=> Building science/clipper Started : Thursday, 7 MAR 2019 at 12:58:25 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 -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" MAKE=gmake XDG_DATA_HOME=/construction/science/clipper XDG_CONFIG_HOME=/construction/science/clipper HOME=/construction/science/clipper TMPDIR="/tmp" PATH=/construction/science/clipper/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 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" CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- 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} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/construction/science/clipper XDG_CONFIG_HOME=/construction/science/clipper HOME=/construction/science/clipper TMPDIR="/tmp" PATH=/construction/science/clipper/.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 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 NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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 -------------------------------------------------- DESTDIR=/construction/science/clipper/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/clipper" EXAMPLESDIR="share/examples/clipper" DATADIR="share/clipper" WWWDIR="www/clipper" ETCDIR="etc/clipper" -------------------------------------------------- -- 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 -------------------------------------------------- -- /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 -------------------------------------------------------------------------------- ===> License LGPL3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> clipper-2.1.20180802_1 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 ===> clipper-2.1.20180802_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of clipper-2.1.20180802_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clipper-2.1.20180802_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clipper-2.1.20180802_1 for building => SHA256 Checksum OK for clipper-2.1.20180802.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clipper-2.1.20180802_1 for building ===> Extracting for clipper-2.1.20180802_1 => SHA256 Checksum OK for clipper-2.1.20180802.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for clipper-2.1.20180802_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> clipper-2.1.20180802_1 depends on executable: gfortran5 - not found ===> Installing existing package /packages/All/gcc5-5.5.0_6.txz Installing gcc5-5.5.0_6... `-- Installing binutils-2.32,1... | `-- Installing gettext-runtime-0.19.8.1_2... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done `-- Extracting binutils-2.32,1: .......... done `-- Installing gmp-6.1.2_1... `-- Extracting gmp-6.1.2_1: .......... done `-- Installing mpc-1.1.0_2... | `-- Installing mpfr-4.0.2... | `-- Extracting mpfr-4.0.2: .......... done `-- Extracting mpc-1.1.0_2: ......... done Extracting gcc5-5.5.0_6: .......... done Message from gcc5-5.5.0_6: 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/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unsupported by upstream. Use GCC 7 or newer instead.. ===> clipper-2.1.20180802_1 depends on executable: gfortran5 - found ===> Returning to build of clipper-2.1.20180802_1 ===> clipper-2.1.20180802_1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... Extracting gmake-4.2.1_3: .......... done ===> clipper-2.1.20180802_1 depends on executable: gmake - found ===> Returning to build of clipper-2.1.20180802_1 ===> clipper-2.1.20180802_1 depends on file: /usr/local/bin/as - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> clipper-2.1.20180802_1 depends on shared library: libccp4c.so - not found ===> Installing existing package /packages/All/libccp4-6.5.1_2.txz Installing libccp4-6.5.1_2... `-- Installing mmdb2-2.0.19... `-- Extracting mmdb2-2.0.19: .......... done Extracting libccp4-6.5.1_2: .......... done ===> clipper-2.1.20180802_1 depends on shared library: libccp4c.so - found (/usr/local/lib/libccp4c.so) ===> Returning to build of clipper-2.1.20180802_1 ===> clipper-2.1.20180802_1 depends on shared library: libmmdb2.so - found (/usr/local/lib/libmmdb2.so) ===> clipper-2.1.20180802_1 depends on shared library: libsfftw.so - not found ===> Installing existing package /packages/All/fftw-float-2.1.5_20.txz Installing fftw-float-2.1.5_20... Extracting fftw-float-2.1.5_20: .......... done Message from fftw-float-2.1.5_20: ===> 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> clipper-2.1.20180802_1 depends on shared library: libsfftw.so - found (/usr/local/lib/libsfftw.so) ===> Returning to build of clipper-2.1.20180802_1 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for clipper-2.1.20180802_1 configure: loading site script /xports/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... x86_64-portbld-dragonfly5.5 checking host system type... x86_64-portbld-dragonfly5.5 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) 262144 