=>> Building biology/babel build started at Thu Apr 4 09:06:42 BST 2024 port directory: /usr/ports/biology/babel package name: babel-1.6_4 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 964 Nov 1 06:56 /usr/ports/biology/babel/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: bf70e962a3 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 11 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/11/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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 babel-1.6_4: 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/babel/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/babel/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/babel/work/.cache HOME=/wrkdirs/usr/ports/biology/babel/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/babel/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/babel/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/babel/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/babel/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/babel/work/.cache HOME=/wrkdirs/usr/ports/biology/babel/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/babel/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/babel/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=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/babel" EXAMPLESDIR="share/examples/babel" DATADIR="share/babel" WWWDIR="www/babel" ETCDIR="etc/babel" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/babel DOCSDIR=/usr/local/share/doc/babel EXAMPLESDIR=/usr/local/share/examples/babel WWWDIR=/usr/local/www/babel ETCDIR=/usr/local/etc/babel --End SUB_LIST-- ---Begin make.conf--- 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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 --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The babel 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 ===> babel-1.6_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> babel-1.6_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of babel-1.6_4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The babel 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 babel-1.6_4 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The babel 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 babel-1.6_4 for building => SHA256 Checksum OK for babel-1.6.tar.Z. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The babel 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 babel-1.6_4 for building ===> Extracting for babel-1.6_4 => SHA256 Checksum OK for babel-1.6.tar.Z. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for babel-1.6_4 ===> Applying FreeBSD patches for babel-1.6_4 from /usr/ports/biology/babel/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for babel-1.6_4 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for babel-1.6_4 cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c addh.c -o addh.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c addh2.c -o addh2.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c aromatic.c -o aromatic.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c assbnd.c -o assbnd.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c asstypes.c -o asstypes.o asstypes.c:639:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ asstypes.c:659:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ asstypes.c:681:2: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 3 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c block.c -o block.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c bndord.c -o bndord.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c bo.c -o bo.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c buildct.c -o buildct.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c combine.c -o combine.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c convert.c -o convert.o convert.c:263:12: warning: comparison of array 'target' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (target != NULL) ^~~~~~ ~~~~ convert.c:401:43: warning: data argument not used by format string [-Wformat-extra-args] fprintf(stderr,"Structure %5d ",in_count,Multi); ~~~~~~~~~~~~~~~~ ^ ./bblmacs.h:153:29: note: expanded from macro 'Multi' #define Multi mol->control->multi ^ convert.c:595:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 3 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c delatms.c -o delatms.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c delh2o.c -o delh2o.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c filesrch.c -o filesrch.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c fileutil.c -o fileutil.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c gastchg.c -o gastchg.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c htoend.c -o htoend.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c int2cart.c -o int2cart.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c intcart.c -o intcart.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c menus.c -o menus.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c miniums.c -o miniums.