[Debian-med-packaging] Bug#1066653: prime-phylo: FTBFS: gb.tab.c:1096:16: error: implicit declaration of function ‘yylex’ [-Werror=implicit-function-declaration]

[Lucas Nussbaum]

Source: prime-phylo
Version: 1.0.11-10
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20240313 ftbfs-trixie ftbfs-impfuncdef

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

This is most likely caused by a change in dpkg 1.22.6, that enabled
-Werror=implicit-function-declaration. For more information, see
https://wiki.debian.org/qa.debian.org/FTBFS#A2024-03-13_-Werror.3Dimplicit-function-declaration

Relevant part (hopefully):
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -MF CMakeFiles/prime-phylo-sfile.dir/sfile.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c
> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c: In function ‘yyparse’:
> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:1096:16: error: implicit declaration of function ‘yylex’ [-Werror=implicit-function-declaration]
>  1096 |       yychar = yylex ();
>       |                ^~~~~
> gb.y: In function ‘yyerror’:
> gb.y:291:70: error: implicit declaration of function ‘linenumber’ [-Werror=implicit-function-declaration]
> gb.y: In function ‘add_to_seq’:
> gb.y:402:9: warning: unused variable ‘new_buf’ [-Wunused-variable]
> /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c: In function ‘main’:
> /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c:17:10: error: implicit declaration of function ‘strcmp’ [-Werror=implicit-function-declaration]
>    17 |     if (!strcmp(argv[opt], "-d")) {
>       |          ^~~~~~
> /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c:8:1: note: include ‘<string.h>’ or provide a declaration of ‘strcmp’
>     7 | #include "gb.tab.h"
>   +++ |+#include <string.h>
>     8 | 
> seqreader.l: In function ‘seq_read’:
> seqreader.l:270:9: warning: unused variable ‘code’ [-Wunused-variable]
> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c: At top level:
> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1864:16: warning: ‘input’ defined but not used [-Wunused-function]
>  1864 |     static int input  (void)
>       |                ^~~~~
> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1821:17: warning: ‘yyunput’ defined but not used [-Wunused-function]
>  1821 |     static void yyunput (int c, char * yy_bp )
>       |                 ^~~~~~~
> /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c: In function ‘seq_print’:
> /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:265:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
>   265 |       printf("%9d", char_counter + 1);
>       |              ^~~~~  ~~~~~~~~~~~~~~~~
>       |                                  |
>       |                                  long int
> /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable ‘date’ set but not used [-Wunused-but-set-variable]
>   212 |   char *top, *date;
>       |               ^~~~
> cc1: some warnings being treated as errors
> make[3]: *** [src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make:90: src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o] Error 1


The full build log is available from:
http://qa-logs.debian.net/2024/03/13/prime-phylo_1.0.11-10_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240313;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.