=>> Building science/clipper build started at Mon Apr 1 08:31:24 BST 2024 port directory: /usr/ports/science/clipper package name: clipper-2.1.20180802_4 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 802 Apr 24 2023 /usr/ports/science/clipper/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 8d3e020ed0 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 18 ---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/18/.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--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --enable-shared --disable-static --enable-phs --enable-cns --enable-mmdb --enable-minimol --enable-cif --enable-ccp4 --enable-fortran --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran13" F90="gfortran13" FC="gfortran13" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc13" MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/science/clipper/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/clipper/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/clipper/work/.cache HOME=/wrkdirs/usr/ports/science/clipper/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/science/clipper/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/clipper/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CMAKE_PREFIX_PATH="/usr/local" CCACHE_DIR="/root/.ccache" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran13" F90="gfortran13" FC="gfortran13" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc13" XDG_DATA_HOME=/wrkdirs/usr/ports/science/clipper/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/clipper/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/clipper/work/.cache HOME=/wrkdirs/usr/ports/science/clipper/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/science/clipper/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/clipper/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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-- OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/clipper" EXAMPLESDIR="share/examples/clipper" DATADIR="share/clipper" WWWDIR="www/clipper" ETCDIR="etc/clipper" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/clipper DOCSDIR=/usr/local/share/doc/clipper EXAMPLESDIR=/usr/local/share/examples/clipper WWWDIR=/usr/local/www/clipper ETCDIR=/usr/local/etc/clipper --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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> clipper-2.1.20180802_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 ===> clipper-2.1.20180802_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of clipper-2.1.20180802_4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by clipper-2.1.20180802_4 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by clipper-2.1.20180802_4 for building => SHA256 Checksum OK for clipper-2.1.20180802.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by clipper-2.1.20180802_4 for building ===> Extracting for clipper-2.1.20180802_4 => SHA256 Checksum OK for clipper-2.1.20180802.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 clipper-2.1.20180802_4 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> clipper-2.1.20180802_4 depends on executable: gfortran13 - not found ===> Installing existing package /packages/All/gcc13-13.2.0_4.pkg [pkg-builder.dan.net.uk] Installing gcc13-13.2.0_4... [pkg-builder.dan.net.uk] `-- Installing binutils-2.40_5,1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting binutils-2.40_5,1: .......... done [pkg-builder.dan.net.uk] `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | `-- Installing mpfr-4.2.1,1... [pkg-builder.dan.net.uk] | `-- Extracting mpfr-4.2.1,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] Extracting gcc13-13.2.0_4: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) ===== Message from gcc13-13.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> clipper-2.1.20180802_4 depends on executable: gfortran13 - found ===> Returning to build of clipper-2.1.20180802_4 ===> clipper-2.1.20180802_4 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> clipper-2.1.20180802_4 depends on package: gmake>=4.4.1 - found ===> Returning to build of clipper-2.1.20180802_4 ===> clipper-2.1.20180802_4 depends on file: /usr/local/bin/as - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> clipper-2.1.20180802_4 depends on shared library: libccp4c.so - not found ===> Installing existing package /packages/All/libccp4-6.5.1_5.pkg [pkg-builder.dan.net.uk] Installing libccp4-6.5.1_5... [pkg-builder.dan.net.uk] `-- Installing mmdb2-2.0.22... [pkg-builder.dan.net.uk] `-- Extracting mmdb2-2.0.22: .......... done [pkg-builder.dan.net.uk] Extracting libccp4-6.5.1_5: .......... done ===> clipper-2.1.20180802_4 depends on shared library: libccp4c.so - found (/usr/local/lib/libccp4c.so) ===> Returning to build of clipper-2.1.20180802_4 ===> clipper-2.1.20180802_4 depends on shared library: libmmdb2.so - found (/usr/local/lib/libmmdb2.so) ===> clipper-2.1.20180802_4 depends on shared library: libsfftw.so - not found ===> Installing existing package /packages/All/fftw-float-2.1.5_23.pkg [pkg-builder.dan.net.uk] Installing fftw-float-2.1.5_23... [pkg-builder.dan.net.uk] Extracting fftw-float-2.1.5_23: .......... done ===== Message from fftw-float-2.1.5_23: -- ===> NOTICE: The fftw-float 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 ===> clipper-2.1.20180802_4 depends on shared library: libsfftw.so - found (/usr/local/lib/libsfftw.so) ===> Returning to build of clipper-2.1.20180802_4 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for clipper-2.1.20180802_4 configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking whether gmake supports nested variables... yes checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by gmake... GNU checking dependency style of cc... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking the archiver (/usr/local/bin/ar) interface... ar checking build system type... amd64-portbld-freebsd13.2 checking host system type... amd64-portbld-freebsd13.2 checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/local/bin/ld checking if the linker (/usr/local/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/local/bin/nm checking the name lister (/usr/local/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 524288 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking how to convert amd64-portbld-freebsd13.2 file names to amd64-portbld-freebsd13.2 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd13.2 file names to toolchain format... func_convert_file_noop checking for /usr/local/bin/ld option to reload object files... -r checking for objdump... /usr/local/bin/objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... /usr/local/bin/ranlib checking command to parse /usr/local/bin/nm output from cc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... cpp checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/local/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd13.2 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/local/bin/ld checking if the linker (/usr/local/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd13.2 ld.so checking how to hardcode library paths into programs... immediate checking whether to enable maintainer-specific portions of Makefiles... no checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran13 accepts -g... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gfortran13 option to produce PIC... -fPIC checking if gfortran13 PIC flag -fPIC works... yes checking if gfortran13 static flag -static works... yes checking if gfortran13 supports -c -o file.o... yes checking if gfortran13 supports -c -o file.o... (cached) yes checking whether the gfortran13 linker (/usr/local/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd13.2 ld.so checking how to hardcode library paths into programs... immediate checking how to get verbose linking output from gfortran13... -v checking for Fortran 77 libraries of gfortran13... -L/usr/local/lib/gcc13 -L/usr/local/lib -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd13.2/13.2.0 -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd13.2/13.2.0/../../../../../x86_64-portbld-freebsd13.2/lib -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd13.2/13.2.0/../../.. -lgfortran -lm -lssp_nonshared -lquadmath checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking for library containing cos... -lm checking for prefixed single-precision FFTW2 (sfftw.h)... yes checking for the pthreads library -lpthreads... no checking for the pthreads library -lpthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... -D_THREAD_SAFE checking for PTHREAD_PRIO_INHERIT... yes checking for MMDB_CCIF_Init in -lmmdb2... yes checking mmdb2/mmdb_manager.h usability... yes checking mmdb2/mmdb_manager.h presence... yes checking for mmdb2/mmdb_manager.h... yes checking for ccp4_banner in -lccp4c... yes checking ccp4/ccp4_general.h usability... yes checking ccp4/ccp4_general.h presence... yes checking for ccp4/ccp4_general.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating clipper/Makefile config.status: creating clipper/core/Makefile config.status: creating clipper/contrib/Makefile config.status: creating examples/Makefile config.status: creating clipper.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands Configuration Summary ------------------------------ core: yes contrib: yes phs: yes cns: yes mmdb: yes minimol: yes cif: yes ccp4: yes cctbx: no fortran: yes =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for clipper-2.1.20180802_4 gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1' Making all in clipper gmake[2]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper' Making all in core gmake[3]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/core' /bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../.. -D_THREAD_SAFE -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-atomsf.lo -MD -MP -MF .deps/libclipper_core_la-atomsf.Tpo -c -o libclipper_core_la-atomsf.lo `test -f 'atomsf.cpp' || echo './'`atomsf.cpp libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -D_THREAD_SAFE -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-atomsf.lo -MD -MP -MF .deps/libclipper_core_la-atomsf.Tpo -c atomsf.cpp -fPIC -DPIC -o .libs/libclipper_core_la-atomsf.o atomsf.cpp:406:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ atomsf.cpp:436:82: note: in