------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gmp-6.2.0.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/mpfr-4.0.2.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/mpc-1.1.0_2.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/gettext-runtime-0.20.1.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/binutils-2.33.1_2,1.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/gcc8-8.4.0.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor ===== Message from gcc8-8.4.0: -- 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/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/gmake-4.2.1_3.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/mmdb2-2.0.20.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/libccp4-6.5.1_4.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/fftw-float-2.1.5_22.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor ===== Message from fftw-float-2.1.5_22: -- ===> 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 UNFLAVORED devel/binutils -> use devel/binutils@native UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:16 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> clipper-2.1.20180802_3 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> clipper-2.1.20180802_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by clipper-2.1.20180802_3 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> clipper-2.1.20180802_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by clipper-2.1.20180802_3 for building => SHA256 Checksum OK for clipper-2.1.20180802.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> clipper-2.1.20180802_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by clipper-2.1.20180802_3 for building ===> Extracting for clipper-2.1.20180802_3 => SHA256 Checksum OK for clipper-2.1.20180802.tar.gz. Extracted Memory Use: 12.68M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for clipper-2.1.20180802_3 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> clipper-2.1.20180802_3 depends on executable: gfortran8 - found ===> clipper-2.1.20180802_3 depends on executable: gmake - found ===> clipper-2.1.20180802_3 depends on file: /usr/local/bin/as - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> clipper-2.1.20180802_3 depends on shared library: libccp4c.so - found (/usr/local/lib/libccp4c.so) ===> clipper-2.1.20180802_3 depends on shared library: libmmdb2.so - found (/usr/local/lib/libmmdb2.so) ===> clipper-2.1.20180802_3 depends on shared library: libsfftw.so - found (/usr/local/lib/libsfftw.so) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> clipper-2.1.20180802_3 depends on executable: gfortran8 - found ===> clipper-2.1.20180802_3 depends on executable: gmake - found ===> clipper-2.1.20180802_3 depends on file: /usr/local/bin/as - found ===> clipper-2.1.20180802_3 depends on shared library: libccp4c.so - found (/usr/local/lib/libccp4c.so) ===> clipper-2.1.20180802_3 depends on shared library: libmmdb2.so - found (/usr/local/lib/libmmdb2.so) ===> clipper-2.1.20180802_3 depends on shared library: libsfftw.so - found (/usr/local/lib/libsfftw.so) ===> Configuring for clipper-2.1.20180802_3 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-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 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-dragonfly5.9 file names to x86_64-portbld-dragonfly5.9 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly5.9 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... dragonfly5.9 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... dragonfly5.9 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 gfortran8 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 gfortran8 option to produce PIC... -fPIC checking if gfortran8 PIC flag -fPIC works... yes checking if gfortran8 static flag -static works... yes checking if gfortran8 supports -c -o file.o... yes checking if gfortran8 supports -c -o file.o... (cached) yes