=>> Building biology/fastdnaml build started at Fri Oct 3 20:23:51 EDT 2025 port directory: /usr/ports/biology/fastdnaml package name: fastdnaml-1.2.2_2 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 843 Aug 27 2024 /usr/ports/biology/fastdnaml/Makefile Ports top last git commit: a936fb9b16ba Ports top unclean checkout: no Port dir last git commit: fb16dfecae4a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500064 Jail OSVERSION: 1500064 Job Id: 15 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500064 UNAME_v=FreeBSD 15.0-ALPHA3 1500064 UNAME_r=15.0-ALPHA3 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/15/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_c_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for fastdnaml-1.2.2_2: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastdnaml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastdnaml/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastdnaml/work/.cache HOME=/wrkdirs/usr/ports/biology/fastdnaml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fastdnaml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastdnaml/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastdnaml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastdnaml/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastdnaml/work/.cache HOME=/wrkdirs/usr/ports/biology/fastdnaml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fastdnaml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastdnaml/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTDOCS="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/fastdnaml" EXAMPLESDIR="share/examples/fastdnaml" DATADIR="share/fastdnaml" WWWDIR="www/fastdnaml" ETCDIR="etc/fastdnaml" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fastdnaml DOCSDIR=/usr/local/share/doc/fastdnaml EXAMPLESDIR=/usr/local/share/examples/fastdnaml WWWDIR=/usr/local/www/fastdnaml ETCDIR=/usr/local/etc/fastdnaml --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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://docs.freebsd.org/en/articles/contributing/#ports-contributing =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastdnaml-1.2.2_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.3.1.pkg [pkg.DaveG.ca] Installing pkg-2.3.1... [pkg.DaveG.ca] Extracting pkg-2.3.1: .......... done ===> fastdnaml-1.2.2_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fastdnaml-1.2.2_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by fastdnaml-1.2.2_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by fastdnaml-1.2.2_2 for building => SHA256 Checksum OK for fastDNAml_1.2.2.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> 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. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for fastdnaml-1.2.2_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastdnaml-1.2.2_2 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> fastdnaml-1.2.2_2 depends on file: /usr/local/bin/ccache - found ===> Returning to build of fastdnaml-1.2.2_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for fastdnaml-1.2.2_2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for fastdnaml-1.2.2_2 --- fastDNAml.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c fastDNAml.c In file included from fastDNAml.c:207: ./fastDNAml.h:222:10: warning: incompatible redeclaration of library function 'malloc' [-Wincompatible-library-redeclaration] 222 | char *malloc(); | ^ ./fastDNAml.h:222:10: note: 'malloc' is a builtin with type 'void *(unsigned long)' fastDNAml.c:313:28: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 313 | if (! (tpl = (topol *) Malloc(sizeof(topol))) || | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:314:35: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 314 | ! (tpl->links = (connptr) Malloc((2*maxtips-3) * sizeof(connect))) || | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:316:30: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 316 | = (double *) Malloc(nsites * sizeof(double))))) { | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:342:5: warning: call to undeclared library function 'free' with type 'void (void *)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 342 | Free(tpl->links); | ^ ./fastDNAml.h:228:28: note: expanded from macro 'Free' 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^ fastDNAml.c:342:5: note: include the header or explicitly provide a declaration for 'free' ./fastDNAml.h:228:28: note: expanded from macro 'Free' 228 | #define Free(x) (void) free((char *) (x)) /* BSD */ | ^ fastDNAml.c:442:19: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 442 | if (tpl_log_f = tpl->log_f) { | ~~~~~~~~~~^~~~~~~~~~~~ fastDNAml.c:442:19: note: place parentheses around the assignment to silence this