Source: readseq Version: 1-14 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 -o readseq -I/usr/include/ncbi -g -O2 > -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. > -fstack-protector-strong -fstack-clash-protection -Wformat > -Werror=format-security -fcf-protection -g -O2 -DNCBI -I/usr/include/ncbi > -DARB readseq.c ureadseq.c ureadasn.c -lncbi -lncbiobj -lncbicdr -lncbiacc > -lncbitool -lncbimmdb -lncbiid1 -lnetcli -lm -Wl,-z,relro -Wl,-z,now > readseq.c: In function ‘formatstr’: > readseq.c:267:41: warning: return discards ‘const’ qualifier from pointer > target type [-Wdiscarded-qualifiers] > 267 | case kASNseqset : return formats[kASN1-1]; > | ~~~~~~~^~~~~~~~~ > readseq.c:269:45: warning: return discards ‘const’ qualifier from pointer > target type [-Wdiscarded-qualifiers] > 269 | case kPhylipSequential: return formats[kPhylip-1]; > | ~~~~~~~^~~~~~~~~~~ > readseq.c:273:22: warning: return discards ‘const’ qualifier from pointer > target type [-Wdiscarded-qualifiers] > 273 | else return formats[format-1]; > | ~~~~~~~^~~~~~~~~~ > readseq.c: In function ‘Nlm_Main’: > readseq.c:801:5: error: implicit declaration of function ‘gets’; did you mean > ‘fgets’? [-Werror=implicit-function-declaration] > 801 | gets(oname= onamestore); > | ^~~~ > | fgets > readseq.c:936:33: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 936 | sprintf( stemp,"%s_%d", oname, whichSeq); > | ~^ ~~~~~~~~ > | | | > | int long int > | %ld > readseq.c:938:48: warning: format ‘%d’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 938 | fprintf( stderr,"Writing sequence %d to file %s\n", > whichSeq, stemp); > | ~^ > ~~~~~~~~ > | | | > | int long > int > | %ld > readseq.c:980:39: warning: format ‘%d’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, > format= %s, id= %s\n", > | ~^ > | | > | int > | %ld > 981 | whichSeq, seqlen, checksum, formatstr(format), > seqidptr); > | ~~~~~~~~ > | | > | long int > readseq.c:980:51: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, > format= %s, id= %s\n", > | ~^ > | | > | int > | %ld > 981 | whichSeq, seqlen, checksum, formatstr(format), > seqidptr); > | ~~~~~~ > | | > | long int > readseq.c:980:65: warning: format ‘%X’ expects argument of type ‘unsigned > int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] > 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, > format= %s, id= %s\n", > | ~^ > | | > | > unsigned int > | %lX > 981 | whichSeq, seqlen, checksum, formatstr(format), > seqidptr); > | ~~~~~~~~ > | | > | long unsigned int > readseq.c:998:53: warning: format ‘%d’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, > seqlen); > | ~^ ~ > | | | > | int long int > | %ld > readseq.c:998:56: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, > seqlen); > | ~^ ~~~~~~ > | | | > | int long > int > | %ld > readseq.c:999:39: warning: format ‘%d’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 999 | else fprintf(foo," %d %d YF\n", i, seqlen); > | ~^ ~ > | | | > | int long int > | %ld > readseq.c:999:42: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 999 | else fprintf(foo," %d %d YF\n", i, seqlen); > | ~^ ~~~~~~ > | | | > | int long int > | %ld > readseq.c:1117:31: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", > /* GSt + RL */ > | ~^ > | | > | int > | %ld > 1118 | cp, seqlen, timestr, checkall); > | ~~~~~~ > | | > | long int > readseq.c:1117:55: warning: format ‘%d’ expects argument of type ‘int’, but > argument 6 has type ‘long unsigned int’ [-Wformat=] > 1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", > /* GSt + RL */ > | ~^ > | | > | int > | %ld > 1118 | cp, seqlen, timestr, checkall); > | ~~~~~~~~ > | | > | long unsigned int > readseq.c:1133:42: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1133 | if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen); > | ~^ ~~~~~~ > | | | > | int long int > | %ld > readseq.c:1134:28: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1134 | else fprintf(foo," %d %d YF\n", seqout, seqlen); > | ~^ ~~~~~~ > | | | > | int long int > | %ld > readseq.c:1158:49: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1158 | fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, > seqlen); > | ~^ ~~~~~~ > | | | > | int long > int > | %ld > cc1: some warnings being treated as errors > ureadseq.c: In function ‘seqFileFormatFp’: > ureadseq.c:1535:19: warning: format ‘%d’ expects argument of type ‘int *’, > but argument 3 has type ‘long int *’ [-Wformat=] > 1535 | sscanf( sp, "%d%d", &nspp, &nlen); > | ~^ ~~~~~ > | | | > | int * long int * > | %ld > ureadseq.c:1535:21: warning: format ‘%d’ expects argument of type ‘int *’, > but argument 4 has type ‘long int *’ [-Wformat=] > 1535 | sscanf( sp, "%d%d", &nspp, &nlen); > | ~^ ~~~~~ > | | | > | int * long int * > | %ld > ureadseq.c: In function ‘writeSeq’: > ureadseq.c:1784:22: warning: format ‘%d’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 1784 | sprintf(numform, "%d", seqlen); > | ~^ ~~~~~~ > | | | > | int long int > | %ld > ureadseq.c:1813:43: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1813 | fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen); > | ~^ ~~~~~~ > | | | > | int long int > | %ld > ureadseq.c:1814:38: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", > seqname, seqlen, checksum); > | ~^ > ~~~~~~ > | | > | > | int > long int > | %ld > ureadseq.c:1814:48: warning: format ‘%X’ expects argument of type ‘unsigned > int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] > 1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", > seqname, seqlen, checksum); > | ~^ > ~~~~~~~~ > | | > | > | unsigned int > long unsigned int > | %lX > ureadseq.c:1828:42: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", > seqname, seqlen, checksum); > | ~^ > ~~~~~~ > | | > | > | int > long int > | %ld > ureadseq.c:1828:52: warning: format ‘%X’ expects argument of type ‘unsigned > int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] > 1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", > seqname, seqlen, checksum); > | ~^ > ~~~~~~~~ > | | > | > | unsigned int > long unsigned int > | %lX > ureadseq.c:1838:53: warning: format ‘%d’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 1838 | for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j); > | ~~~^ ~ > | | | > | | long int > | int > | %10ld > ureadseq.c:1848:26: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, > checksum); > | ~^ ~~~~~~ > | | | > | int long int > | %ld > ureadseq.c:1848:36: warning: format ‘%X’ expects argument of type ‘unsigned > int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] > 1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, > checksum); > | ~^ > ~~~~~~~~ > | | | > | unsigned int > long unsigned int > | %lX > ureadseq.c:1857:31: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, > seqlen, checksum); > | ~^ > ~~~~~~ > | | | > | int long > int > | %ld > ureadseq.c:1857:41: warning: format ‘%X’ expects argument of type ‘unsigned > int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] > 1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, > seqlen, checksum); > | ~^ > ~~~~~~~~ > | | > | > | unsigned int > long unsigned int > | %lX > ureadseq.c:1858:37: warning: format ‘%d’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 1858 | fprintf(outf,"SQ %d BP\n", seqlen); > | ~^ ~~~~~~ > | | | > | int long int > | %ld > ureadseq.c:1869:38: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", > idword, seqlen, checksum); > | ~^ > ~~~~~~ > | | > | > | int > long int > | %ld > ureadseq.c:1869:58: warning: format ‘%d’ expects argument of type ‘int’, but > argument 5 has type ‘long unsigned int’ [-Wformat=] > 1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", > idword, seqlen, checksum); > | ~^ > ~~~~~~~~ > | | > | > | int > long unsigned int > | %ld > ureadseq.c:1878:42: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", > seqname, seqlen, checksum); > | ~^ > ~~~~~~ > | | > | > | int > long int > | %ld > ureadseq.c:1878:52: warning: format ‘%X’ expects argument of type ‘unsigned > int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] > 1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", > seqname, seqlen, checksum); > | ~^ > ~~~~~~~~ > | | > | > | unsigned int > long unsigned int > | %lX > ureadseq.c:1884:26: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, > checksum); > | ~^ ~~~~~~ > | | | > | int long int > | %ld > ureadseq.c:1884:36: warning: format ‘%X’ expects argument of type ‘unsigned > int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] > 1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, > checksum); > | ~^ > ~~~~~~~~ > | | | > | unsigned int > long unsigned int > | %lX > ureadseq.c:1915:53: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1915 | fprintf(outf," repr raw, mol %s, length %d, topology > linear,\n", cp, seqlen); > | ~^ > ~~~~~~ > | | > | > | int > long int > | %ld > ureadseq.c:1937:41: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, > seqlen, checksum); > | ~~^ > ~~~~~~ > | | | > | int > long int > | %6ld > ureadseq.c:1937:53: warning: format ‘%X’ expects argument of type ‘unsigned > int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] > 1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, > seqlen, checksum); > | ~~^ > ~~~~~~~~ > | | > | > | unsigned int > long unsigned int > | %8lX > ureadseq.c:1954:42: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, > seqlen, checksum); > | ~~^ > ~~~~~~ > | | | > | int > long int > | %6ld > ureadseq.c:1954:54: warning: format ‘%X’ expects argument of type ‘unsigned > int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] > 1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, > seqlen, checksum); > | ~~^ > ~~~~~~~~ > | | > | > | unsigned int > long unsigned int > | %8lX > ureadseq.c:1960:40: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: > 