instantiation of member function 'clipper::ScatteringFactorsTraits::sf' requested here case SF_WAASMAIER_KIRFEL: return ScatteringFactorsTraits::sf(element); ^ atomsf.cpp:406:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ atomsf.cpp:437:68: note: in instantiation of member function 'clipper::ScatteringFactorsTraits::sf' requested here case SF_ELECTRON: return ScatteringFactorsTraits::sf(element); ^ 2 warnings generated. mv -f .deps/libclipper_core_la-atomsf.Tpo .deps/libclipper_core_la-atomsf.Plo /bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../.. -D_THREAD_SAFE -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-coords.lo -MD -MP -MF .deps/libclipper_core_la-coords.Tpo -c -o libclipper_core_la-coords.lo `test -f 'coords.cpp' || echo './'`coords.cpp libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -D_THREAD_SAFE -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-coords.lo -MD -MP -MF .deps/libclipper_core_la-coords.Tpo -c coords.cpp -fPIC -DPIC -o .libs/libclipper_core_la-coords.o mv -f .deps/libclipper_core_la-coords.Tpo .deps/libclipper_core_la-coords.Plo /bin/sh ../../libtool --tag=CXX 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core/.libs/libclipper-core.so contrib/.libs/libclipper-contrib.so /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -fstack-protector-strong -Wl,-soname -Wl,libclipper-fortran.so.2 -o fortran/.libs/libclipper-fortran.so.2.0.1 libtool: link: (cd "fortran/.libs" && rm -f "libclipper-fortran.so.2" && ln -s "libclipper-fortran.so.2.0.1" "libclipper-fortran.so.2") libtool: link: (cd "fortran/.libs" && rm -f "libclipper-fortran.so" && ln -s "libclipper-fortran.so.2.0.1" "libclipper-fortran.so") libtool: link: ( cd "fortran/.libs" && rm -f "libclipper-fortran.la" && ln -s "../libclipper-fortran.la" "libclipper-fortran.la" ) gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper' gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper' Making all in examples gmake[2]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/examples' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/examples' gmake[2]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1' gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1' gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> clipper-2.1.20180802_4 depends on executable: gfortran13 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for clipper-2.1.20180802_4 ===> Generating temporary packing list Making install in clipper gmake[1]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper' Making install in core gmake[2]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/core' gmake[3]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/core' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib' /bin/sh ../../libtool --mode=install /usr/bin/install -c libclipper-core.la '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libclipper-core.so.2.0.1 /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-core.so.2.0.1 libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-core.so.2.0.1 libclipper-core.so.2 || { rm -f libclipper-core.so.2 && ln -s libclipper-core.so.2.0.1 libclipper-core.so.2; }; }) libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-core.so.2.0.1 libclipper-core.so || { rm -f libclipper-core.so && ln -s libclipper-core.so.2.0.1 libclipper-core.so; }; }) libtool: install: /usr/bin/install -c .libs/libclipper-core.lai /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-core.la libtool: install: warning: remember to run `libtool --finish /usr/local/lib' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/core' install -m 0644 atomsf.h container_types.h nxmap_operator.h cell.h coords.h ramachandran.h clipper_instance.h derivs.h resol_basisfn.h clipper_memory.h fftmap.h resol_fn.h clipper_message.h fftmap_sparse.h resol_targetfn.h clipper_precision.h hkl_compute.h rotation.h clipper_stats.h hkl_data.h spacegroup.h clipper_sysdep.h hkl_datatypes.h spacegroup_data.h clipper_test.h hkl_info.h symop.h clipper_types.h hkl_lookup.h clipper_util.h hkl_operators.h container.h map_interp.h xmap.h container_hkl.h map_utils.h container_map.h nxmap.h clipper_thread.h test_core.h '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/core' install -m 0644 test_data.h '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/core' gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/core' gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/core' Making install in contrib gmake[2]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/contrib' gmake[3]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/contrib' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib' /bin/sh ../../libtool --mode=install /usr/bin/install -c libclipper-contrib.la '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib' libtool: install: warning: relinking `libclipper-contrib.la' libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/contrib; /bin/sh /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/libtool --tag CXX --mode=relink c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib -o libclipper-contrib.la -rpath /usr/local/lib convolution_search.lo sfcalc.lo edcalc.lo sfcalc_obs.lo fffear.lo sfscale.lo function_object_bases.lo sfweight.lo mapfilter.lo skeleton.lo originmatch.lo test_contrib.lo ../core/libclipper-core.la -lm -inst-prefix-dir /wrkdirs/usr/ports/science/clipper/work/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/crtbeginS.o .libs/convolution_search.o .libs/sfcalc.o .libs/edcalc.o .libs/sfcalc_obs.o .libs/fffear.o .libs/sfscale.o .libs/function_object_bases.o .libs/sfweight.o .libs/mapfilter.o .libs/skeleton.o .libs/originmatch.o .libs/test_contrib.