warning 442 | if (tpl_log_f = tpl->log_f) { | ^ | ( ) fastDNAml.c:442:19: note: use '==' to turn this assignment into an equality comparison 442 | if (tpl_log_f = tpl->log_f) { | ^ | == fastDNAml.c:522:13: warning: passing arguments to 'hookup' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 522 | hookup(r->p, r->q, r->z); | ^ fastDNAml.c:533:19: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 533 | if (tpl_log_f = tpl->log_f) { | ~~~~~~~~~~^~~~~~~~~~~~ fastDNAml.c:533:19: note: place parentheses around the assignment to silence this warning 533 | if (tpl_log_f = tpl->log_f) { | ^ | ( ) fastDNAml.c:533:19: note: use '==' to turn this assignment into an equality comparison 533 | if (tpl_log_f = tpl->log_f) { | ^ | == fastDNAml.c:542:20: warning: passing arguments to 'initrav' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 542 | return (initrav(tr, tr->start) && initrav(tr, tr->start->back)); | ^ fastDNAml.c:542:46: warning: passing arguments to 'initrav' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 542 | return (initrav(tr, tr->start) && initrav(tr, tr->start->back)); | ^ fastDNAml.c:560:32: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 560 | bt->byScore = (topol **) Malloc((newkeep+1) * sizeof(topol *)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:561:32: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 561 | bt->byTopol = (topol **) Malloc((newkeep+1) * sizeof(topol *)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:605:3: warning: non-void function does not return a value [-Wreturn-type] 605 | } /* resetBestTree */ | ^ fastDNAml.c:637:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 637 | if (cmp = cmpSubtopol(p10, p1d, p20, p2d)) return cmp; /* Subtrees */ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastDNAml.c:637:15: note: place parentheses around the assignment to silence this warning 637 | if (cmp = cmpSubtopol(p10, p1d, p20, p2d)) return cmp; /* Subtrees */ | ^ | ( ) fastDNAml.c:637:15: note: use '==' to turn this assignment into an equality comparison 637 | if (cmp = cmpSubtopol(p10, p1d, p20, p2d)) return cmp; /* Subtrees */ | ^ | == fastDNAml.c:689:24: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 689 | cmp = (* cmpFunc)(item, list[mid-1]); | ^ fastDNAml.c:698:25: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 698 | cmp = (* cmpFunc)(item, list[lo-1]); | ^ fastDNAml.c:769:19: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 769 | if (tpl_log_f = tpl->log_f) { | ~~~~~~~~~~^~~~~~~~~~~~ fastDNAml.c:769:19: note: place parentheses around the assignment to silence this warning 769 | if (tpl_log_f = tpl->log_f) { | ^ | ( ) fastDNAml.c:769:19: note: use '==' to turn this assignment into an equality comparison 769 | if (tpl_log_f = tpl->log_f) { | ^ | == fastDNAml.c:1293:33: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1293 | rdta->wgt = (int *) Malloc((rdta->sites + 1) * sizeof(int)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1294:33: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1294 | rdta->wgt2 = (int *) Malloc((rdta->sites + 1) * sizeof(int)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1295:33: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1295 | rdta->sitecat = (int *) Malloc((rdta->sites + 1) * sizeof(int)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1296:33: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1296 | cdta->alias = (int *) Malloc((rdta->sites + 1) * sizeof(int)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1297:33: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1297 | cdta->aliaswgt = (int *) Malloc((rdta->sites + 1) * sizeof(int)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1298:33: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1298 | cdta->patcat = (int *) Malloc((rdta->sites + 1) * sizeof(int)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1299:33: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1299 | cdta->patrat = (double *) Malloc((rdta->sites + 1) * sizeof(double)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1300:33: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1300 | cdta->wr = (double *) Malloc((rdta->sites + 1) * sizeof(double)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1301:33: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1301 | cdta->wr2 = (double *) Malloc((rdta->sites + 1) * sizeof(double)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1443:33: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1443 | if (! (rdta->y = (yType **) Malloc((rdta->numsp + 1) * sizeof(yType *)))) { | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1449:27: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1449 | if (! (y0 = (yType *) Malloc((rdta->numsp + 1) * size * sizeof(yType)))) { | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1471:26: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1471 | if (!