checking whether the gfortran8 linker (/usr/local/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... dragonfly5.9 ld.so checking how to hardcode library paths into programs... immediate checking how to get verbose linking output from gfortran8... -v checking for Fortran 77 libraries of gfortran8... -L/usr/local/lib/gcc8 -L/usr/local/lib -L/usr/local/bin -L/usr/local/lib/gcc8/gcc/x86_64-portbld-dragonfly5.9/8.4.0 -L/usr/local/lib/gcc8/gcc/x86_64-portbld-dragonfly5.9/8.4.0/../../../../../x86_64-portbld-dragonfly5.9/lib -L/usr/local/lib/gcc8/gcc/x86_64-portbld-dragonfly5.9/8.4.0/../../.. -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 SUCCEEDED 00:00:12 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for clipper-2.1.20180802_3 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 /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 /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-clipper_instance.lo -MD -MP -MF .deps/libclipper_core_la-clipper_instance.Tpo -c -o libclipper_core_la-clipper_instance.lo `test -f 'clipper_instance.cpp' || echo './'`clipper_instance.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-fftmap.lo -MD -MP -MF .deps/libclipper_core_la-fftmap.Tpo -c -o libclipper_core_la-fftmap.lo `test -f 'fftmap.cpp' || echo './'`fftmap.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-resol_basisfn.lo -MD -MP -MF .deps/libclipper_core_la-resol_basisfn.Tpo -c -o libclipper_core_la-resol_basisfn.lo `test -f 'resol_basisfn.cpp' || echo './'`resol_basisfn.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-clipper_memory.lo -MD -MP -MF .deps/libclipper_core_la-clipper_memory.Tpo -c -o libclipper_core_la-clipper_memory.lo `test -f 'clipper_memory.cpp' || echo './'`clipper_memory.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-clipper_instance.lo -MD -MP -MF .deps/libclipper_core_la-clipper_instance.Tpo -c clipper_instance.cpp -fPIC -DPIC -o .libs/libclipper_core_la-clipper_instance.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-fftmap.lo -MD -MP -MF .deps/libclipper_core_la-fftmap.Tpo -c fftmap.cpp -fPIC -DPIC -o .libs/libclipper_core_la-fftmap.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-clipper_memory.lo -MD -MP -MF .deps/libclipper_core_la-clipper_memory.Tpo -c clipper_memory.cpp -fPIC -DPIC -o .libs/libclipper_core_la-clipper_memory.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-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-ramachandran.lo -MD -MP -MF .deps/libclipper_core_la-ramachandran.Tpo -c ramachandran.cpp -fPIC -DPIC -o .libs/libclipper_core_la-ramachandran.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 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-resol_basisfn.lo -MD -MP -MF .deps/libclipper_core_la-resol_basisfn.Tpo -c resol_basisfn.cpp -fPIC -DPIC -o .libs/libclipper_core_la-resol_basisfn.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-fftmap_sparse.lo -MD -MP -MF .deps/libclipper_core_la-fftmap_sparse.Tpo -c -o libclipper_core_la-fftmap_sparse.lo `test -f 'fftmap_sparse.cpp' || echo './'`fftmap_sparse.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-fftmap_sparse.lo -MD -MP -MF .deps/libclipper_core_la-fftmap_sparse.Tpo -c fftmap_sparse.cpp -fPIC -DPIC -o .libs/libclipper_core_la-fftmap_sparse.o mv -f .deps/libclipper_core_la-nxmap_operator.Tpo .deps/libclipper_core_la-nxmap_operator.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-resol_fn.lo -MD -MP -MF .deps/libclipper_core_la-resol_fn.Tpo -c -o libclipper_core_la-resol_fn.lo `test -f 'resol_fn.cpp' || echo './'`resol_fn.cpp mv -f .deps/libclipper_core_la-clipper_memory.Tpo .deps/libclipper_core_la-clipper_memory.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-clipper_message.lo -MD -MP -MF .deps/libclipper_core_la-clipper_message.Tpo -c -o libclipper_core_la-clipper_message.lo `test -f 'clipper_message.cpp' || echo './'`clipper_message.