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking how to convert x86_64-portbld-dragonfly5.5 file names to x86_64-portbld-dragonfly5.5 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly5.5 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... no 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... dragonfly5.5 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... dragonfly5.5 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 gfortran5 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 gfortran5 option to produce PIC... -fPIC checking if gfortran5 PIC flag -fPIC works... yes checking if gfortran5 static flag -static works... yes checking if gfortran5 supports -c -o file.o... yes checking if gfortran5 supports -c -o file.o... (cached) yes checking whether the gfortran5 linker (/usr/local/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... dragonfly5.5 ld.so checking how to hardcode library paths into programs... immediate checking how to get verbose linking output from gfortran5... -v checking for Fortran 77 libraries of gfortran5... -L/usr/local/lib/gcc5 -L/usr/local/lib -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.5/5.5.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.5/5.5.0/../../../../../x86_64-portbld-dragonfly5.5/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.5/5.5.0/../../.. -lgfortran -lm -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... no 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 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for clipper-2.1.20180802_1 gmake[1]: Entering directory '/construction/science/clipper/clipper-2.1' gmake all-recursive gmake[2]: Entering directory '/construction/science/clipper/clipper-2.1' Making all in clipper gmake[3]: Entering directory '/construction/science/clipper/clipper-2.1/clipper' Making all in core gmake[4]: Entering directory '/construction/science/clipper/clipper-2.1/clipper/core' /bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -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 /bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -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 /bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-nxmap_operator.lo -MD -MP -MF .deps/libclipper_core_la-nxmap_operator.Tpo -c -o libclipper_core_la-nxmap_operator.lo `test -f 'nxmap_operator.cpp' || echo './'`nxmap_operator.cpp /bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-cell.lo -MD -MP -MF .deps/libclipper_core_la-cell.Tpo -c -o libclipper_core_la-cell.lo `test -f 'cell.cpp' || echo './'`cell.cpp /bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-derivs.lo -MD -MP -MF .deps/libclipper_core_la-derivs.Tpo -c -o libclipper_core_la-derivs.lo `test -f 'derivs.cpp' || echo './'`derivs.cpp libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -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 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-cell.lo -MD -MP -MF .deps/libclipper_core_la-cell.Tpo -c cell.cpp -fPIC -DPIC -o .libs/libclipper_core_la-cell.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-derivs.lo -MD -MP -MF .deps/libclipper_core_la-derivs.Tpo -c derivs.cpp -fPIC -DPIC -o .libs/libclipper_core_la-derivs.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -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 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-nxmap_operator.lo -MD -MP -MF .deps/libclipper_core_la-nxmap_operator.Tpo -c nxmap_operator.cpp -fPIC -DPIC -o .libs/libclipper_core_la-nxmap_operator.o atomsf.cpp: In member function 'const clipper::ScatteringFactorsData& clipper::ScatteringFactors::operator[](const clipper::String&) const': atomsf.cpp:438:33: warning: control reaches end of non-void function [-Wreturn-type] default: Message::message(Message_fatal("unimplemented type")); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atomsf.cpp: In static member function 'static const clipper::ScatteringFactorsData& clipper::ScatteringFactorsTraits::sf(const clipper::String&, int) [with clipper::ScatteringFactorsType TYPE = (clipper::ScatteringFactorsType)0]': atomsf.cpp:379:10: warning: control reaches end of non-void function [-Wreturn-type] String atyp; ^~~~ atomsf.cpp: In static member function 'static const clipper::ScatteringFactorsData& clipper::ScatteringFactorsTraits::sf(const clipper::String&, int) [with clipper::ScatteringFactorsType TYPE = (clipper::ScatteringFactorsType)1]': atomsf.cpp:379:10: warning: control reaches end of non-void function [-Wreturn-type] String atyp; ^~~~ mv -f .deps/libclipper_core_la-derivs.Tpo .deps/libclipper_core_la-derivs.Plo /bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-ramachandran.lo -MD -MP -MF .deps/libclipper_core_la-ramachandran.Tpo -c -o libclipper_core_la-ramachandran.lo `test -f 'ramachandran.cpp' || echo './'`ramachandran.cpp libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-ramachandran.lo -MD -MP -MF .deps/libclipper_core_la-ramachandran.Tpo -c ramachandran.cpp -fPIC -DPIC -o .libs/libclipper_core_la-ramachandran.o mv -f .deps/libclipper_core_la-nxmap_operator.Tpo 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-Wl,/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc5 -B/usr/local/bin -Wl,-soname -Wl,libclipper-phs.so.2 -o phs/.libs/libclipper-phs.so.2.0.1 libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o mmdb/.libs/clipper_mmdb.o -Wl,-rpath -Wl,/construction/science/clipper/clipper-2.1/clipper/core/.libs -Wl,-rpath -Wl,/usr/local/lib -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -lmmdb2 -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc5 -B/usr/local/bin -Wl,-soname -Wl,libclipper-mmdb.so.2 -o mmdb/.libs/libclipper-mmdb.so.2.0.1 libtool: link: 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rm -f "libclipper-cif.so" && ln -s "libclipper-cif.so.2.0.1" "libclipper-cif.so") 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" ) /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -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 libtool: link: ( cd 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-Wl,libclipper-minimol.so.2 -o minimol/.libs/libclipper-minimol.so.2.0.1 libtool: link: (cd "minimol/.libs" && rm -f "libclipper-minimol.so.2" && ln -s "libclipper-minimol.so.2.0.1" "libclipper-minimol.so.2") libtool: link: (cd "minimol/.libs" && rm -f "libclipper-minimol.so" && ln -s "libclipper-minimol.so.2.0.1" "libclipper-minimol.so") libtool: link: ( cd "minimol/.libs" && rm -f "libclipper-minimol.la" && ln -s "../libclipper-minimol.la" "libclipper-minimol.la" ) /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -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 libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o ccp4/.libs/ccp4_mtz_types.o 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/usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -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 libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o cns/.libs/cns_hkl_io.o cns/.libs/cns_map_io.o -Wl,-rpath -Wl,/construction/science/clipper/clipper-2.1/clipper/core/.libs -Wl,-rpath -Wl,/usr/local/lib -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc5 -B/usr/local/bin -Wl,-soname -Wl,libclipper-cns.so.2 -o cns/.libs/libclipper-cns.so.2.0.1 libtool: link: (cd "cns/.libs" && rm -f "libclipper-cns.so.2" && ln -s "libclipper-cns.so.2.0.1" "libclipper-cns.so.2") libtool: link: (cd "cns/.libs" && rm -f "libclipper-cns.so" && ln -s "libclipper-cns.so.2.0.1" "libclipper-cns.so") libtool: link: ( cd "cns/.libs" && rm -f "libclipper-cns.la" && ln -s "../libclipper-cns.la" "libclipper-cns.la" ) gmake[4]: Leaving directory '/construction/science/clipper/clipper-2.1/clipper' gmake[3]: Leaving directory '/construction/science/clipper/clipper-2.1/clipper' Making all in examples gmake[3]: Entering directory '/construction/science/clipper/clipper-2.1/examples' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/science/clipper/clipper-2.1/examples' gmake[3]: Entering directory '/construction/science/clipper/clipper-2.1' gmake[3]: Nothing to be done for 'all-am'. gmake[3]: Leaving directory '/construction/science/clipper/clipper-2.1' gmake[2]: Leaving directory '/construction/science/clipper/clipper-2.1' gmake[1]: Leaving directory '/construction/science/clipper/clipper-2.1' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> clipper-2.1.20180802_1 depends on executable: gfortran5 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for clipper-2.1.20180802_1 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/science/clipper/clipper-2.1' Making install in clipper gmake[2]: Entering directory '/construction/science/clipper/clipper-2.1/clipper' Making install in core gmake[3]: Entering directory '/construction/science/clipper/clipper-2.1/clipper/core' gmake[4]: Entering directory '/construction/science/clipper/clipper-2.1/clipper/core' /bin/mkdir -p '/construction/science/clipper/stage/usr/local/lib' /bin/sh ../../libtool --mode=install /usr/bin/install -c libclipper-core.la '/construction/science/clipper/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libclipper-core.so.2.0.1 /construction/science/clipper/stage/usr/local/lib/libclipper-core.so.2.0.1 libtool: install: (cd /construction/science/clipper/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 /construction/science/clipper/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 /construction/science/clipper/stage/usr/local/lib/libclipper-core.la libtool: install: warning: remember to run `libtool --finish /usr/local/lib' /bin/mkdir -p '/construction/science/clipper/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 '/construction/science/clipper/stage/usr/local/include/clipper/core' install -m 0644 test_data.h '/construction/science/clipper/stage/usr/local/include/clipper/core' gmake[4]: Leaving directory '/construction/science/clipper/clipper-2.1/clipper/core' gmake[3]: Leaving directory '/construction/science/clipper/clipper-2.1/clipper/core' Making