[Debian-med-packaging] Bug#1066563: ncbi-seg: FTBFS: genwin.c:93:8: error: implicit declaration of function ‘blastdb’ [-Werror=implicit-function-declaration]
Lucas Nussbaum
lucas at debian.org
Wed Mar 13 11:53:52 GMT 2024
Source: ncbi-seg
Version: 0.0.20000620-6
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):
> gcc -DPACKAGE_NAME=\"ncbi-seg\" -DPACKAGE_TARNAME=\"ncbi-seg\" -DPACKAGE_VERSION=\"0.0.20000620\" -DPACKAGE_STRING=\"ncbi-seg\ 0.0.20000620\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"ncbi-seg\" -DVERSION=\"0.0.20000620\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o genwin.o genwin.c
> sed -e 's|__datadir__|/usr/share|g;s|__docdir__|/usr/share/doc/ncbi-seg|g;s|__pkgdatadir__|/usr/share/ncbi-seg|g;s|__PREFIX__|/usr|g;s|__sysconfdir__|/etc|g;s|__VERSION__|0.0.20000620|g;' "ncbi-seg.pod" | \
> pod2man -c 'User Commands' -r "0.0.20000620" -name NCBI-SEG > "ncbi-seg.1"
> In file included from seg.c:10:
> genwin.h:146:8: warning: type defaults to ‘int’ in declaration of ‘closedbase’ [-Wimplicit-int]
> 146 | extern closedbase();
> | ^~~~~~~~~~
> genwin.h:149:8: warning: type defaults to ‘int’ in declaration of ‘closeseq’ [-Wimplicit-int]
> 149 | extern closeseq();
> | ^~~~~~~~
> genwin.h:152:8: warning: type defaults to ‘int’ in declaration of ‘shiftwin’ [-Wimplicit-int]
> 152 | extern shiftwin(), closewin();
> | ^~~~~~~~
> In file included from genwin.c:9:
> genwin.h:146:8: warning: type defaults to ‘int’ in declaration of ‘closedbase’ [-Wimplicit-int]
> 146 | extern closedbase();
> | ^~~~~~~~~~
> genwin.h:152:20: warning: type defaults to ‘int’ in declaration of ‘closewin’ [-Wimplicit-int]
> 152 | extern shiftwin(), closewin();
> | ^~~~~~~~
> genwin.h:154:8: warning: type defaults to ‘int’ in declaration of ‘compon’ [-Wimplicit-int]
> 154 | extern compon(), stateon(), enton();
> | ^~~~~~
> genwin.h:154:18: warning: type defaults to ‘int’ in declaration of ‘stateon’ [-Wimplicit-int]
> 154 | extern compon(), stateon(), enton();
> | ^~~~~~~
> genwin.h:149:8: warning: type defaults to ‘int’ in declaration of ‘closeseq’ [-Wimplicit-int]
> 149 | extern closeseq();
> | ^~~~~~~~
> genwin.h:154:29: warning: type defaults to ‘int’ in declaration of ‘enton’ [-Wimplicit-int]
> 154 | extern compon(), stateon(), enton();
> | ^~~~~
> genwin.h:152:8: warning: type defaults to ‘int’ in declaration of ‘shiftwin’ [-Wimplicit-int]
> 152 | extern shiftwin(), closewin();
> | ^~~~~~~~
> genwin.h:158:8: warning: type defaults to ‘int’ in declaration of ‘closemat’ [-Wimplicit-int]
> 158 | extern closemat();
> | ^~~~~~~~
> genwin.h:152:20: warning: type defaults to ‘int’ in declaration of ‘closewin’ [-Wimplicit-int]
> 152 | extern shiftwin(), closewin();
> | ^~~~~~~~
> genwin.h:154:8: warning: type defaults to ‘int’ in declaration of ‘compon’ [-Wimplicit-int]
> 154 | extern compon(), stateon(), enton();
> | ^~~~~~
> genwin.h:160:8: warning: type defaults to ‘int’ in declaration of ‘upper’ [-Wimplicit-int]
> 160 | extern upper(), lower(), findchar();
> | ^~~~~
> genwin.h:154:18: warning: type defaults to ‘int’ in declaration of ‘stateon’ [-Wimplicit-int]
> 154 | extern compon(), stateon(), enton();
> | ^~~~~~~
> genwin.h:160:17: warning: type defaults to ‘int’ in declaration of ‘lower’ [-Wimplicit-int]
> 160 | extern upper(), lower(), findchar();
> | ^~~~~
> genwin.h:154:29: warning: type defaults to ‘int’ in declaration of ‘enton’ [-Wimplicit-int]
> 154 | extern compon(), stateon(), enton();
> | ^~~~~
> genwin.h:160:26: warning: type defaults to ‘int’ in declaration of ‘findchar’ [-Wimplicit-int]
> 160 | extern upper(), lower(), findchar();
> | ^~~~~~~~
> genwin.h:158:8: warning: type defaults to ‘int’ in declaration of ‘closemat’ [-Wimplicit-int]
> 158 | extern closemat();
> | ^~~~~~~~
> genwin.h:160:8: warning: type defaults to ‘int’ in declaration of ‘upper’ [-Wimplicit-int]
> 160 | extern upper(), lower(), findchar();
> | ^~~~~
> genwin.h:160:17: warning: type defaults to ‘int’ in declaration of ‘lower’ [-Wimplicit-int]
> 160 | extern upper(), lower(), findchar();
> | ^~~~~