(p0 = (nodeptr) Malloc((tips + 3*inter) * sizeof(node)))) { | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1476:35: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1476 | if (!(tr->nodep = (nodeptr *) Malloc((2*tr->mxtips) * sizeof(nodeptr)))) { | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1519:28: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1519 | tr->log_f = (double *) Malloc(nsites * sizeof(double)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1551:13: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 1551 | if (p = tr->nodep[i]) { | ~~^~~~~~~~~~~~~~ fastDNAml.c:1551:13: note: place parentheses around the assignment to silence this warning 1551 | if (p = tr->nodep[i]) { | ^ | ( ) fastDNAml.c:1551:13: note: use '==' to turn this assignment into an equality comparison 1551 | if (p = tr->nodep[i]) { | ^ | == fastDNAml.c:1552:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 1552 | if (q = p->next) { | ~~^~~~~~~~~ fastDNAml.c:1552:15: note: place parentheses around the assignment to silence this warning 1552 | if (q = p->next) { | ^ | ( ) fastDNAml.c:1552:15: note: use '==' to turn this assignment into an equality comparison 1552 | if (q = p->next) { | ^ | == fastDNAml.c:1717:21: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 1717 | while (ch = *nameptr++) {putchar(ch); k--;} | ~~~^~~~~~~~~~~~ fastDNAml.c:1717:21: note: place parentheses around the assignment to silence this warning 1717 | while (ch = *nameptr++) {putchar(ch); k--;} | ^ | ( ) fastDNAml.c:1717:21: note: use '==' to turn this assignment into an equality comparison 1717 | while (ch = *nameptr++) {putchar(ch); k--;} | ^ | == fastDNAml.c:1779:43: warning: passing arguments to 'randum' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1779 | cdta->aliaswgt[(int) (nonzero*randum(& adef->boot)) + 1]++; | ^ fastDNAml.c:2019:20: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2019 | x = (xarray *) Malloc(sizeof(xarray)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:2021:31: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2021 | data = (likelivector *) Malloc(npat * sizeof(likelivector)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:2500:31: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2500 | if ((abi = (double *) Malloc(scratch_size)) && | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:2501:31: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2501 | (bci = (double *) Malloc(scratch_size)) && | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:2502:31: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2502 | (sumci = (double *) Malloc(scratch_size))) ; | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:501:11: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 501 | void hookup(); | ^ fastDNAml.c:2693:6: note: conflicting prototype is here 2693 | void hookup (nodeptr p, nodeptr q, double z) | ^ fastDNAml.c:502:14: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 502 | boolean initrav(); | ^ fastDNAml.c:2811:9: note: conflicting prototype is here 2811 | boolean initrav (tree *tr, nodeptr p) | ^ fastDNAml.c:2856:8: warning: incompatible redeclaration of library function 'strchr' [-Wincompatible-library-redeclaration] 2856 | char * strchr (char *str, int chr) | ^ fastDNAml.c:2856:8: note: 'strchr' is a builtin with type 'char *(const char *, int)' fastDNAml.c:2860:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 2860 | while (c = *str) {if (c == chr) return str; str++;} | ~~^~~~~~ fastDNAml.c:2860:14: note: place parentheses around the assignment to silence this warning 2860 | while (c = *str) {if (c == chr) return str; str++;} | ^ | ( ) fastDNAml.c:2860:14: note: use '==' to turn this assignment into an equality comparison 2860 | while (c = *str) {if (c == chr) return str; str++;} | ^ | == fastDNAml.c:2865:8: warning: incompatible redeclaration of library function 'strstr' [-Wincompatible-library-redeclaration] 2865 | char * strstr (char *str1, char *str2) | ^ fastDNAml.c:2865:8: note: 'strstr' is a builtin with type 'char *(const char *, const char *)' fastDNAml.c:2886:15: warning: call to undeclared library function 'strlen' with type 'unsigned long (const char *)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 2886 | string += strlen(key); | ^ fastDNAml.c:2886:15: note: include the header or explicitly provide a declaration for 'strlen' fastDNAml.c:3231:47: warning: call to undeclared function 'getpid'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 3231 | (void) sprintf(name_pid, "%s.