install in contrib gmake[3]: Entering directory '/construction/science/clipper/clipper-2.1/clipper/contrib' gmake[4]: Entering directory '/construction/science/clipper/clipper-2.1/clipper/contrib' /bin/mkdir -p '/construction/science/clipper/stage/usr/local/lib' /bin/sh ../../libtool --mode=install /usr/bin/install -c libclipper-contrib.la '/construction/science/clipper/stage/usr/local/lib' libtool: install: warning: relinking `libclipper-contrib.la' libtool: install: (cd /construction/science/clipper/clipper-2.1/clipper/contrib; /bin/sh /construction/science/clipper/clipper-2.1/libtool --tag CXX --mode=relink c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/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/gcc5 -L/usr/local/lib ../core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage/usr/local/lib/libclipper-contrib.so.2.0.1 libtool: install: (cd /construction/science/clipper/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 /construction/science/clipper/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 /construction/science/clipper/stage/usr/local/lib/libclipper-contrib.la libtool: install: warning: remember to run `libtool --finish /usr/local/lib' /bin/mkdir -p '/construction/science/clipper/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 '/construction/science/clipper/stage/usr/local/include/clipper/contrib' gmake[4]: Leaving directory '/construction/science/clipper/clipper-2.1/clipper/contrib' gmake[3]: Leaving directory '/construction/science/clipper/clipper-2.1/clipper/contrib' gmake[3]: Entering directory '/construction/science/clipper/clipper-2.1/clipper' gmake[4]: Entering directory '/construction/science/clipper/clipper-2.1/clipper' /bin/mkdir -p '/construction/science/clipper/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 '/construction/science/clipper/stage/usr/local/lib' libtool: install: warning: relinking `mmdb/libclipper-mmdb.la' libtool: install: (cd /construction/science/clipper/clipper-2.1/clipper; /bin/sh /construction/science/clipper/clipper-2.1/libtool --tag CXX --mode=relink c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o mmdb/.libs/clipper_mmdb.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -lmmdb2 -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage/usr/local/lib/libclipper-mmdb.so.2.0.1 libtool: install: (cd /construction/science/clipper/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 /construction/science/clipper/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 /construction/science/clipper/stage/usr/local/lib/libclipper-mmdb.la libtool: install: warning: relinking `minimol/libclipper-minimol.la' libtool: install: (cd /construction/science/clipper/clipper-2.1/clipper; /bin/sh /construction/science/clipper/clipper-2.1/libtool --tag CXX --mode=relink c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/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/gcc5 -L/usr/local/lib core/.libs/libclipper-core.so mmdb/.libs/libclipper-mmdb.so /construction/science/clipper/clipper-2.1/clipper/core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -lmmdb2 -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage/usr/local/lib/libclipper-minimol.so.2.0.1 libtool: install: (cd /construction/science/clipper/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 /construction/science/clipper/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 /construction/science/clipper/stage/usr/local/lib/libclipper-minimol.la libtool: install: warning: relinking `phs/libclipper-phs.la' libtool: install: (cd /construction/science/clipper/clipper-2.1/clipper; /bin/sh /construction/science/clipper/clipper-2.1/libtool --tag CXX --mode=relink c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o phs/.libs/phs_io.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage/usr/local/lib/libclipper-phs.so.2.0.1 libtool: install: (cd /construction/science/clipper/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 /construction/science/clipper/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 /construction/science/clipper/stage/usr/local/lib/libclipper-phs.la libtool: install: warning: relinking `cif/libclipper-cif.la' libtool: install: (cd /construction/science/clipper/clipper-2.1/clipper; /bin/sh /construction/science/clipper/clipper-2.1/libtool --tag CXX --mode=relink c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o cif/.libs/cif_data_io.