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c molwt.c -o molwt.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c nodummy.c -o nodummy.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c orient.c -o orient.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c precip.c -o precip.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c printbad.c -o printbad.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c progress.c -o progress.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdalch.c -o rdalch.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdampout.c -o rdampout.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdbalst.c -o rdbalst.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdbgf.c -o rdbgf.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdboogie.c -o rdboogie.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdc3d.c -o rdc3d.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdcacao.c -o rdcacao.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdcadpac.c -o rdcadpac.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdcharmm.c -o rdcharmm.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdcsd.c -o rdcsd.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rddock.c -o rddock.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rddpdb.c -o rddpdb.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdelmnts.c -o rdelmnts.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdfdat.c -o rdfdat.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdfeat.c -o rdfeat.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdfract.c -o rdfract.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdg96.c -o rdg96.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdgamout.c -o rdgamout.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdgauout.c -o rdgauout.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdgzmat.c -o rdgzmat.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdhin.c -o rdhin.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdinsite.c -o rdinsite.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdint.c -o rdint.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdirc.c -o rdirc.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdisis.c -o rdisis.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdm3d.c -o rdm3d.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdmacmod.c -o rdmacmod.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdmacmol.c -o rdmacmol.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdmdl.c -o rdmdl.o rdmdl.c:65:19: warning: format specifies type 'long *' but the argument has type 'int *' [-Wformat] &dummyi,&dummyi,&dummyi,&dummyi,&dummyi,&dummyi) == 9) ^~~~~~~ rdmdl.c:65:27: warning: format specifies type 'long *' but the argument has type 'int *' [-Wformat] &dummyi,&dummyi,&dummyi,&dummyi,&dummyi,&dummyi) == 9) ^~~~~~~ rdmdl.c:65:35: warning: format specifies type 'long *' but the argument has type 'int *' [-Wformat] &dummyi,&dummyi,&dummyi,&dummyi,&dummyi,&dummyi) == 9) ^~~~~~~ rdmdl.c:65:43: warning: format specifies type 'long *' but the argument has type 'int *' [-Wformat] &dummyi,&dummyi,&dummyi,&dummyi,&dummyi,&dummyi) == 9) ^~~~~~~ rdmdl.c:65:51: warning: format specifies type 'long *' but the argument has type 'int *' [-Wformat] &dummyi,&dummyi,&dummyi,&dummyi,&dummyi,&dummyi) == 9) ^~~~~~~ rdmdl.c:65:59: warning: data argument not used by format string [-Wformat-extra-args] &dummyi,&dummyi,&dummyi,&dummyi,&dummyi,&dummyi) == 9) ^ 6 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdmicro.c -o rdmicro.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdmm2.c -o rdmm2.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdmm2in.c -o rdmm2in.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdmm3.c -o rdmm3.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdmolen.c -o rdmolen.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdmopac.c -o rdmopac.o rdmopac.c:128:32: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat] sscanf(mop_line,"%*s%*s%f",&Charge(i)); ~~ ^~~~~~~~~~ %lf 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdmopcrt.c -o rdmopcrt.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdpcmod.c -o rdpcmod.o rdpcmod.c:75:20: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare] while ((start != '\0') && (!done)) ^~~~ (void *)0 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdpdb.c -o rdpdb.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdprep.c -o rdprep.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdpsgout.c -o rdpsgout.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdpsgvin.c -o rdpsgvin.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdquanta.c -o rdquanta.o rdquanta.c:312:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdschak.c -o rdschak.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdshelx.c -o rdshelx.o rdshelx.c:43:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdsmiles.c -o rdsmiles.o rdsmiles.c:14:7: warning: address of array 'smiles_string' will always evaluate to 'true' [-Wpointer-bool-conversion] if (smiles_string) ~~ ^~~~~~~~~~~~~ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdspart.c -o rdspart.