--- Begin Message ---
Source: ncbi-tools6
Version: 6.1.20170106+dfsg2-1
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):
> x86_64-linux-gnu-gcc -c -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF
> asn2gnb2.c
> In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25,
> from ../include/ncbilcl.h:150,
> from ../include/ncbi.h:57,
> from asn2gnb2.c:42:
> /usr/include/features.h:195:3: warning: #warning "_BSD_SOURCE and
> _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
> 195 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use
> _DEFAULT_SOURCE"
> | ^~~~~~~
> asn2gnb2.c: In function ‘s_LocusAddSuffix’:
> asn2gnb2.c:217:11: warning: variable ‘ch’ set but not used
> [-Wunused-but-set-variable]
> 217 | Char ch;
> | ^~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:1361:66: warning: suggest parentheses around ‘&&’ within ‘||’
> [-Wparentheses]
> 1361 | } else if ((moltype >= 2 && moltype <= 8) || moltype >= 10 &&
> moltype <= 11) {
> |
> ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
> asn2gnb2.c: In function ‘IsSuccessor’:
> asn2gnb2.c:1742:15: warning: comparison between pointer and zero character
> constant [-Wpointer-compare]
> 1742 | while (accp != '\0' && prevp != '\0') {
> | ^~
> asn2gnb2.c:1742:10: note: did you mean to dereference the pointer?
> 1742 | while (accp != '\0' && prevp != '\0') {
> | ^
> asn2gnb2.c:1742:34: warning: comparison between pointer and zero character
> constant [-Wpointer-compare]
> 1742 | while (accp != '\0' && prevp != '\0') {
> | ^~
> asn2gnb2.c:1742:28: note: did you mean to dereference the pointer?
> 1742 | while (accp != '\0' && prevp != '\0') {
> | ^
> asn2gnb2.c: In function ‘IsProjectAccn’:
> asn2gnb2.c:1767:38: warning: comparison between pointer and zero character
> constant [-Wpointer-compare]
> 1767 | for (ptr = acc, letters = 0; ptr != '\0' && IS_ALPHA(*ptr);
> ++ptr, ++letters) continue;
> | ^~
> asn2gnb2.c:1767:34: note: did you mean to dereference the pointer?
> 1767 | for (ptr = acc, letters = 0; ptr != '\0' && IS_ALPHA(*ptr);
> ++ptr, ++letters) continue;
> | ^
> asn2gnb2.c: In function ‘AddDblinkBlock’:
> asn2gnb2.c:2892:22: warning: variable ‘parentID’ set but not used
> [-Wunused-but-set-variable]
> 2892 | Int4 parentID;
> | ^~~~~~~~
> asn2gnb2.c: In function ‘AddSPBlock’:
> asn2gnb2.c:3409:14: error: implicit declaration of function ‘PrintDate’
> [-Werror=implicit-function-declaration]
> 3409 | string = PrintDate (spb->created);
> | ^~~~~~~~~
> asn2gnb2.c:3409:12: warning: assignment to ‘Nlm_CharPtr’ {aka ‘char *’} from
> ‘int’ makes pointer from integer without a cast [-Wint-conversion]
> 3409 | string = PrintDate (spb->created);
> | ^
> asn2gnb2.c:3417:12: warning: assignment to ‘Nlm_CharPtr’ {aka ‘char *’} from
> ‘int’ makes pointer from integer without a cast [-Wint-conversion]
> 3417 | string = PrintDate (spb->sequpd);
> | ^
> asn2gnb2.c:3424:12: warning: assignment to ‘Nlm_CharPtr’ {aka ‘char *’} from
> ‘int’ makes pointer from integer without a cast [-Wint-conversion]
> 3424 | string = PrintDate (spb->annotupd);
> | ^
> asn2gnb2.c: In function ‘AddSourceOrganismBlock’:
> asn2gnb2.c:5056:22: warning: variable ‘common’ set but not used
> [-Wunused-but-set-variable]
> 5056 | CharPtr common;
> | ^~~~~~
> asn2gnb2.c: In function ‘GetRefsOnBioseq’:
> asn2gnb2.c:5893:22: warning: variable ‘strand’ set but not used
> [-Wunused-but-set-variable]
> 5893 | Uint1 strand;
> | ^~~~~~
> asn2gnb2.c:5890:22: warning: variable ‘split’ set but not used
> [-Wunused-but-set-variable]
> 5890 | Boolean split;
> | ^~~~~
> asn2gnb2.c:5884:22: warning: variable ‘right’ set but not used
> [-Wunused-but-set-variable]
> 5884 | Int4 right;
> | ^~~~~
> asn2gnb2.c:5878:22: warning: variable ‘left’ set but not used
> [-Wunused-but-set-variable]
> 5878 | Int4 left;
> | ^~~~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:239:24: warning: ‘%d’ directive writing between 1 and 10 bytes
> into a region of size 6 [-Wformat-overflow=]
> 239 | sprintf(segCountStr,"%d",awp->numsegs);
> | ^~
> In function ‘s_LocusAddSuffix’,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9:
> asn2gnb2.c:239:23: note: directive argument in the range [2, 2147483647]
> 239 | sprintf(segCountStr,"%d",awp->numsegs);
> | ^~~~
> In file included from /usr/include/stdio.h:906,
> from ../include/ncbilcl.h:154:
> In function ‘sprintf’,
> inlined from ‘s_LocusAddSuffix’ at asn2gnb2.c:239:3,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note:
> ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of
> size 6
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:244:25: warning: ‘%0*d’ directive writing between 1 and 32768
> bytes into a region of size 4 [-Wformat-overflow=]
> 244 | sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg);
> | ^~~~
> In function ‘s_LocusAddSuffix’,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9:
> asn2gnb2.c:244:23: note: directive argument in the range [0, 65535]
> 244 | sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg);
> | ^~~~~~~
> In function ‘sprintf’,
> inlined from ‘s_LocusAddSuffix’ at asn2gnb2.c:244:5,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note:
> ‘__builtin___sprintf_chk’ output between 3 and 32770 bytes into a destination
> of size 5
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:246:24: warning: ‘%0*d’ directive writing between 1 and 32768
> bytes into a region of size 5 [-Wformat-overflow=]