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -lmmdb2 -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage/usr/local/lib/libclipper-cif.so.2.0.1 libtool: install: (cd /construction/science/clipper/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 /construction/science/clipper/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 /construction/science/clipper/stage/usr/local/lib/libclipper-cif.la libtool: install: warning: relinking `ccp4/libclipper-ccp4.la' libtool: install: (cd /construction/science/clipper/clipper-2.1/clipper; /bin/sh /construction/science/clipper/clipper-2.1/libtool --tag CXX --mode=relink c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/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/gcc5 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -lccp4c -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage/usr/local/lib/libclipper-ccp4.so.2.0.1 libtool: install: (cd /construction/science/clipper/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 /construction/science/clipper/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 /construction/science/clipper/stage/usr/local/lib/libclipper-ccp4.la libtool: install: warning: relinking `cns/libclipper-cns.la' libtool: install: (cd /construction/science/clipper/clipper-2.1/clipper; /bin/sh /construction/science/clipper/clipper-2.1/libtool --tag CXX --mode=relink c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o cns/.libs/cns_hkl_io.o cns/.libs/cns_map_io.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage/usr/local/lib/libclipper-cns.so.2.0.1 libtool: install: (cd /construction/science/clipper/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 /construction/science/clipper/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 /construction/science/clipper/stage/usr/local/lib/libclipper-cns.la libtool: install: warning: relinking `fortran/libclipper-fortran.la' libtool: install: (cd /construction/science/clipper/clipper-2.1/clipper; /bin/sh /construction/science/clipper/clipper-2.1/libtool --tag CXX --mode=relink c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage) libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o fortran/.libs/f_interface.o -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/lib core/.libs/libclipper-core.so contrib/.libs/libclipper-contrib.so /construction/science/clipper/clipper-2.1/clipper/core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc5 -B/usr/local/bin -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 /construction/science/clipper/stage/usr/local/lib/libclipper-fortran.so.2.0.1 libtool: install: (cd /construction/science/clipper/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 /construction/science/clipper/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 /construction/science/clipper/stage/usr/local/lib/libclipper-fortran.la libtool: install: warning: remember to run `libtool --finish /usr/local/lib' /bin/mkdir -p '/construction/science/clipper/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 '/construction/science/clipper/stage/usr/local/include/clipper/ccp4' /bin/mkdir -p '/construction/science/clipper/stage/usr/local/include/clipper/cif' install -m 0644 cif/cif_data_io.h '/construction/science/clipper/stage/usr/local/include/clipper/cif' /bin/mkdir -p '/construction/science/clipper/stage/usr/local/include/clipper/cns' install -m 0644 cns/cns_hkl_io.h cns/cns_map_io.h '/construction/science/clipper/stage/usr/local/include/clipper/cns' /bin/mkdir -p '/construction/science/clipper/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 '/construction/science/clipper/stage/usr/local/include/clipper/minimol' /bin/mkdir -p '/construction/science/clipper/stage/usr/local/include/clipper/mmdb' install -m 0644 mmdb/clipper_mmdb.h '/construction/science/clipper/stage/usr/local/include/clipper/mmdb' /bin/mkdir -p '/construction/science/clipper/stage/usr/local/include/clipper/phs' install -m 0644 phs/phs_io.h '/construction/science/clipper/stage/usr/local/include/clipper/phs' /bin/mkdir -p '/construction/science/clipper/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 '/construction/science/clipper/stage/usr/local/include/clipper' gmake[4]: Leaving directory '/construction/science/clipper/clipper-2.1/clipper' gmake[3]: Leaving directory '/construction/science/clipper/clipper-2.1/clipper' gmake[2]: Leaving directory '/construction/science/clipper/clipper-2.1/clipper' Making install in examples gmake[2]: Entering directory '/construction/science/clipper/clipper-2.1/examples' gmake[3]: Entering directory '/construction/science/clipper/clipper-2.1/examples' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/science/clipper/clipper-2.1/examples' gmake[2]: Leaving directory '/construction/science/clipper/clipper-2.1/examples' gmake[2]: Entering directory '/construction/science/clipper/clipper-2.1' gmake[3]: Entering directory '/construction/science/clipper/clipper-2.1' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/construction/science/clipper/stage/usr/local/lib/pkgconfig' install -m 0644 clipper.pc '/construction/science/clipper/stage/usr/local/lib/pkgconfig' gmake[3]: Leaving directory '/construction/science/clipper/clipper-2.1' gmake[2]: Leaving directory '/construction/science/clipper/clipper-2.1' gmake[1]: Leaving directory '/construction/science/clipper/clipper-2.1' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for clipper-2.1.20180802_1 file sizes/checksums [110]: .. done packing files [110]: .. done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 7 MAR 2019 at 13:00:29 UTC Duration: 00:02:03