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -L/usr/local/lib ../core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -fstack-protector-strong -Wl,-soname -Wl,libclipper-contrib.so.2 -o .libs/libclipper-contrib.so.2.0.1 libtool: install: /usr/bin/install -c .libs/libclipper-contrib.so.2.0.1T /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-contrib.so.2.0.1 libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-contrib.so.2.0.1 libclipper-contrib.so.2 || { rm -f libclipper-contrib.so.2 && ln -s libclipper-contrib.so.2.0.1 libclipper-contrib.so.2; }; }) libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-contrib.so.2.0.1 libclipper-contrib.so || { rm -f libclipper-contrib.so && ln -s libclipper-contrib.so.2.0.1 libclipper-contrib.so; }; }) libtool: install: /usr/bin/install -c .libs/libclipper-contrib.lai /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-contrib.la libtool: install: warning: remember to run `libtool --finish /usr/local/lib' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/contrib' install -m 0644 convolution_search.h mapfilter.h sfscale.h edcalc.h originmatch.h sfweight.h fffear.h sfcalc.h skeleton.h function_object_bases.h sfcalc_obs.h test_contrib.h '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/contrib' gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/contrib' gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/contrib' gmake[2]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper' gmake[3]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c mmdb/libclipper-mmdb.la minimol/libclipper-minimol.la phs/libclipper-phs.la cif/libclipper-cif.la ccp4/libclipper-ccp4.la cns/libclipper-cns.la fortran/libclipper-fortran.la '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib' libtool: install: warning: relinking `mmdb/libclipper-mmdb.la' libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper; /bin/sh /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/libtool --tag CXX --mode=relink c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib -o mmdb/libclipper-mmdb.la -rpath /usr/local/lib mmdb/clipper_mmdb.lo core/libclipper-core.la -lmmdb2 -lm -inst-prefix-dir /wrkdirs/usr/ports/science/clipper/work/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/crtbeginS.o mmdb/.libs/clipper_mmdb.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -lmmdb2 -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -fstack-protector-strong -Wl,-soname -Wl,libclipper-mmdb.so.2 -o mmdb/.libs/libclipper-mmdb.so.2.0.1 libtool: install: /usr/bin/install -c mmdb/.libs/libclipper-mmdb.so.2.0.1T /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-mmdb.so.2.0.1 libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-mmdb.so.2.0.1 libclipper-mmdb.so.2 || { rm -f libclipper-mmdb.so.2 && ln -s libclipper-mmdb.so.2.0.1 libclipper-mmdb.so.2; }; }) libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-mmdb.so.2.0.1 libclipper-mmdb.so || { rm -f libclipper-mmdb.so && ln -s libclipper-mmdb.so.2.0.1 libclipper-mmdb.so; }; }) libtool: install: /usr/bin/install -c mmdb/.libs/libclipper-mmdb.lai /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-mmdb.la libtool: install: warning: relinking `minimol/libclipper-minimol.la' libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper; /bin/sh /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/libtool --tag CXX --mode=relink c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib -o minimol/libclipper-minimol.la -rpath /usr/local/lib minimol/minimol.lo minimol/container_minimol.lo minimol/minimol_data.lo minimol/minimol_io.lo minimol/minimol_seq.lo minimol/minimol_utils.lo core/libclipper-core.la mmdb/libclipper-mmdb.la -lmmdb2 -lm -inst-prefix-dir /wrkdirs/usr/ports/science/clipper/work/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/crtbeginS.o minimol/.libs/minimol.o minimol/.libs/container_minimol.o minimol/.libs/minimol_data.o minimol/.libs/minimol_io.o minimol/.libs/minimol_seq.o minimol/.libs/minimol_utils.