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-clipper_message.lo -MD -MP -MF .deps/libclipper_core_la-clipper_message.Tpo -c clipper_message.cpp -fPIC -DPIC -o .libs/libclipper_core_la-clipper_message.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-resol_fn.lo -MD -MP -MF .deps/libclipper_core_la-resol_fn.Tpo -c resol_fn.cpp -fPIC -DPIC -o .libs/libclipper_core_la-resol_fn.o 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../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libclipper_core_la-hkl_compute.lo -MD -MP -MF .deps/libclipper_core_la-hkl_compute.Tpo -c -o libclipper_core_la-hkl_compute.lo `test -f 'hkl_compute.cpp' || echo './'`hkl_compute.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-hkl_compute.lo -MD -MP -MF .deps/libclipper_core_la-hkl_compute.Tpo -c hkl_compute.cpp -fPIC -DPIC -o .libs/libclipper_core_la-hkl_compute.o mv -f .deps/libclipper_core_la-resol_basisfn.Tpo .deps/libclipper_core_la-resol_basisfn.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-resol_targetfn.lo -MD -MP -MF .deps/libclipper_core_la-resol_targetfn.Tpo -c -o libclipper_core_la-resol_targetfn.lo `test -f 'resol_targetfn.cpp' || echo './'`resol_targetfn.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-resol_targetfn.lo -MD -MP -MF .deps/libclipper_core_la-resol_targetfn.Tpo -c resol_targetfn.cpp -fPIC -DPIC -o .libs/libclipper_core_la-resol_targetfn.o mv -f .deps/libclipper_core_la-fftmap.Tpo .deps/libclipper_core_la-fftmap.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-clipper_stats.lo -MD -MP -MF .deps/libclipper_core_la-clipper_stats.Tpo -c -o libclipper_core_la-clipper_stats.lo `test -f 'clipper_stats.cpp' || echo './'`clipper_stats.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-clipper_stats.lo -MD -MP -MF .deps/libclipper_core_la-clipper_stats.Tpo -c clipper_stats.cpp -fPIC -DPIC -o .libs/libclipper_core_la-clipper_stats.o mv -f .deps/libclipper_core_la-cell.Tpo .deps/libclipper_core_la-cell.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-hkl_data.lo -MD -MP -MF .deps/libclipper_core_la-hkl_data.Tpo -c -o libclipper_core_la-hkl_data.lo `test -f 'hkl_data.cpp' || echo './'`hkl_data.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-hkl_data.lo -MD -MP -MF .deps/libclipper_core_la-hkl_data.Tpo -c hkl_data.cpp -fPIC -DPIC -o .libs/libclipper_core_la-hkl_data.o mv -f .deps/libclipper_core_la-clipper_message.Tpo .deps/libclipper_core_la-clipper_message.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-rotation.lo -MD -MP -MF .deps/libclipper_core_la-rotation.Tpo -c -o libclipper_core_la-rotation.lo `test -f 'rotation.cpp' || echo './'`rotation.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-rotation.lo -MD -MP -MF .deps/libclipper_core_la-rotation.Tpo -c rotation.cpp -fPIC -DPIC -o .libs/libclipper_core_la-rotation.o mv -f .deps/libclipper_core_la-ramachandran.Tpo .deps/libclipper_core_la-ramachandran.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-clipper_test.lo -MD -MP -MF .deps/libclipper_core_la-clipper_test.Tpo -c -o libclipper_core_la-clipper_test.lo `test -f 'clipper_test.cpp' || echo './'`clipper_test.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-clipper_test.lo -MD -MP -MF .deps/libclipper_core_la-clipper_test.Tpo -c clipper_test.cpp -fPIC -DPIC -o .libs/libclipper_core_la-clipper_test.o mv -f .deps/libclipper_core_la-clipper_stats.Tpo .deps/libclipper_core_la-clipper_stats.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-hkl_datatypes.lo -MD -MP -MF .deps/libclipper_core_la-hkl_datatypes.Tpo -c -o libclipper_core_la-hkl_datatypes.lo `test -f 'hkl_datatypes.cpp' || echo './'`hkl_datatypes.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-hkl_datatypes.lo -MD -MP -MF .deps/libclipper_core_la-hkl_datatypes.Tpo -c hkl_datatypes.cpp -fPIC -DPIC -o .libs/libclipper_core_la-hkl_datatypes.o mv -f .deps/libclipper_core_la-fftmap_sparse.Tpo .deps/libclipper_core_la-fftmap_sparse.