[Debian-med-packaging] Bug#978918: vsearch: ftbfs with autoconf 2.70

[Matthias Klose]

Package: src:vsearch
Version: 2.15.0-1
Severity: normal
Tags: sid bookworm
User: doko at debian.org
Usertags: ftbfs-ac270

[This bug report is not targeted to the upcoming bullseye release]

The package fails to build in a test rebuild on at least amd64 with
autoconf 2.70, but succeeds to build with autoconf 2.69. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.

The full build log can be found at:
http://qa-logs.debian.net/2020/09/26.ac270/vsearch_2.15.0-1_unstable_ac270.log
The last lines of the build log are at the end of this report.

To build with autoconf 2.70, please install the autoconf package from
experimental:  apt-get -t=experimental install autoconf 

[...]
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h: In function ‘void* _mm_malloc(size_t, size_t)’:
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h:42:12: error: ‘malloc’ was not declared in this scope
   42 |     return malloc (__size);
      |            ^~~~~~
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h:28:1: note: ‘malloc’ is defined in header ‘<cstdlib>’; did you forget to ‘#include <cstdlib>’?
   27 | #include <stdlib.h>
  +++ |+#include <cstdlib>
   28 | 
In file included from /usr/lib/gcc/x86_64-linux-gnu/10/include/xmmintrin.h:34,
                 from /usr/lib/gcc/x86_64-linux-gnu/10/include/immintrin.h:29,
                 from /usr/lib/gcc/x86_64-linux-gnu/10/include/x86intrin.h:32,
                 from vsearch.h:103,
                 from allpairs.cc:61:
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h: In function ‘void* _mm_malloc(size_t, size_t)’:
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h:42:12: error: ‘malloc’ was not declared in this scope
   42 |     return malloc (__size);
      |            ^~~~~~
In file included from /usr/lib/gcc/x86_64-linux-gnu/10/include/xmmintrin.h:34,
                 from /usr/lib/gcc/x86_64-linux-gnu/10/include/immintrin.h:29,
                 from /usr/lib/gcc/x86_64-linux-gnu/10/include/x86intrin.h:32,
                 from vsearch.h:103,
                 from align.cc:61:
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h: In function ‘void* _mm_malloc(size_t, size_t)’:
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h:42:12: error: ‘malloc’ was not declared in this scope
   42 |     return malloc (__size);
      |            ^~~~~~
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h:28:1: note: ‘malloc’ is defined in header ‘<cstdlib>’; did you forget to ‘#include <cstdlib>’?
   27 | #include <stdlib.h>
  +++ |+#include <cstdlib>
   28 | 
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h:28:1: note: ‘malloc’ is defined in header ‘<cstdlib>’; did you forget to ‘#include <cstdlib>’?
   27 | #include <stdlib.h>
  +++ |+#include <cstdlib>
   28 | 
In file included from /usr/lib/gcc/x86_64-linux-gnu/10/include/xmmintrin.h:34,
                 from /usr/lib/gcc/x86_64-linux-gnu/10/include/immintrin.h:29,
                 from /usr/lib/gcc/x86_64-linux-gnu/10/include/x86intrin.h:32,
                 from vsearch.h:103,
                 from align_simd.cc:61:
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h: In function ‘void* _mm_malloc(size_t, size_t)’:
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h:42:12: error: ‘malloc’ was not declared in this scope
   42 |     return malloc (__size);
      |            ^~~~~~
/usr/lib/gcc/x86_64-linux-gnu/10/include/mm_malloc.h:28:1: note: ‘malloc’ is defined in header ‘<cstdlib>’; did you forget to ‘#include <cstdlib>’?
   27 | #include <stdlib.h>
  +++ |+#include <cstdlib>
   28 | 
arch.cc: In function ‘void* xrealloc(void*, size_t)’:
arch.cc:225:14: error: ‘realloc’ was not declared in this scope
  225 |   void * t = realloc(ptr, size);
      |              ^~~~~~~
arch.cc:62:1: note: ‘realloc’ is defined in header ‘<cstdlib>’; did you forget to ‘#include <cstdlib>’?
   61 | #include "vsearch.h"
  +++ |+#include <cstdlib>
   62 | 
make[4]: *** [Makefile:729: arch.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: *** [Makefile:729: align_simd.o] Error 1
make[4]: *** [Makefile:729: align.o] Error 1
make[4]: *** [Makefile:729: allpairs.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: *** [Makefile:374: all-recursive] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:315: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 returned exit code 2
make[1]: *** [debian/rules:28: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:25: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2