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdspmm.c -o rdspmm.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdspsemi.c -o rdspsemi.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdsybmol.c -o rdsybmol.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdsybyl.c -o rdsybyl.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdtypes.c -o rdtypes.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdunichm.c -o rdunichm.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdwiz.c -o rdwiz.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdxed.c -o rdxed.o rdxed.c:62:5: warning: format specifies type 'double *' but the argument has type 'float *' [-Wformat] &chge); ^~~~~ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rdxyz.c -o rdxyz.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c renum.c -o renum.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c report.c -o report.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c rings.c -o rings.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c ringutil.c -o ringutil.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c sets.c -o sets.o sets.c:211:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] LowBit(s,bit); ^~~~~~~~~~~~~ ./bbltyp.h:342:13: note: expanded from macro 'LowBit' if (m = (set & 0x0000ffff)) {set = m; bit -= 16;}\ ~~^~~~~~~~~~~~~~~~~~~~ sets.c:211:10: note: place parentheses around the assignment to silence this warning ./bbltyp.h:342:13: note: expanded from macro 'LowBit' if (m = (set & 0x0000ffff)) {set = m; bit -= 16;}\ ^ sets.c:211:10: note: use '==' to turn this assignment into an equality comparison ./bbltyp.h:342:13: note: expanded from macro 'LowBit' if (m = (set & 0x0000ffff)) {set = m; bit -= 16;}\ ^ sets.c:211:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] LowBit(s,bit); ^~~~~~~~~~~~~ ./bbltyp.h:343:13: note: expanded from macro 'LowBit' if (m = (set & 0x00ff00ff)) {set = m; bit -= 8;}\ ~~^~~~~~~~~~~~~~~~~~~~ sets.c:211:10: note: place parentheses around the assignment to silence this warning ./bbltyp.h:343:13: note: expanded from macro 'LowBit' if (m = (set & 0x00ff00ff)) {set = m; bit -= 8;}\ ^ sets.c:211:10: note: use '==' to turn this assignment into an equality comparison ./bbltyp.h:343:13: note: expanded from macro 'LowBit' if (m = (set & 0x00ff00ff)) {set = m; bit -= 8;}\ ^ sets.c:211:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] LowBit(s,bit); ^~~~~~~~~~~~~ ./bbltyp.h:344:13: note: expanded from macro 'LowBit' if (m = (set & 0x0f0f0f0f)) {set = m; bit -= 4;}\ ~~^~~~~~~~~~~~~~~~~~~~ sets.c:211:10: note: place parentheses around the assignment to silence this warning ./bbltyp.h:344:13: note: expanded from macro 'LowBit' if (m = (set & 0x0f0f0f0f)) {set = m; bit -= 4;}\ ^ sets.c:211:10: note: use '==' to turn this assignment into an equality comparison ./bbltyp.h:344:13: note: expanded from macro 'LowBit' if (m = (set & 0x0f0f0f0f)) {set = m; bit -= 4;}\ ^ sets.c:211:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] LowBit(s,bit); ^~~~~~~~~~~~~ ./bbltyp.h:345:13: note: expanded from macro 'LowBit' if (m = (set & 0x33333333)) {set = m; bit -= 2;}\ ~~^~~~~~~~~~~~~~~~~~~~ sets.c:211:10: note: place parentheses around the assignment to silence this warning ./bbltyp.h:345:13: note: expanded from macro 'LowBit' if (m = (set & 0x33333333)) {set = m; bit -= 2;}\ ^ sets.c:211:10: note: use '==' to turn this assignment into an equality comparison ./bbltyp.h:345:13: note: expanded from macro 'LowBit' if (m = (set & 0x33333333)) {set = m; bit -= 2;}\ ^ sets.c:211:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] LowBit(s,bit); ^~~~~~~~~~~~~ ./bbltyp.h:346:13: note: expanded from macro 'LowBit' if (m = (set & 0x55555555)) {set = m; bit -= 1;}}}\ ~~^~~~~~~~~~~~~~~~~~~~ sets.c:211:10: note: place parentheses around the assignment to silence this warning ./bbltyp.h:346:13: note: expanded from macro 'LowBit' if (m = (set & 0x55555555)) {set = m; bit -= 1;}}}\ ^ sets.c:211:10: note: use '==' to turn this assignment into an equality comparison ./bbltyp.h:346:13: note: expanded from macro 'LowBit' if (m = (set & 0x55555555)) {set = m; bit -= 1;}}}\ ^ sets.c:223:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] LowBit(s, bit); ^~~~~~~~~~~~~~ ./bbltyp.h:342:13: note: expanded from macro 'LowBit' if (m = (set & 0x0000ffff)) {set = m; bit -= 16;}\ ~~^~~~~~~~~~~~~~~~~~~~ sets.c:223:10: note: place parentheses around the assignment to silence this warning ./bbltyp.h:342:13: note: expanded from macro 'LowBit' if (m = (set & 0x0000ffff)) {set = m; bit -= 16;}\ ^ sets.c:223:10: note: use '==' to turn this assignment into an equality comparison ./bbltyp.h:342:13: note: expanded from macro 'LowBit' if (m = (set & 0x0000ffff)) {set = m; bit -= 16;}\ ^ sets.c:223:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] LowBit(s, bit); ^~~~~~~~~~~~~~ ./bbltyp.h:343:13: note: expanded from macro 'LowBit' if (m = (set & 0x00ff00ff)) {set = m; bit -= 8;}\ ~~^~~~~~~~~~~~~~~~~~~~ sets.c:223:10: note: place parentheses around the assignment to silence this warning ./bbltyp.h:343:13: note: expanded from macro 'LowBit' if (m = (set & 0x00ff00ff)) {set = m; bit -= 8;}\ ^ sets.c:223:10: note: use '==' to turn this assignment into an equality comparison ./bbltyp.h:343:13: note: expanded from macro 'LowBit' if (m = (set & 0x00ff00ff)) {set = m; bit -= 8;}\ ^ sets.c:223:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] LowBit(s, bit); ^~~~~~~~~~~~~~ ./bbltyp.h:344:13: note: expanded from macro 'LowBit' if (m = (set & 0x0f0f0f0f)) {set = m; bit -= 4;}\ ~~^~~~~~~~~~~~~~~~~~~~ sets.c:223:10: note: place parentheses around the assignment to silence this warning ./bbltyp.h:344:13: note: expanded from macro 'LowBit' if (m = (set & 0x0f0f0f0f)) {set = m; bit -= 4;}\ ^ sets.c:223:10: note: use '==' to turn this assignment into an equality comparison ./bbltyp.h:344:13: note: expanded from macro 'LowBit' if (m = (set & 0x0f0f0f0f)) {set = m; bit -= 4;}\ ^ sets.c:223:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] LowBit(s, bit); ^~~~~~~~~~~~~~ ./bbltyp.h:345:13: note: expanded from macro 'LowBit' if (m = (set & 0x33333333)) {set = m; bit -= 2;}\ ~~^~~~~~~~~~~~~~~~~~~~ sets.c:223:10: note: place parentheses around the assignment to silence this warning ./bbltyp.h:345:13: note: expanded from macro 'LowBit' if (m = (set & 0x33333333)) {set = m; bit -= 2;}\ ^ sets.c:223:10: note: use '==' to turn this assignment into an equality comparison ./bbltyp.h:345:13: note: expanded from macro 'LowBit' if (m = (set & 0x33333333)) {set = m; bit -= 2;}\ ^ sets.c:223:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] LowBit(s, bit); ^~~~~~~~~~~~~~ ./bbltyp.h:346:13: note: expanded from macro 'LowBit' if (m = (set & 0x55555555)) {set = m; bit -= 1;}}}\ ~~^~~~~~~~~~~~~~~~~~~~ sets.c:223:10: note: place parentheses around the assignment to silence this warning ./bbltyp.h:346:13: note: expanded from macro 'LowBit' if (m = (set & 0x55555555)) {set = m; bit -= 1;}}}\ ^ sets.c:223:10: note: use '==' to turn this assignment into an equality comparison ./bbltyp.h:346:13: note: expanded from macro 'LowBit' if (m = (set & 0x55555555)) {set = m; bit -= 1;}}}\ ^ 10 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c smilesto.c -o smilesto.o smilesto.c:82:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] else if(bord = strchr(bondchr, smiles[i])) state = (enum state_typ) next[state][Tok_Bond]; ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ smilesto.c:82:20: note: place parentheses around the assignment to silence this warning else if(bord = strchr(bondchr, smiles[i])) state = (enum state_typ) next[state][Tok_Bond]; ^ ( ) smilesto.c:82:20: note: use '==' to turn this assignment into an equality comparison else if(bord = strchr(bondchr, smiles[i])) state = (enum state_typ) next[state][Tok_Bond]; ^ == 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c spline.c -o spline.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c strngutl.c -o strngutl.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c tokenst.c -o tokenst.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c tosmiles.c -o tosmiles.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c tree.c -o tree.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c typbybo.c -o typbybo.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c umslist.c -o umslist.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c utils.c -o utils.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c vectors.c -o vectors.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wralch.c -o wralch.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrbalst.c -o wrbalst.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrbgf.c -o wrbgf.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrbmin.c -o wrbmin.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrbox.c -o wrbox.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrc3d.c -o wrc3d.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrcacao.c -o wrcacao.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrcache.c -o wrcache.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrcacint.c -o wrcacint.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrchdrw.c -o wrchdrw.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrcontmp.c -o wrcontmp.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrcsr.c -o wrcsr.o wrcsr.c:16:1: warning: non-void function does not return a value [-Wreturn-type] } ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrcssr.c -o wrcssr.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrdock.c -o wrdock.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrdpdb.c -o wrdpdb.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrfeat.c -o wrfeat.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrfh.c -o wrfh.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrg96.c -o wrg96.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrgamess.c -o wrgamess.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrgau.c -o wrgau.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrgaucrt.c -o wrgaucrt.