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-spacegroup.lo -MD -MP -MF .deps/libclipper_core_la-spacegroup.Tpo -c -o libclipper_core_la-spacegroup.lo `test -f 'spacegroup.cpp' || echo './'`spacegroup.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-spacegroup.lo -MD -MP -MF .deps/libclipper_core_la-spacegroup.Tpo -c spacegroup.cpp -fPIC -DPIC -o .libs/libclipper_core_la-spacegroup.o mv -f .deps/libclipper_core_la-clipper_test.Tpo .deps/libclipper_core_la-clipper_test.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-clipper_types.lo -MD -MP -MF .deps/libclipper_core_la-clipper_types.Tpo -c -o libclipper_core_la-clipper_types.lo `test -f 'clipper_types.cpp' || echo './'`clipper_types.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-clipper_types.lo -MD -MP -MF .deps/libclipper_core_la-clipper_types.Tpo -c clipper_types.cpp -fPIC -DPIC -o .libs/libclipper_core_la-clipper_types.o mv -f .deps/libclipper_core_la-resol_targetfn.Tpo .deps/libclipper_core_la-resol_targetfn.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-hkl_info.lo -MD -MP -MF .deps/libclipper_core_la-hkl_info.Tpo -c -o libclipper_core_la-hkl_info.lo `test -f 'hkl_info.cpp' || echo './'`hkl_info.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-hkl_info.lo -MD -MP -MF .deps/libclipper_core_la-hkl_info.Tpo -c hkl_info.cpp -fPIC -DPIC -o .libs/libclipper_core_la-hkl_info.o mv -f .deps/libclipper_core_la-resol_fn.Tpo .deps/libclipper_core_la-resol_fn.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-spacegroup_data.lo -MD -MP -MF .deps/libclipper_core_la-spacegroup_data.Tpo -c -o libclipper_core_la-spacegroup_data.lo `test -f 'spacegroup_data.cpp' || echo './'`spacegroup_data.cpp mv -f .deps/libclipper_core_la-hkl_data.Tpo .deps/libclipper_core_la-hkl_data.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-clipper_util.lo -MD -MP -MF .deps/libclipper_core_la-clipper_util.Tpo -c -o libclipper_core_la-clipper_util.lo `test -f 'clipper_util.cpp' || echo './'`clipper_util.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-spacegroup_data.lo -MD -MP -MF .deps/libclipper_core_la-spacegroup_data.Tpo -c spacegroup_data.cpp -fPIC -DPIC -o .libs/libclipper_core_la-spacegroup_data.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-clipper_util.lo -MD -MP -MF .deps/libclipper_core_la-clipper_util.Tpo -c clipper_util.cpp -fPIC -DPIC -o .libs/libclipper_core_la-clipper_util.o mv -f .deps/libclipper_core_la-hkl_compute.Tpo .deps/libclipper_core_la-hkl_compute.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-hkl_lookup.lo -MD -MP -MF .deps/libclipper_core_la-hkl_lookup.Tpo -c -o libclipper_core_la-hkl_lookup.lo `test -f 'hkl_lookup.cpp' || echo './'`hkl_lookup.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-hkl_lookup.lo -MD -MP -MF .deps/libclipper_core_la-hkl_lookup.Tpo -c hkl_lookup.cpp -fPIC -DPIC -o .libs/libclipper_core_la-hkl_lookup.o mv -f .deps/libclipper_core_la-clipper_instance.Tpo .deps/libclipper_core_la-clipper_instance.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-symop.lo -MD -MP -MF .deps/libclipper_core_la-symop.Tpo -c -o libclipper_core_la-symop.lo `test -f 'symop.cpp' || echo './'`symop.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-symop.lo -MD -MP -MF .deps/libclipper_core_la-symop.Tpo -c symop.cpp -fPIC -DPIC -o .libs/libclipper_core_la-symop.o mv -f .deps/libclipper_core_la-clipper_util.Tpo .deps/libclipper_core_la-clipper_util.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-container.lo -MD -MP -MF .deps/libclipper_core_la-container.Tpo -c -o libclipper_core_la-container.lo `test -f 'container.cpp' || echo './'`container.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-container.lo -MD -MP -MF .deps/libclipper_core_la-container.Tpo -c container.cpp -fPIC -DPIC -o .libs/libclipper_core_la-container.o mv -f .deps/libclipper_core_la-spacegroup_data.Tpo .deps/libclipper_core_la-spacegroup_data.