Your message dated Sun, 07 Apr 2024 09:34:04 +0000
with message-id <e1rtoua-006q2o...@fasolo.debian.org>
and subject line Bug#1066709: fixed in fastdnaml 1.2.2-16
has caused the Debian Bug report #1066709,
regarding fastdnaml: FTBFS: fastDNAml.h:228:28: error: implicit declaration of
function ‘free’ [-Werror=implicit-function-declaration]
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
1066709: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066709
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: fastdnaml
Version: 1.2.2-15
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):
> cd source && cc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> fastDNAml.c -o fastDNAml -lm -Wl,-z,relro -Wl,-z,now
> In file included from fastDNAml.c:207:
> fastDNAml.h:222:10: warning: conflicting types for built-in function
> ‘malloc’; expected ‘void *(long unsigned int)’
> [-Wbuiltin-declaration-mismatch]
> 222 | char *malloc();
> | ^~~~~~
> fastDNAml.h:1:1: note: ‘malloc’ is declared in header ‘<stdlib.h>’
> +++ |+#include <stdlib.h>
> 1 | /* fastDNAml.h */
> fastDNAml.c: In function ‘freeTopol’:
> fastDNAml.h:228:28: error: implicit declaration of function ‘free’
> [-Werror=implicit-function-declaration]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:342:5: note: in expansion of macro ‘Free’
> 342 | Free(tpl->links);
> | ^~~~
> fastDNAml.c:208:1: note: include ‘<stdlib.h>’ or provide a declaration of
> ‘free’
> 207 | #include "fastDNAml.h" /* Requires version 1.2 */
> +++ |+#include <stdlib.h>
> 208 |
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in
> function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:342:5: note: in expansion of macro ‘Free’
> 342 | Free(tpl->links);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of
> ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:342:5: note: in expansion of macro ‘Free’
> 342 | Free(tpl->links);
> | ^~~~
> fastDNAml.c: In function ‘freeTreeNode’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in
> function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1533:23: note: in expansion of macro ‘Free’
> 1533 | if (p->x->lv) Free(p->x->lv);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of
> ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1533:23: note: in expansion of macro ‘Free’
> 1533 | if (p->x->lv) Free(p->x->lv);
> | ^~~~
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in
> function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1534:9: note: in expansion of macro ‘Free’
> 1534 | Free(p->x);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of
> ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1534:9: note: in expansion of macro ‘Free’
> 1534 | Free(p->x);
> | ^~~~
> fastDNAml.c: In function ‘freeTree’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in
> function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1560:5: note: in expansion of macro ‘Free’
> 1560 | Free(tr->nodep[1]); /* Free the actual nodes */
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of
> ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1560:5: note: in expansion of macro ‘Free’
> 1560 | Free(tr->nodep[1]); /* Free the actual nodes */
> | ^~~~
> fastDNAml.c: In function ‘setupxarray’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in
> function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:2028:9: note: in expansion of macro ‘Free’
> 2028 | Free(x);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of
> ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:2028:9: note: in expansion of macro ‘Free’
> 2028 | Free(x);
> | ^~~~
> fastDNAml.c: In function ‘makenewz’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in
> function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:2604:5: note: in expansion of macro ‘Free’
> 2604 | Free(abi);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of
> ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:2604:5: note: in expansion of macro ‘Free’
> 2604 | Free(abi);
> | ^~~~
> fastDNAml.c: In function ‘readKeyValue’:
> fastDNAml.c:2886:15: error: implicit declaration of function ‘strlen’
> [-Werror=implicit-function-declaration]
> 2886 | string += strlen(key);
> | ^~~~~~
> fastDNAml.c:208:1: note: include ‘<string.h>’ or provide a declaration of
> ‘strlen’
> 207 | #include "fastDNAml.h" /* Requires version 1.2 */
> +++ |+#include <string.h>
> 208 |
> fastDNAml.c:2886:15: warning: incompatible implicit declaration of built-in
> function ‘strlen’ [-Wbuiltin-declaration-mismatch]
> 2886 | string += strlen(key);
> | ^~~~~~
> fastDNAml.c:2886:15: note: include ‘<string.h>’ or provide a declaration of
> ‘strlen’
> fastDNAml.c: In function ‘fopen_pid’:
> fastDNAml.c:3231:47: error: implicit declaration of function ‘getpid’
> [-Werror=implicit-function-declaration]
> 3231 | (void) sprintf(name_pid, "%s.%d", filenm, getpid());
> | ^~~~~~
> fastDNAml.c: In function ‘treeOut’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in
> function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:3683:5: note: in expansion of macro ‘Free’
> 3683 | Free(treestr);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of
> ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:3683:5: note: in expansion of macro ‘Free’
> 3683 | Free(treestr);
> | ^~~~
> fastDNAml.c: In function ‘cmpBestTrees’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in
> function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:4535:5: note: in expansion of macro ‘Free’
> 4535 | Free(log_f0);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of
> ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:4535:5: note: in expansion of macro ‘Free’
> 4535 | Free(log_f0);
> | ^~~~
> fastDNAml.c: In function ‘makeDenovoTree’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in
> function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:4765:5: note: in expansion of macro ‘Free’
> 4765 | Free(enterorder);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of
> ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:4765:5: note: in expansion of macro ‘Free’
> 4765 | Free(enterorder);
> | ^~~~
> fastDNAml.c: At top level:
> fastDNAml.c:4775:3: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 4775 | main ()
> | ^~~~
> cc1: some warnings being treated as errors
> make[1]: *** [Makefile:4: fastDNAml] Error 1
The full build log is available from:
http://qa-logs.debian.net/2024/03/13/fastdnaml_1.2.2-15_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 ---
--- Begin Message ---
Source: fastdnaml
Source-Version: 1.2.2-16
Done: Nilesh Patra <nil...@iki.fi>
We believe that the bug you reported is fixed in the latest version of
fastdnaml, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1066...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <nil...@iki.fi> (supplier of updated fastdnaml package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sun, 07 Apr 2024 14:47:48 +0530
Source: fastdnaml
Architecture: source
Version: 1.2.2-16
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nil...@iki.fi>
Closes: 1066709
Changes:
fastdnaml (1.2.2-16) unstable; urgency=medium
.
* Team Upload.
* Add patch to fix FTBFS with
implicit-function-declaration (Closes: #1066709)
* Bump Standards-Version to 4.6.2 (no changes needed)
Checksums-Sha1:
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214486f3b741b13fd191d3f1a124293ff3c8d604 8544 fastdnaml_1.2.2-16.debian.tar.xz
86b81024e984f1d67e142d38b2f515f7c912846b 5369
fastdnaml_1.2.2-16_amd64.buildinfo
Checksums-Sha256:
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Files:
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5247c6589a20c9387a7c05937c1fb5c7 8544 science optional
fastdnaml_1.2.2-16.debian.tar.xz
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fastdnaml_1.2.2-16_amd64.buildinfo
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