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrhin.c -o wrhin.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wricon.c -o wricon.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrint.c -o wrint.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrisis.c -o wrisis.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrm3d.c -o wrm3d.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrmaccs.c -o wrmaccs.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrmacmod.c -o wrmacmod.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrmcmol.c -o wrmcmol.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrmdl.c -o wrmdl.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrmicro.c -o wrmicro.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrmimic.c -o wrmimic.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrmiv.c -o wrmiv.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrmm2.c -o wrmm2.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrmm3.c -o wrmm3.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrmopac.c -o wrmopac.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrpcmod.c -o wrpcmod.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrpdb.c -o wrpdb.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrpsgv.c -o wrpsgv.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrpsgvz.c -o wrpsgvz.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrsmiles.c -o wrsmiles.o wrsmiles.c:45:49: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat] printf("OUT OF MEMORY AT %s %s \n",__FILE__,__LINE__); ~~ ^~~~~~~~ %d :100:1: note: expanded from here 45 ^~ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrspart.c -o wrspart.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrsybmol.c -o wrsybmol.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrsybyl.c -o wrsybyl.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrtinker.c -o wrtinker.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrtorlst.c -o wrtorlst.o wrtorlst.c:36:59: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat] printf("Memory Allocation Error at %s %s \n",__FILE__,__LINE__); ~~ ^~~~~~~~ %d :100:1: note: expanded from here 36 ^~ wrtorlst.c:74:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrunichm.c -o wrunichm.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrwiz.c -o wrwiz.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrxed.c -o wrxed.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c wrxyz.c -o wrxyz.o cc addh.o addh2.o aromatic.o assbnd.o asstypes.o block.o bndord.o bo.o buildct.o combine.o convert.o delatms.o delh2o.o filesrch.o fileutil.o gastchg.o htoend.o int2cart.o intcart.o menus.o miniums.o molwt.o nodummy.o orient.o precip.o printbad.o progress.o rdalch.o rdampout.o rdbalst.o rdbgf.o rdboogie.o rdc3d.o rdcacao.o rdcadpac.o rdcharmm.o rdcsd.o rddock.o rddpdb.o rdelmnts.o rdfdat.o rdfeat.o rdfract.o rdg96.o rdgamout.o rdgauout.o rdgzmat.o rdhin.o rdinsite.o rdint.o rdirc.o rdisis.o rdm3d.o rdmacmod.o rdmacmol.o rdmdl.o rdmicro.o rdmm2.o rdmm2in.o rdmm3.o rdmolen.o rdmopac.o rdmopcrt.o rdpcmod.o rdpdb.o rdprep.o rdpsgout.o rdpsgvin.o rdquanta.o rdschak.o rdshelx.o rdsmiles.o rdspart.o rdspmm.o rdspsemi.o rdsybmol.o rdsybyl.o rdtypes.o rdunichm.o rdwiz.o rdxed.o rdxyz.o renum.o report.o rings.o ringutil.o sets.o smilesto.o spline.o strngutl.o tokenst.o tosmiles.o tree.o typbybo.o umslist.o utils.o vectors.o wralch.o wrbalst.o wrbgf.o wrbmin.o wrbox.o wrc3d.o wrcacao.o wrcache.o wrcacint.o wrchdrw.o wrcontmp.o wrcsr.o wrcssr.o wrdock.o wrdpdb.o wrfeat.o wrfh.o wrg96.o wrgamess.o wrgau.o wrgaucrt.o wrhin.o wricon.o wrint.o wrisis.o wrm3d.o wrmaccs.o wrmacmod.o wrmcmol.o wrmdl.o wrmicro.o wrmimic.o wrmiv.o wrmm2.o wrmm3.o wrmopac.o wrpcmod.o wrpdb.o wrpsgv.o wrpsgvz.o wrsmiles.o wrspart.o wrsybmol.o wrsybyl.o wrtinker.o wrtorlst.o wrunichm.o wrwiz.o wrxed.o wrxyz.o -o babel -lm /usr/bin/sed -e 's%@PREFIX@%/usr/local%g' /usr/ports/biology/babel/files/babel.sh >/wrkdirs/usr/ports/biology/babel/work/babel-1.6/babel.sh =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for babel-1.6_4 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/babel/work/babel-1.6/babel /wrkdirs/usr/ports/biology/babel/work/stage/usr/local/libexec install -m 555 /wrkdirs/usr/ports/biology/babel/work/babel-1.6/babel.sh /wrkdirs/usr/ports/biology/babel/work/stage/usr/local/bin/babel install -m 0644 /wrkdirs/usr/ports/biology/babel/work/babel-1.6/*.lis /wrkdirs/usr/ports/biology/babel/work/stage/usr/local/share/babel install -m 0644 /wrkdirs/usr/ports/biology/babel/work/babel-1.6/README.1ST /wrkdirs/usr/ports/biology/babel/work/stage/usr/local/share/doc/babel ====> 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=2024-04-04T08:06:46+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=bf70e962a3' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for babel-1.6_4 ===> Building babel-1.6_4 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for babel-1.6_4 build of biology/babel | babel-1.6_4 ended at Thu Apr 4 09:48:04 BST 2024 build time: 00:42:06