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -L/usr/local/lib core/.libs/libclipper-core.so mmdb/.libs/libclipper-mmdb.so /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -lmmdb2 -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -fstack-protector-strong -Wl,-soname -Wl,libclipper-minimol.so.2 -o minimol/.libs/libclipper-minimol.so.2.0.1 libtool: install: /usr/bin/install -c minimol/.libs/libclipper-minimol.so.2.0.1T /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-minimol.so.2.0.1 libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-minimol.so.2.0.1 libclipper-minimol.so.2 || { rm -f libclipper-minimol.so.2 && ln -s libclipper-minimol.so.2.0.1 libclipper-minimol.so.2; }; }) libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-minimol.so.2.0.1 libclipper-minimol.so || { rm -f libclipper-minimol.so && ln -s libclipper-minimol.so.2.0.1 libclipper-minimol.so; }; }) libtool: install: /usr/bin/install -c minimol/.libs/libclipper-minimol.lai /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-minimol.la libtool: install: warning: relinking `phs/libclipper-phs.la' libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper; /bin/sh /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/libtool --tag CXX --mode=relink c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib -o phs/libclipper-phs.la -rpath /usr/local/lib phs/phs_io.lo core/libclipper-core.la -lm -inst-prefix-dir /wrkdirs/usr/ports/science/clipper/work/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/crtbeginS.o phs/.libs/phs_io.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -fstack-protector-strong -Wl,-soname -Wl,libclipper-phs.so.2 -o phs/.libs/libclipper-phs.so.2.0.1 libtool: install: /usr/bin/install -c phs/.libs/libclipper-phs.so.2.0.1T /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-phs.so.2.0.1 libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-phs.so.2.0.1 libclipper-phs.so.2 || { rm -f libclipper-phs.so.2 && ln -s libclipper-phs.so.2.0.1 libclipper-phs.so.2; }; }) libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-phs.so.2.0.1 libclipper-phs.so || { rm -f libclipper-phs.so && ln -s libclipper-phs.so.2.0.1 libclipper-phs.so; }; }) libtool: install: /usr/bin/install -c phs/.libs/libclipper-phs.lai /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-phs.la libtool: install: warning: relinking `cif/libclipper-cif.la' libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper; /bin/sh /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/libtool --tag CXX --mode=relink c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib -o cif/libclipper-cif.la -rpath /usr/local/lib cif/cif_data_io.lo core/libclipper-core.la -lmmdb2 -lm -inst-prefix-dir /wrkdirs/usr/ports/science/clipper/work/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/crtbeginS.o cif/.libs/cif_data_io.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -lmmdb2 -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -fstack-protector-strong -Wl,-soname -Wl,libclipper-cif.so.2 -o cif/.libs/libclipper-cif.so.2.0.1 libtool: install: /usr/bin/install -c cif/.libs/libclipper-cif.so.2.0.1T /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-cif.so.2.0.1 libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-cif.so.2.0.1 libclipper-cif.so.2 || { rm -f libclipper-cif.so.2 && ln -s libclipper-cif.so.2.0.1 libclipper-cif.so.2; }; }) libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-cif.so.2.0.1 libclipper-cif.so || { rm -f libclipper-cif.so && ln -s libclipper-cif.so.2.0.1 libclipper-cif.so; }; }) libtool: install: /usr/bin/install -c cif/.libs/libclipper-cif.lai /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-cif.la libtool: install: warning: relinking `ccp4/libclipper-ccp4.la' libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper; /bin/sh /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/libtool --tag CXX --mode=relink c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib -o ccp4/libclipper-ccp4.la -rpath /usr/local/lib ccp4/ccp4_mtz_types.lo ccp4/ccp4_mtz_io.lo ccp4/ccp4_map_io.lo ccp4/ccp4_utils.lo core/libclipper-core.la -lccp4c -lm -inst-prefix-dir /wrkdirs/usr/ports/science/clipper/work/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/crtbeginS.o ccp4/.libs/ccp4_mtz_types.o ccp4/.libs/ccp4_mtz_io.o ccp4/.libs/ccp4_map_io.o ccp4/.libs/ccp4_utils.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -lccp4c -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -fstack-protector-strong -Wl,-soname -Wl,libclipper-ccp4.so.2 -o ccp4/.libs/libclipper-ccp4.so.2.0.1 libtool: install: /usr/bin/install -c ccp4/.libs/libclipper-ccp4.so.2.0.1T /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-ccp4.so.2.0.1 libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-ccp4.so.2.0.1 libclipper-ccp4.so.2 || { rm -f libclipper-ccp4.so.2 && ln -s libclipper-ccp4.so.2.0.1 libclipper-ccp4.so.2; }; }) libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-ccp4.so.2.0.1 libclipper-ccp4.so || { rm -f libclipper-ccp4.so && ln -s libclipper-ccp4.so.2.0.1 libclipper-ccp4.so; }; }) libtool: install: /usr/bin/install -c ccp4/.libs/libclipper-ccp4.lai /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-ccp4.la libtool: install: warning: relinking `cns/libclipper-cns.la' libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper; /bin/sh /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/libtool --tag CXX --mode=relink c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib -o cns/libclipper-cns.la -rpath /usr/local/lib cns/cns_hkl_io.lo cns/cns_map_io.lo core/libclipper-core.la -lm -inst-prefix-dir /wrkdirs/usr/ports/science/clipper/work/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/crtbeginS.o cns/.libs/cns_hkl_io.o cns/.libs/cns_map_io.