------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- ===> NOTICE: The fastdnaml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> fastdnaml-1.2.2_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> NOTICE: The fastdnaml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> fastdnaml-1.2.2_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by fastdnaml-1.2.2_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> NOTICE: The fastdnaml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> fastdnaml-1.2.2_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by fastdnaml-1.2.2_2 for building => SHA256 Checksum OK for fastDNAml_1.2.2.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> NOTICE: The fastdnaml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> fastdnaml-1.2.2_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by fastdnaml-1.2.2_2 for building ===> Extracting for fastdnaml-1.2.2_2 => SHA256 Checksum OK for fastDNAml_1.2.2.tar.gz. Extracted Memory Use: 0.46M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for fastdnaml-1.2.2_2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> Configuring for fastdnaml-1.2.2_2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for fastdnaml-1.2.2_2 --- fastDNAml.o --- cc -pipe -O2 -fno-strict-aliasing -c fastDNAml.c In file included from fastDNAml.c:207: fastDNAml.h:222:10: warning: conflicting types for built-in function 'malloc' [-Wbuiltin-declaration-mismatch] char *malloc(); ^~~~~~ fastDNAml.c: In function 'freeTopol': fastDNAml.h:228:28: warning: implicit declaration of function 'free' [-Wimplicit-function-declaration] #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:342:5: note: in expansion of macro 'Free' Free(tpl->links); ^~~~ fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:342:5: note: in expansion of macro 'Free' Free(tpl->links); ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:342:5: note: in expansion of macro 'Free' Free(tpl->links); ^~~~ fastDNAml.c: In function 'freeTreeNode': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:1533:23: note: in expansion of macro 'Free' if (p->x->lv) Free(p->x->lv); ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:1533:23: note: in expansion of macro 'Free' if (p->x->lv) Free(p->x->lv); ^~~~ fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:1534:9: note: in expansion of macro 'Free' Free(p->x); ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:1534:9: note: in expansion of macro 'Free' Free(p->x); ^~~~ fastDNAml.c: In function 'freeTree': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:1560:5: note: in expansion of macro 'Free' Free(tr->nodep[1]); /* Free the actual nodes */ ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:1560:5: note: in expansion of macro 'Free' 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' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:2028:9: note: in expansion of macro 'Free' Free(x); ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:2028:9: note: in expansion of macro 'Free' Free(x); ^~~~ fastDNAml.c: In function 'makenewz': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:2604:5: note: in expansion of macro 'Free' Free(abi); ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:2604:5: note: in expansion of macro 'Free' Free(abi); ^~~~ fastDNAml.c: In function 'readKeyValue': fastDNAml.c:2886:15: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration] string += strlen(key); ^~~~~~ fastDNAml.c:2886:15: warning: incompatible implicit declaration of built-in function 'strlen' fastDNAml.c:2886:15: note: include '' or provide a declaration of 'strlen' fastDNAml.c:208:1: +#include fastDNAml.c:2886:15: string += strlen(key); ^~~~~~ fastDNAml.c: In function 'fopen_pid': fastDNAml.c:3231:47: warning: implicit declaration of function 'getpid'; did you mean 'getxtip'? [-Wimplicit-function-declaration] (void) sprintf(name_pid, "%s.%d", filenm, getpid()); ^~~~~~ getxtip In file included from fastDNAml.c:207: fastDNAml.c: In function 'treeOut': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:3683:5: note: in expansion of macro 'Free' Free(treestr); ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:3683:5: note: in expansion of macro 'Free' Free(treestr); ^~~~ fastDNAml.c: In function 'cmpBestTrees': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:4535:5: note: in expansion of macro 'Free' Free(log_f0); ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:4535:5: note: in expansion of macro 'Free' Free(log_f0); ^~~~ fastDNAml.c: In function 'makeDenovoTree': fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:4765:5: note: in expansion of macro 'Free' Free(enterorder); ^~~~ fastDNAml.h:228:28: note: include '' or provide a declaration of 'free' #define Free(x) (void) free((char *) (x)) /* BSD */ ^~~~ fastDNAml.c:4765:5: note: in expansion of macro 'Free' Free(enterorder); ^~~~ fastDNAml.c: At top level: fastDNAml.c:4775:3: warning: return type defaults to 'int' [-Wimplicit-int] main () ^~~~ --- fastDNAml --- cc -pipe -O2 -fno-strict-aliasing -o fastDNAml fastDNAml.o -lm SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for fastdnaml-1.2.2_2 ===> Generating temporary packing list install -s -m 555 /construction/biology/fastdnaml/fastDNAml_1.2.2/source/fastDNAml /construction/biology/fastdnaml/stage/usr/local/bin install -m 555 /construction/biology/fastdnaml/fastDNAml_1.2.2/scripts/* /construction/biology/fastdnaml/stage/usr/local/bin/fastdnaml install -m 0644 /construction/biology/fastdnaml/fastDNAml_1.2.2/docs/*.txt /construction/biology/fastdnaml/stage/usr/local/share/doc/fastdnaml ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for fastdnaml-1.2.2_2 file sizes/checksums [36]: 0% file sizes/checksums [36]: 100% packing files [36]: 0% packing files [36]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:00:04