Source: repeatmasker-recon Version: 1.08-7 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 -g -O2 -Werror=implicit-function-declaration > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O > -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro famdef.c -o famdef > In file included from msps.h:4, > from ele.h:1, > from edgeredef.c:1: > seqlist.h: In function ‘GetSeqNames’: > seqlist.h:39:16: error: implicit declaration of function ‘isspace’ > [-Werror=implicit-function-declaration] > 39 | while (isspace(*name_start)) name_start++; > | ^~~~~~~ > seqlist.h:4:1: note: include ‘<ctype.h>’ or provide a declaration of ‘isspace’ > 3 | #include "string.h" > +++ |+#include <ctype.h> > 4 | > msps.h: In function ‘scan_msp’: > msps.h:116:25: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 3 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ ~~~~~~~~~~~ > | | | > | long int * int32_t * > {aka int *} > | %d > msps.h:116:32: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 5 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka int *} > | %d > msps.h:116:36: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 6 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka int *} > | %d > msps.h:116:43: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 8 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka > int *} > | %d > msps.h:116:47: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 9 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > > ~~~~~~~~~~~~~~~~~~~ > | | > > | > | long int * > > int32_t * {aka int *} > | %d > In file included from msps.h:4, > from imagespread.c:2: > seqlist.h: In function ‘GetSeqNames’: > seqlist.h:39:16: error: implicit declaration of function ‘isspace’ > [-Werror=implicit-function-declaration] > 39 | while (isspace(*name_start)) name_start++; > | ^~~~~~~ > seqlist.h:4:1: note: include ‘<ctype.h>’ or provide a declaration of ‘isspace’ > 3 | #include "string.h" > +++ |+#include <ctype.h> > 4 | > msps.h: In function ‘scan_msp’: > msps.h:116:25: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 3 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ ~~~~~~~~~~~ > | | | > | long int * int32_t * > {aka int *} > | %d > msps.h:116:32: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 5 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka int *} > | %d > In file included from msps.h:4, > from ele.h:1, > from eleredef.c:5: > seqlist.h: In function ‘GetSeqNames’: > msps.h:116:36: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 6 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka int *} > | %d > seqlist.h:39:16: error: implicit declaration of function ‘isspace’ > [-Werror=implicit-function-declaration] > 39 | while (isspace(*name_start)) name_start++; > | ^~~~~~~ > seqlist.h:4:1: note: include ‘<ctype.h>’ or provide a declaration of ‘isspace’ > 3 | #include "string.h" > +++ |+#include <ctype.h> > 4 | > seqlist.h: In function ‘GetSeqNames’: > seqlist.h:19:3: warning: ignoring return value of ‘fgets’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 19 | fgets(line, 255, seq_list); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ > msps.h:116:43: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 8 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka > int *} > | %d > msps.h:116:47: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 9 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > > ~~~~~~~~~~~~~~~~~~~ > | | > > | > | long int * > > int32_t * {aka int *} > | %d > msps.h: In function ‘scan_msp’: > msps.h:116:25: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 3 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ ~~~~~~~~~~~ > | | | > | long int * int32_t * > {aka int *} > | %d > msps.h:116:32: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 5 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka int *} > | %d > msps.h:116:36: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 6 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka int *} > | %d > msps.h:116:43: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 8 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka > int *} > | %d > msps.h:116:47: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 9 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > > ~~~~~~~~~~~~~~~~~~~ > | | > > | > | long int * > > int32_t * {aka int *} > | %d > seqlist.h: In function ‘GetSeqNames’: > seqlist.h:19:3: warning: ignoring return value of ‘fgets’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 19 | fgets(line, 255, seq_list); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ > edgeredef.c: In function ‘general_edge_redef’: > edgeredef.c:200:5: warning: ignoring return value of ‘system’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 200 | system(command); > | ^~~~~~~~~~~~~~~ > eleredef.c: In function ‘main’: > eleredef.c:239:70: warning: format ‘%d’ expects argument of type ‘int’, but > argument 2 has type ‘long unsigned int’ [-Wformat=] > 239 | printf("eleredef: Error! Could not allocate memory for img_ptr: > %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) ); > | > ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > | > | | > | > int long unsigned int > | > %ld > seqlist.h: In function ‘GetSeqNames’: > seqlist.h:19:3: warning: ignoring return value of ‘fgets’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 19 | fgets(line, 255, seq_list); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ > In file included from msps.h:4, > from eledef.c:1: > seqlist.h: In function ‘GetSeqNames’: > seqlist.h:39:16: error: implicit declaration of function ‘isspace’ > [-Werror=implicit-function-declaration] > 39 | while (isspace(*name_start)) name_start++; > | ^~~~~~~ > seqlist.h:4:1: note: include ‘<ctype.h>’ or provide a declaration of ‘isspace’ > 3 | #include "string.h" > +++ |+#include <ctype.h> > 4 | > In file included from msps.h:4, > from ele.h:1, > from famdef.c:1: > seqlist.h: In function ‘GetSeqNames’: > seqlist.h:39:16: error: implicit declaration of function ‘isspace’ > [-Werror=implicit-function-declaration] > 39 | while (isspace(*name_start)) name_start++; > | ^~~~~~~ > seqlist.h:4:1: note: include ‘<ctype.h>’ or provide a declaration of ‘isspace’ > 3 | #include "string.h" > +++ |+#include <ctype.h> > 4 | > msps.h: In function ‘scan_msp’: > msps.h: In function ‘scan_msp’: > msps.h:116:25: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 3 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ ~~~~~~~~~~~ > | | | > | long int * int32_t * > {aka int *} > | %d > msps.h:116:25: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 3 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ ~~~~~~~~~~~ > | | | > | long int * int32_t * > {aka int *} > | %d > msps.h:116:32: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 5 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka int *} > | %d > msps.h:116:32: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 5 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka int *} > | %d > msps.h:116:36: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 6 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka int *} > | %d > msps.h:116:36: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 6 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka int *} > | %d > msps.h:116:43: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 8 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka > int *} > | %d > msps.h:116:43: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 8 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > > ~~~~~~~~~~~~~~~~~~~ > | | > | > | long int * > int32_t * {aka > int *} > | %d > msps.h:116:47: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 9 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > > ~~~~~~~~~~~~~~~~~~~ > | | > > | > | long int * > > int32_t * {aka int *} > | %d > msps.h:116:47: warning: format ‘%ld’ expects argument of type ‘long int *’, > but argument 9 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] > 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), > &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, > &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { > | ~~^ > > ~~~~~~~~~~~~~~~~~~~ > | | > > | > | long int * > > int32_t * {aka int *} > | %d > seqlist.h: In function ‘GetSeqNames’: > seqlist.h:19:3: warning: ignoring return value of ‘fgets’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 19 | fgets(line, 255, seq_list); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ > eledef.c: In function ‘main’: > eledef.c:95:13: warning: ignoring return value of ‘freopen’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 95 | freopen(ele_name, "w", all_ele);\ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > eledef.c:246:7: note: in expansion of macro ‘DUMBBELL’ > 246 | DUMBBELL; > | ^~~~~~~~ > eledef.c:95:13: warning: ignoring return value of ‘freopen’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 95 | freopen(ele_name, "w", all_ele);\ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > eledef.c:253:5: note: in expansion of macro ‘DUMBBELL’ > 253 | DUMBBELL; > | ^~~~~~~~ > seqlist.h: In function ‘GetSeqNames’: > seqlist.h:19:3: warning: ignoring return value of ‘fgets’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 19 | fgets(line, 255, seq_list); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ > cc1: some warnings being treated as errors > make[1]: *** [<builtin>: imagespread] Error 1 The full build log is available from: http://qa-logs.debian.net/2024/03/13/repeatmasker-recon_1.08-7_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.