h:334: first defined here
/usr/bin/ld: phylip.o:./src/phylip.h:354: multiple definition of `firstplotblock'; clique.o:./src/phylip.h:354: first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile.unx:280: clique] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: error: cd src && make -j1 "INSTALL=install --strip-program=true" -f Makefile.unx all returned exit code 2
make[1]: *** [debian/rules:18: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:15: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2