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -fstack-protector-strong -Wl,-soname -Wl,libclipper-cns.so.2 -o cns/.libs/libclipper-cns.so.2.0.1 libtool: install: /usr/bin/install -c cns/.libs/libclipper-cns.so.2.0.1T /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-cns.so.2.0.1 libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-cns.so.2.0.1 libclipper-cns.so.2 || { rm -f libclipper-cns.so.2 && ln -s libclipper-cns.so.2.0.1 libclipper-cns.so.2; }; }) libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-cns.so.2.0.1 libclipper-cns.so || { rm -f libclipper-cns.so && ln -s libclipper-cns.so.2.0.1 libclipper-cns.so; }; }) libtool: install: /usr/bin/install -c cns/.libs/libclipper-cns.lai /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-cns.la libtool: install: warning: relinking `fortran/libclipper-fortran.la' libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper; /bin/sh /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/libtool --tag CXX --mode=relink c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib -o fortran/libclipper-fortran.la -rpath /usr/local/lib fortran/f_interface.lo core/libclipper-core.la contrib/libclipper-contrib.la -lm -inst-prefix-dir /wrkdirs/usr/ports/science/clipper/work/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/crtbeginS.o fortran/.libs/f_interface.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc13 -L/usr/local/lib core/.libs/libclipper-core.so contrib/.libs/libclipper-contrib.so /wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper/core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -fstack-protector-strong -Wl,-soname -Wl,libclipper-fortran.so.2 -o fortran/.libs/libclipper-fortran.so.2.0.1 libtool: install: /usr/bin/install -c fortran/.libs/libclipper-fortran.so.2.0.1T /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-fortran.so.2.0.1 libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-fortran.so.2.0.1 libclipper-fortran.so.2 || { rm -f libclipper-fortran.so.2 && ln -s libclipper-fortran.so.2.0.1 libclipper-fortran.so.2; }; }) libtool: install: (cd /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib && { ln -s -f libclipper-fortran.so.2.0.1 libclipper-fortran.so || { rm -f libclipper-fortran.so && ln -s libclipper-fortran.so.2.0.1 libclipper-fortran.so; }; }) libtool: install: /usr/bin/install -c fortran/.libs/libclipper-fortran.lai /wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/libclipper-fortran.la libtool: install: warning: remember to run `libtool --finish /usr/local/lib' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/ccp4' install -m 0644 ccp4/ccp4_map_io.h ccp4/ccp4_mtz_io.h ccp4/ccp4_mtz_types.h ccp4/ccp4_utils.h '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/ccp4' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/cif' install -m 0644 cif/cif_data_io.h '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/cif' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/cns' install -m 0644 cns/cns_hkl_io.h cns/cns_map_io.h '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/cns' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/minimol' install -m 0644 minimol/container_minimol.h minimol/minimol_data.h minimol/minimol_seq.h minimol/minimol.h minimol/minimol_io.h minimol/minimol_utils.h '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/minimol' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/mmdb' install -m 0644 mmdb/clipper_mmdb.h '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/mmdb' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/phs' install -m 0644 phs/phs_io.h '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper/phs' /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper' install -m 0644 clipper-ccp4.h clipper-contrib.h clipper-phs.h clipper-cctbx.h clipper-minimol.h clipper.h clipper-cif.h clipper-mmdb.h minimal-clipper-hkl.h clipper-cns.h minimal-clipper-map.h '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/include/clipper' gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper' gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper' gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/clipper' Making install in examples gmake[1]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/examples' gmake[2]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/examples' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/examples' gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1/examples' gmake[1]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1' gmake[2]: Entering directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1' gmake[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/pkgconfig' install -m 0644 clipper.pc '/wrkdirs/usr/ports/science/clipper/work/stage/usr/local/lib/pkgconfig' gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1' gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/clipper/work/clipper-2.1' ====> 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=2024-04-01T07:31:24+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=8d3e020ed0' '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 clipper-2.1.20180802_4 ===> Building clipper-2.1.20180802_4 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for clipper-2.1.20180802_4 build of science/clipper | clipper-2.1.20180802_4 ended at Mon Apr 1 08:35:20 BST 2024 build time: 00:03:57