%d", filenm, getpid()); | ^ fastDNAml.c:3255:14: warning: passing arguments to 'treeOut' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3255 | treeOut(checkpointf, tr, treeNewick); | ^ fastDNAml.c:3536:17: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 3536 | while (ch = *nameptr++) {putchar(ch); k--;} | ~~~^~~~~~~~~~~~ fastDNAml.c:3536:17: note: place parentheses around the assignment to silence this warning 3536 | while (ch = *nameptr++) {putchar(ch); k--;} | ^ | ( ) fastDNAml.c:3536:17: note: use '==' to turn this assignment into an equality comparison 3536 | while (ch = *nameptr++) {putchar(ch); k--;} | ^ | == fastDNAml.c:3632:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 3632 | while (c = *nameptr++) { | ~~^~~~~~~~~~~~ fastDNAml.c:3632:16: note: place parentheses around the assignment to silence this warning 3632 | while (c = *nameptr++) { | ^ | ( ) fastDNAml.c:3632:16: note: use '==' to turn this assignment into an equality comparison 3632 | while (c = *nameptr++) { | ^ | == fastDNAml.c:3251:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 3251 | void treeOut(); | ^ fastDNAml.c:3667:6: note: conflicting prototype is here 3667 | void treeOut (FILE *treefile, tree *tr, int form) | ^ fastDNAml.c:3673:24: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3673 | treestr = (char *) Malloc((tr->ntips * (nmlngth+32)) + 256); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:3681:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] 3681 | while (c = *cptr++) putc(c, treefile); | ~~^~~~~~~~~ fastDNAml.c:3681:14: note: place parentheses around the assignment to silence this warning 3681 | while (c = *cptr++) putc(c, treefile); | ^ | ( ) fastDNAml.c:3681:14: note: use '==' to turn this assignment into an equality comparison 3681 | while (c = *cptr++) putc(c, treefile); | ^ | == fastDNAml.c:4493:32: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4493 | if (! (log_f0 = (double *) Malloc(sizeof(double) * tr->cdta->endsite))) { | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:1772:13: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 1772 | double randum(); | ^ fastDNAml.c:4611:8: note: conflicting prototype is here 4611 | double randum (long *seed) | ^ fastDNAml.c:4645:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a previous declaration [-Wdeprecated-non-prototype] 4645 | double randum(); | ^ fastDNAml.c:4611:8: note: conflicting prototype is here 4611 | double randum (long *seed) | ^ fastDNAml.c:4648:26: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4648 | enterorder = (int *) Malloc(sizeof(int) * (tr->mxtips + 1)); | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:4775:3: warning: type specifier missing, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int] 4775 | main () | ^ | int fastDNAml.c:4863:31: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4863 | if (! (adef = (analdef *) Malloc(sizeof(analdef)))) { | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:4868:31: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4868 | if (! (rdta = (rawdata *) Malloc(sizeof(rawdata)))) { | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:4873:36: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4873 | if (! (cdta = (cruncheddata *) Malloc(sizeof(cruncheddata)))) { | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:4878:28: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4878 | if ((tr = (tree *) Malloc(sizeof(tree))) && | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ fastDNAml.c:4879:28: warning: passing arguments to 'malloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4879 | (bt = (bestlist *) Malloc(sizeof(bestlist)))) ; | ^ ./fastDNAml.h:225:27: note: expanded from macro 'Malloc' 225 | #define Malloc(x) malloc((unsigned) (x)) /* BSD */ | ^ 63 warnings generated. --- fastDNAml --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o fastDNAml fastDNAml.o -lm =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for fastdnaml-1.2.2_2 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/fastdnaml/work/fastDNAml_1.2.2/source/fastDNAml /wrkdirs/usr/ports/biology/fastdnaml/work/stage/usr/local/bin install -m 555 /wrkdirs/usr/ports/biology/fastdnaml/work/fastDNAml_1.2.2/scripts/* /wrkdirs/usr/ports/biology/fastdnaml/work/stage/usr/local/bin/fastdnaml install -m 0644 /wrkdirs/usr/ports/biology/fastdnaml/work/fastDNAml_1.2.2/docs/*.txt /wrkdirs/usr/ports/biology/fastdnaml/work/stage/usr/local/share/doc/fastdnaml ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-10-04T00:23:51+0000' 'PKG_NOTE_ports_top_git_hash=a936fb9b16ba' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=fb16dfecae4a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for fastdnaml-1.2.2_2 ===> Building fastdnaml-1.2.2_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for fastdnaml-1.2.2_2 build of biology/fastdnaml | fastdnaml-1.2.2_2 ended at Fri Oct 3 20:24:19 EDT 2025 build time: 00:00:31