+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/fastDNAml-1.2.2/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/fastDNAml-1.2.2/work.log WARNING: [license.mk] Every package should define a LICENSE. ===> Building for fastDNAml-1.2.2 --- fastDNAml.o --- cc -O -c fastDNAml.c 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 '' +++ |+#include 1 | /* fastDNAml.h */ fastDNAml.c: In function 'freeTopol': fastDNAml.h:228:28: error: implicit declaration of function 'free' [-Wimplicit-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 '' or provide a declaration of 'free' 207 | #include "fastDNAml.h" /* Requires version 1.2 */ +++ |+#include 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 '' 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 '' 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 '' 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 '' 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 '' 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 '' 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' [-Wimplicit-function-declaration] 2886 | string += strlen(key); | ^~~~~~ fastDNAml.c:208:1: note: include '' or provide a declaration of 'strlen' 207 | #include "fastDNAml.h" /* Requires version 1.2 */ +++ |+#include 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 '' or provide a declaration of 'strlen' fastDNAml.c: In function 'fopen_pid': fastDNAml.c:3231:47: error: implicit declaration of function 'getpid' [-Wimplicit-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 '' 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 '' 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 '' 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: error: return type defaults to 'int' [-Wimplicit-int] 4775 | main () | ^~~~ *** [fastDNAml.o] Error code 1 bmake: stopped making "all" in /home/pbulk/build/biology/fastDNAml/work/fastDNAml_1.2.2/source bmake: 1 error bmake: stopped making "all" in /home/pbulk/build/biology/fastDNAml/work/fastDNAml_1.2.2/source *** Error code 2 Stop. bmake[1]: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/fastDNAml *** Error code 1 Stop. bmake: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/fastDNAml