=> Building biology/fastdnaml Started : Thursday, 7 MAR 2019 at 18:14:11 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> 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 -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/fastdnaml XDG_CONFIG_HOME=/construction/biology/fastdnaml HOME=/construction/biology/fastdnaml TMPDIR="/tmp" PATH=/construction/biology/fastdnaml/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/fastdnaml XDG_CONFIG_HOME=/construction/biology/fastdnaml HOME=/construction/biology/fastdnaml TMPDIR="/tmp" PATH=/construction/biology/fastdnaml/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " DESTDIR=/construction/biology/fastdnaml/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/fastdnaml" EXAMPLESDIR="share/examples/fastdnaml" DATADIR="share/fastdnaml" WWWDIR="www/fastdnaml" ETCDIR="etc/fastdnaml" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- 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 ===> License GPLv2+ accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> fastdnaml-1.2.2_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> fastdnaml-1.2.2_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fastdnaml-1.2.2_2 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- 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 ===> License GPLv2+ accepted by the user ===> Fetching all distfiles required by fastdnaml-1.2.2_2 for building -------------------------------------------------------------------------------- -- 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 ===> License GPLv2+ accepted by the user ===> Fetching all distfiles required by fastdnaml-1.2.2_2 for building => SHA256 Checksum OK for fastDNAml_1.2.2.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- 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 ===> License GPLv2+ accepted by the user ===> 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. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for fastdnaml-1.2.2_2 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for fastdnaml-1.2.2_2 -------------------------------------------------------------------------------- -- 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 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- 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) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for fastdnaml-1.2.2_2 file sizes/checksums [39]: . done packing files [39]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 7 MAR 2019 at 18:14:23 UTC Duration: 00:00:11