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-hkl_operators.lo -MD -MP -MF .deps/libclipper_core_la-hkl_operators.Tpo -c -o libclipper_core_la-hkl_operators.lo `test -f 'hkl_operators.cpp' || echo './'`hkl_operators.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-hkl_operators.lo -MD -MP -MF .deps/libclipper_core_la-hkl_operators.Tpo -c hkl_operators.cpp -fPIC -DPIC -o .libs/libclipper_core_la-hkl_operators.o mv -f .deps/libclipper_core_la-coords.Tpo .deps/libclipper_core_la-coords.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-container_hkl.lo -MD -MP -MF .deps/libclipper_core_la-container_hkl.Tpo -c -o libclipper_core_la-container_hkl.lo `test -f 'container_hkl.cpp' || echo './'`container_hkl.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-container_hkl.lo -MD -MP -MF .deps/libclipper_core_la-container_hkl.Tpo -c container_hkl.cpp -fPIC -DPIC -o .libs/libclipper_core_la-container_hkl.o mv -f .deps/libclipper_core_la-hkl_lookup.Tpo .deps/libclipper_core_la-hkl_lookup.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-map_interp.lo -MD -MP -MF .deps/libclipper_core_la-map_interp.Tpo -c -o libclipper_core_la-map_interp.lo `test -f 'map_interp.cpp' || echo './'`map_interp.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-map_interp.lo -MD -MP -MF .deps/libclipper_core_la-map_interp.Tpo -c map_interp.cpp -fPIC -DPIC -o .libs/libclipper_core_la-map_interp.o mv -f .deps/libclipper_core_la-hkl_datatypes.Tpo .deps/libclipper_core_la-hkl_datatypes.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-container_map.lo -MD -MP -MF .deps/libclipper_core_la-container_map.Tpo -c -o libclipper_core_la-container_map.lo `test -f 'container_map.cpp' || echo './'`container_map.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-container_map.lo -MD -MP -MF .deps/libclipper_core_la-container_map.Tpo -c container_map.cpp -fPIC -DPIC -o .libs/libclipper_core_la-container_map.o mv -f .deps/libclipper_core_la-symop.Tpo .deps/libclipper_core_la-symop.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-map_utils.lo -MD -MP -MF .deps/libclipper_core_la-map_utils.Tpo -c -o libclipper_core_la-map_utils.lo `test -f 'map_utils.cpp' || echo './'`map_utils.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-map_utils.lo -MD -MP -MF .deps/libclipper_core_la-map_utils.Tpo -c map_utils.cpp -fPIC -DPIC -o .libs/libclipper_core_la-map_utils.o mv -f .deps/libclipper_core_la-hkl_info.Tpo .deps/libclipper_core_la-hkl_info.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-xmap.lo -MD -MP -MF .deps/libclipper_core_la-xmap.Tpo -c -o libclipper_core_la-xmap.lo `test -f 'xmap.cpp' || echo './'`xmap.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-xmap.lo -MD -MP -MF .deps/libclipper_core_la-xmap.Tpo -c xmap.cpp -fPIC -DPIC -o .libs/libclipper_core_la-xmap.o mv -f .deps/libclipper_core_la-container.Tpo .deps/libclipper_core_la-container.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-container_types.lo -MD -MP -MF .deps/libclipper_core_la-container_types.Tpo -c -o libclipper_core_la-container_types.lo `test -f 'container_types.cpp' || echo './'`container_types.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-container_types.lo -MD -MP -MF .deps/libclipper_core_la-container_types.Tpo -c container_types.cpp -fPIC -DPIC -o .libs/libclipper_core_la-container_types.o mv -f .deps/libclipper_core_la-container_hkl.Tpo .deps/libclipper_core_la-container_hkl.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-nxmap.lo -MD -MP -MF .deps/libclipper_core_la-nxmap.Tpo -c -o libclipper_core_la-nxmap.lo `test -f 'nxmap.cpp' || echo './'`nxmap.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-nxmap.lo -MD -MP -MF .deps/libclipper_core_la-nxmap.Tpo -c nxmap.cpp -fPIC -DPIC -o .libs/libclipper_core_la-nxmap.o mv -f .deps/libclipper_core_la-map_interp.Tpo .deps/libclipper_core_la-map_interp.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-clipper_thread.lo -MD -MP -MF .deps/libclipper_core_la-clipper_thread.Tpo -c -o libclipper_core_la-clipper_thread.lo `test -f 'clipper_thread.cpp' || echo './'`clipper_thread.