--- Begin Message ---
Source: repeatmasker-recon
Version: 1.08-7
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: [email protected]
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;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&[email protected]&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 ---