> 246 | sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg);
> | ^~~~
> In function ‘s_LocusAddSuffix’,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9:
> asn2gnb2.c:246:23: note: directive argument in the range [0, 65535]
> 246 | sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg);
> | ^~~~~~
> In function ‘sprintf’,
> inlined from ‘s_LocusAddSuffix’ at asn2gnb2.c:246:5,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note:
> ‘__builtin___sprintf_chk’ output between 2 and 32769 bytes into a destination
> of size 5
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:1514:48: warning: ‘" title="Jump to the comment...’ directive
> writing 69 bytes into a region of size between 66 and 106 [-Wformat-overflow=]
> 1514 | sprintf (sect, "<li><a href=\"#comment_%s\" title=\"Jump to the
> comment section of this record\">Comment</a></li>",
> |
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> In function ‘sprintf’,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1514:7:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note:
> ‘__builtin___sprintf_chk’ output between 92 and 132 bytes into a destination
> of size 128
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:1518:46: warning: ‘" title="Jump to the feature...’ directive
> writing 68 bytes into a region of size between 66 and 106 [-Wformat-overflow=]
> 1518 | sprintf (sect, "<li><a href=\"#feature_%s\" title=\"Jump to the
> feature table of this record\">Features</a></li>",
> |
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> In function ‘sprintf’,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1518:5:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note:
> ‘__builtin___sprintf_chk’ output between 91 and 131 bytes into a destination
> of size 128
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:1527:117: warning: ‘__builtin___sprintf_chk’ may write a
> terminating nul past the end of the destination [-Wformat-overflow=]
> 1527 | sprintf (sect, "<li><a href=\"#genome_%s\" title=\"Jump to the
> genome section of this record\">Genome</a></li>",
> |
> ^
> In function ‘sprintf’,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1527:7:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note:
> ‘__builtin___sprintf_chk’ output between 89 and 129 bytes into a destination
> of size 128
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:1532:117: warning: ‘__builtin___sprintf_chk’ may write a
> terminating nul past the end of the destination [-Wformat-overflow=]
> 1532 | sprintf (sect, "<li><a href=\"#contig_%s\" title=\"Jump to the
> contig section of this record\">Contig</a></li>",
> |
> ^
> In function ‘sprintf’,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1532:7:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note:
> ‘__builtin___sprintf_chk’ output between 89 and 129 bytes into a destination
> of size 128
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:1579:81: warning: ‘%s’ directive writing up to 127 bytes into a
> region of size between 68 and 77 [-Wformat-overflow=]
> 1579 | sprintf (sect, "<li class=\"next\"><a href=\"#locus_%ld\"
> title=\"Jump to %s\">Next</a></li>", (long) nextGi, seqid);
> |
> ^~ ~~~~~
> In function ‘sprintf’,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1579:7:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note:
> ‘__builtin___sprintf_chk’ output between 67 and 203 bytes into a destination
> of size 128
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:1587:81: warning: ‘%s’ directive writing up to 127 bytes into a
> region of size between 67 and 77 [-Wformat-overflow=]
> 1587 | sprintf (sect, "<li class=\"next\"><a href=\"#locus_%ld\"
> title=\"Jump to %s\">Next</a></li>", (long) awp->nextGi, seqid);
> |
> ^~ ~~~~~
> In function ‘sprintf’,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1587:7:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note:
> ‘__builtin___sprintf_chk’ output between 67 and 204 bytes into a destination
> of size 128
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:1608:81: warning: ‘%s’ directive writing up to 127 bytes into a
> region of size between 67 and 77 [-Wformat-overflow=]
> 1608 | sprintf (sect, "<li class=\"prev\"><a href=\"#locus_%ld\"
> title=\"Jump to %s\">Previous</a></li>", (long) awp->prevGi, seqid);
> |
> ^~ ~~~~~
> In function ‘sprintf’,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1608:7:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note:
> ‘__builtin___sprintf_chk’ output between 71 and 208 bytes into a destination
> of size 128
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> asn2gnb2.c: In function ‘AddLocusBlock’:
> asn2gnb2.c:1600:81: warning: ‘%s’ directive writing up to 127 bytes into a
> region of size between 68 and 77 [-Wformat-overflow=]
> 1600 | sprintf (sect, "<li class=\"prev\"><a href=\"#locus_%ld\"
> title=\"Jump to %s\">Previous</a></li>", (long) prevGi, seqid);
> |
> ^~ ~~~~~
> In function ‘sprintf’,
> inlined from ‘AddLocusBlock’ at asn2gnb2.c:1600:7:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note:
> ‘__builtin___sprintf_chk’ output between 71 and 207 bytes into a destination
> of size 128
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> cc1: some warnings being treated as errors
> make[3]: *** [makefile:513: asn2gnb2.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2024/03/13/ncbi-tools6_6.1.20170106+dfsg2-1_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 ---
pgpfhWzGJR_td.pgp
