Source: fastdnaml Version: 1.2.2-15 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): > 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;[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.