> genwin.h:160:26: warning: type defaults to ‘int’ in declaration of ‘findchar’ [-Wimplicit-int]
> 160 | extern upper(), lower(), findchar();
> | ^~~~~~~~
> genwin.c:62:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 62 | genwininit()
> | ^~~~~~~~~~
> genwin.c: In function ‘opendbase’:
> genwin.c:93:8: error: implicit declaration of function ‘blastdb’ [-Werror=implicit-function-declaration]
> 93 | if (blastdb(name))
> | ^~~~~~~
> genwin.c: At top level:
> genwin.c:144:8: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 144 | extern closedbase(dbase)
> | ^~~~~~~~~~
> genwin.c:185:8: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 185 | extern closeseq(seq)
> | ^~~~~~~~
> genwin.c:319:8: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 319 | extern closewin(win)
> | ^~~~~~~~
> genwin.c:336:8: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 336 | extern compon(win)
> | ^~~~~~
> genwin.c:364:8: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 364 | extern stateon(win)
> | ^~~~~~~
> genwin.c:389:8: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 389 | extern enton(win)
> | ^~~~~
> genwin.c: In function ‘readentry’:
> genwin.c:510:9: error: implicit declaration of function ‘readhdr’ [-Werror=implicit-function-declaration]
> 510 | if (!readhdr(seq))
> | ^~~~~~~
> genwin.c:528:4: error: implicit declaration of function ‘readseq’ [-Werror=implicit-function-declaration]
> 528 | readseq(seq);
> | ^~~~~~~
> genwin.c: At top level:
> genwin.c:545:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 545 | readhdr(seq)
> | ^~~~~~~
> genwin.c: In function ‘readhdr’:
> genwin.c:670:10: error: implicit declaration of function ‘skipline’ [-Werror=implicit-function-declaration]
> 670 | skipline(fp);
> | ^~~~~~~~
> genwin.c: At top level:
> genwin.c:684:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 684 | skipline(fp)
> | ^~~~~~~~
> genwin.c:718:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 718 | readseq(seq)
> | ^~~~~~~
> genwin.c:794:8: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 794 | extern upper(string, len)
> | ^~~~~
> genwin.c:807:8: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 807 | extern lower(string, len)
> | ^~~~~
> genwin.c:862:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 862 | tfree(ptr)
> | ^~~~~
> seg.c:49:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 49 | main(argc, argv)
> | ^~~~
> seg.c: In function ‘main’:
> seg.c:58:4: error: implicit declaration of function ‘genwininit’ [-Werror=implicit-function-declaration]
> 58 | genwininit();
> | ^~~~~~~~~~
> seg.c:60:4: error: implicit declaration of function ‘getparams’ [-Werror=implicit-function-declaration]
> 60 | getparams(argc, argv);
> | ^~~~~~~~~
> seg.c:61:4: error: implicit declaration of function ‘entropy_init’ [-Werror=implicit-function-declaration]
> 61 | entropy_init(window);
> | ^~~~~~~~~~~~
> seg.c:72:7: error: implicit declaration of function ‘segseq’ [-Werror=implicit-function-declaration]
> 72 | segseq(seq, &segs, 0);
> | ^~~~~~
> seg.c:73:7: error: implicit declaration of function ‘mergesegs’ [-Werror=implicit-function-declaration]
> 73 | mergesegs(seq, segs);
> | ^~~~~~~~~
> seg.c:75:22: error: implicit declaration of function ‘singreport’ [-Werror=implicit-function-declaration]
> 75 | if (singleseq) singreport(seq, segs);
> | ^~~~~~~~~~
> seg.c:76:27: error: implicit declaration of function ‘prettyreport’ [-Werror=implicit-function-declaration]
> 76 | else if (prettyseq) prettyreport(seq, segs);
> | ^~~~~~~~~~~~
> seg.c:77:28: error: implicit declaration of function ‘pretreereport’ [-Werror=implicit-function-declaration]
> 77 | else if (prettytree) pretreereport(seq, segs);
> | ^~~~~~~~~~~~~
> seg.c:78:12: error: implicit declaration of function ‘report’ [-Werror=implicit-function-declaration]
> 78 | else report(seq, segs);
> | ^~~~~~
> seg.c:80:7: error: implicit declaration of function ‘freesegs’ [-Werror=implicit-function-declaration]
> 80 | freesegs(segs);
> | ^~~~~~~~
> seg.c: At top level:
> seg.c:90:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 90 | getparams(argc, argv)
