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.