1.00\n", > | ~~^ > | | > | int > | %6ld > 1961 | idword, seqlen, checksum); > | ~~~~~~ > | | > | long int > ureadseq.c:1960:52: warning: format ‘%d’ expects argument of type ‘int’, but > argument 5 has type ‘long unsigned int’ [-Wformat=] > 1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: > 1.00\n", > | ~~^ > | | > | int > | %5ld > 1961 | idword, seqlen, checksum); > | ~~~~~~~~ > | | > | long unsigned int > ureadseq.c:1972:27: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, > checksum); > | ~^ ~~~~~~ > | | | > | int long int > | %ld > ureadseq.c:1972:37: warning: format ‘%X’ expects argument of type ‘unsigned > int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] > 1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, > checksum); > | ~^ > ~~~~~~~~ > | | | > | unsigned int > long unsigned int > | %lX > ureadseq.c:1979:25: warning: format ‘%d’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 1979 | fprintf(outf,"%4d %-60s\n",seqlen,seqname); > | ~~^ ~~~~~~ > | | | > | int long int > | %4ld > ureadseq.c:2002:27: warning: format ‘%d’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, > checksum); > | ~^ ~~~~~~ > | | | > | int long int > | %ld > ureadseq.c:2002:37: warning: format ‘%X’ expects argument of type ‘unsigned > int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] > 2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, > checksum); > | ~^ > ~~~~~~~~ > | | | > | unsigned int > long unsigned int > | %lX > ureadseq.c:2043:42: warning: format ‘%d’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 2043 | if (numline==1) fprintf(outf,"%-9d ",i+1); > | ~~~^ ~~~ > | | | > | int long int > | %-9ld > ureadseq.c: In function ‘readPAUPinterleaved’: > ureadseq.c:213:22: warning: ‘%s’ directive writing up to 255 bytes into a > region of size between 246 and 251 [-Wformat-overflow=] > 213 | sprintf(si, " %d) %s\n", V->nseq, s); > | ^~ > In function ‘addinfo’, > inlined from ‘readPAUPinterleaved’ at ureadseq.c:813:13: > ureadseq.c:213:3: note: ‘sprintf’ output between 7 and 267 bytes into a > destination of size 256 > 213 | sprintf(si, " %d) %s\n", V->nseq, s); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ureadseq.c: In function ‘writeSeq’: > ureadseq.c:2007:45: warning: ‘%d’ directive writing between 1 and 6 bytes > into a region of size between 2 and 7 [-Wformat-overflow=] > 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds > ",namewidth,namewidth); > | ^~ > ureadseq.c:2007:39: note: directive argument in the range [-32768, 32767] > 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds > ",namewidth,namewidth); > | ^~~~~~~~~~~ > ureadseq.c:2007:21: note: ‘sprintf’ output between 7 and 17 bytes into a > destination of size 10 > 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds > ",namewidth,namewidth); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ureadasn.c: In function ‘listASNSeqs’: > ureadasn.c:189:24: warning: passing argument 1 of ‘AsnIoOpen’ discards > ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] > 189 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto > errxit; > | ^~~~~~~~ > In file included from /usr/include/ncbi/ncbi.h:57, > from ureadasn.c:13: > /usr/include/ncbi/asn.h:384:54: note: expected ‘Nlm_CharPtr’ {aka ‘char *’} > but argument is of type ‘const char *’ > 384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, > CharPtr mode)); > /usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro ‘PROTO’ > 192 | #define PROTO(x) x /* Prototypes are acceptable */ > | ^ > ureadasn.c: In function ‘readASNSeq’: > ureadasn.c:261:24: warning: passing argument 1 of ‘AsnIoOpen’ discards > ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] > 261 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto > errxit; > | ^~~~~~~~ > /usr/include/ncbi/asn.h:384:54: note: expected ‘Nlm_CharPtr’ {aka ‘char *’} > but argument is of type ‘const char *’ > 384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, > CharPtr mode)); > /usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro ‘PROTO’ > 192 | #define PROTO(x) x /* Prototypes are acceptable */ > | ^ > ureadasn.c:262:31: warning: ‘fgets’ writing 255 bytes into a region of size > 200 overflows the destination [-Wstringop-overflow=] > 262 | for (i=0; i<skiplines; i++) fgets( stemp, 255, aip->fp); /* this > may mess up asn routines... */ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ > ureadasn.c:241:15: note: destination object ‘stemp’ of size 200 > 241 | char *seq, stemp[200]; > | ^~~~~ > In file included from ureadasn.c:8: > /usr/include/stdio.h:592:14: note: in a call to function ‘fgets’ declared > with attribute ‘access (write_only, 1, 2)’ > 592 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict > __stream) > | ^~~~~ > make[1]: *** [Makefile:51: build] Error 1 The full build log is available from: http://qa-logs.debian.net/2024/03/13/readseq_1-14_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.