> | ^~~~~~~~~
> seg.c: In function ‘getparams’:
> seg.c:103:7: error: implicit declaration of function ‘usage’ [-Werror=implicit-function-declaration]
> 103 | usage();
> | ^~~~~
> seg.c:137:14: error: implicit declaration of function ‘getopt’; did you mean ‘getsubopt’? [-Werror=implicit-function-declaration]
> 137 | while ((c=getopt(nargc, nargv, "m:olhaxpqc:nt:"))!=-1)
> | ^~~~~~
> | getsubopt
> seg.c: At top level:
> seg.c:210:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 210 | segseq(seq, segs, offset)
> | ^~~~~~
> seg.c: In function ‘segseq’:
> seg.c:233:16: error: implicit declaration of function ‘findlo’ [-Werror=implicit-function-declaration]
> 233 | loi = findlo(i, lowlim, H);
> | ^~~~~~
> seg.c:234:16: error: implicit declaration of function ‘findhi’; did you mean ‘findchar’? [-Werror=implicit-function-declaration]
> 234 | hii = findhi(i, last, H);
> | ^~~~~~
> | findchar
> seg.c:239:10: error: implicit declaration of function ‘trim’ [-Werror=implicit-function-declaration]
> 239 | trim(openwin(seq, leftend, rightend-leftend+1), &leftend, &rightend);
> | ^~~~
> seg.c:252:21: error: implicit declaration of function ‘appendseg’ [-Werror=implicit-function-declaration]
> 252 | else appendseg(*segs, leftsegs);
> | ^~~~~~~~~
> seg.c:273:14: error: implicit declaration of function ‘min’; did you mean ‘main’? [-Werror=implicit-function-declaration]
> 273 | i = min(hii, rightend+downset);
> | ^~~
> | main
> seg.c: In function ‘seqent’:
> seg.c:312:31: error: implicit declaration of function ‘hasdash’ [-Werror=implicit-function-declaration]
> 312 | if (seq->punctuation && hasdash(win))
> | ^~~~~~~
> seg.c:314:10: error: implicit declaration of function ‘shiftwin1’; did you mean ‘shiftwin’? [-Werror=implicit-function-declaration]
> 314 | shiftwin1(win);
> | ^~~~~~~~~
> | shiftwin
> seg.c: At top level:
> seg.c:326:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 326 | hasdash(win)
> | ^~~~~~~
> seg.c:343:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 343 | findlo(i, limit, H)
> | ^~~~~~
> seg.c:360:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 360 | findhi(i, limit, H)
> | ^~~~~~
> seg.c:377:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 377 | trim(seq, leftend, rightend)
> | ^~~~
> seg.c:507:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 507 | mergesegs(seq, segs)
> | ^~~~~~~~~
> seg.c:553:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 553 | report(seq, segs)
> | ^~~~~~
> seg.c: In function ‘report’:
> seg.c:565:7: error: implicit declaration of function ‘seqout’; did you mean ‘seqent’? [-Werror=implicit-function-declaration]
> 565 | seqout(seq, hi, 1, seq->length);
> | ^~~~~~
> | seqent
> seg.c: At top level:
> seg.c:626:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 626 | singreport(seq, segs)
> | ^~~~~~~~~~
> seg.c:663:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 663 | prettyreport(seq, segs)
> | ^~~~~~~~~~~~
> seg.c: In function ‘prettyreport’:
> seg.c:687:9: error: implicit declaration of function ‘space’; did you mean ‘isspace’? [-Werror=implicit-function-declaration]
> 687 | space(leftspace+1);
> | ^~~~~
> | isspace
> seg.c: At top level:
> seg.c:718:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 718 | pretreereport(seq, segs)
> | ^~~~~~~~~~~~~
> seg.c:811:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 811 | space(len)
> | ^~~~~
> seg.c:832:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 832 | seqout(seq, hilo, begin, end)
> | ^~~~~~
> seg.c:906:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 906 | appendseg(segs, seg)
> | ^~~~~~~~~
> seg.c:930:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 930 | freesegs(segs)
> | ^~~~~~~~
> seg.c:945:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 945 | usage()
> | ^~~~~
> cc1: some warnings being treated as errors
> make[1]: *** [Makefile:408: genwin.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2024/03/13/ncbi-seg_0.0.20000620-6_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.
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