Your message dated Sun, 01 Sep 2024 18:52:04 +0000
with message-id <e1skpgc-005sbw...@fasolo.debian.org>
and subject line Bug#1066563: fixed in ncbi-seg 0.0.20000620-7
has caused the Debian Bug report #1066563,
regarding ncbi-seg: FTBFS: genwin.c:93:8: error: implicit declaration of
function ‘blastdb’ [-Werror=implicit-function-declaration]
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1066563: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066563
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: ncbi-seg
Version: 0.0.20000620-6
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@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=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&fusertaguser=lu...@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.
--- End Message ---
--- Begin Message ---
Source: ncbi-seg
Source-Version: 0.0.20000620-7
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
ncbi-seg, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1066...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated ncbi-seg package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 01 Sep 2024 20:11:32 +0200
Source: ncbi-seg
Architecture: source
Version: 0.0.20000620-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1066563
Changes:
ncbi-seg (0.0.20000620-7) unstable; urgency=medium
.
* Team upload.
* d/rules: workaround build failure with gcc-14. (Closes: #1066563)
* d/{control,copyright}: update homepage from ftp to https.
* d/control: declare compliance to standards version 4.7.0.
Checksums-Sha1:
04992a0e6dd64d90dcc70f1f4d41b3204d48b62a 2214 ncbi-seg_0.0.20000620-7.dsc
abd512c45a425619e16b28a4614f2513c90b70f0 11736
ncbi-seg_0.0.20000620-7.debian.tar.xz
Checksums-Sha256:
dcf4ad909ec9767718c7873593f9410630377cabffd82b89bd8784fc446233d3 2214
ncbi-seg_0.0.20000620-7.dsc
b05aee643b9bbc0c654ff0fbf3113adfa89ecf9a979f5c0458726f96c47059a5 11736
ncbi-seg_0.0.20000620-7.debian.tar.xz
Files:
c1237d6cfe4b078017e7e5d726959272 2214 science optional
ncbi-seg_0.0.20000620-7.dsc
ddb90b09f09551ab71526cee9f7cac28 11736 science optional
ncbi-seg_0.0.20000620-7.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=pYsR
-----END PGP SIGNATURE-----
pgpMCoFC0q61J.pgp
Description: PGP signature
--- End Message ---