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-clipper_thread.lo -MD -MP -MF .deps/libclipper_core_la-clipper_thread.Tpo -c clipper_thread.cpp -fPIC -DPIC -o .libs/libclipper_core_la-clipper_thread.o mv -f .deps/libclipper_core_la-container_map.Tpo .deps/libclipper_core_la-container_map.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-test_core.lo -MD -MP -MF .deps/libclipper_core_la-test_core.Tpo -c -o libclipper_core_la-test_core.lo `test -f 'test_core.cpp' || echo './'`test_core.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-test_core.lo -MD -MP -MF .deps/libclipper_core_la-test_core.Tpo -c test_core.cpp -fPIC -DPIC -o .libs/libclipper_core_la-test_core.o mv -f .deps/libclipper_core_la-clipper_thread.Tpo .deps/libclipper_core_la-clipper_thread.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-test_data.lo -MD -MP -MF .deps/libclipper_core_la-test_data.Tpo -c -o libclipper_core_la-test_data.lo `test -f 'test_data.cpp' || echo './'`test_data.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-test_data.lo -MD -MP -MF .deps/libclipper_core_la-test_data.Tpo -c test_data.cpp -fPIC -DPIC -o .libs/libclipper_core_la-test_data.o mv -f .deps/libclipper_core_la-map_utils.Tpo .deps/libclipper_core_la-map_utils.Plo mv -f .deps/libclipper_core_la-container_types.Tpo .deps/libclipper_core_la-container_types.Plo mv -f .deps/libclipper_core_la-nxmap.Tpo .deps/libclipper_core_la-nxmap.Plo mv -f .deps/libclipper_core_la-hkl_operators.Tpo .deps/libclipper_core_la-hkl_operators.Plo mv -f .deps/libclipper_core_la-clipper_types.Tpo .deps/libclipper_core_la-clipper_types.Plo mv -f .deps/libclipper_core_la-spacegroup.Tpo .deps/libclipper_core_la-spacegroup.Plo mv -f .deps/libclipper_core_la-rotation.Tpo .deps/libclipper_core_la-rotation.Plo mv -f .deps/libclipper_core_la-xmap.Tpo .deps/libclipper_core_la-xmap.Plo mv -f .deps/libclipper_core_la-test_data.Tpo .deps/libclipper_core_la-test_data.Plo mv -f .deps/libclipper_core_la-test_core.Tpo .deps/libclipper_core_la-test_core.Plo /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/gcc8 -L/usr/local/lib/gcc8 -B/usr/local/bin -L/usr/local/lib -o libclipper-core.la -rpath /usr/local/lib libclipper_core_la-atomsf.lo libclipper_core_la-coords.lo libclipper_core_la-nxmap_operator.lo libclipper_core_la-cell.lo libclipper_core_la-derivs.lo libclipper_core_la-ramachandran.lo libclipper_core_la-clipper_instance.lo libclipper_core_la-fftmap.lo libclipper_core_la-resol_basisfn.lo libclipper_core_la-clipper_memory.lo libclipper_core_la-fftmap_sparse.lo libclipper_core_la-resol_fn.lo libclipper_core_la-clipper_message.lo libclipper_core_la-hkl_compute.lo libclipper_core_la-resol_targetfn.lo libclipper_core_la-clipper_stats.lo libclipper_core_la-hkl_data.lo libclipper_core_la-rotation.lo libclipper_core_la-clipper_test.lo libclipper_core_la-hkl_datatypes.lo libclipper_core_la-spacegroup.lo libclipper_core_la-clipper_types.lo libclipper_core_la-hkl_info.lo libclipper_core_la-spacegroup_data.lo libclipper_core_la-clipper_util.lo libclipper_core_la-hkl_lookup.lo libclipper_core_la-symop.lo libclipper_core_la-container.lo libclipper_core_la-hkl_operators.lo libclipper_core_la-container_hkl.lo libclipper_core_la-map_interp.lo libclipper_core_la-container_map.lo libclipper_core_la-map_utils.lo libclipper_core_la-xmap.lo libclipper_core_la-container_types.lo libclipper_core_la-nxmap.lo libclipper_core_la-clipper_thread.lo libclipper_core_la-test_core.lo libclipper_core_la-test_data.lo -lsrfftw -lsfftw -lpthread -lm libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o .libs/libclipper_core_la-atomsf.o .libs/libclipper_core_la-coords.o .libs/libclipper_core_la-nxmap_operator.o .libs/libclipper_core_la-cell.o .libs/libclipper_core_la-derivs.o .libs/libclipper_core_la-ramachandran.o .libs/libclipper_core_la-clipper_instance.o .libs/libclipper_core_la-fftmap.o .libs/libclipper_core_la-resol_basisfn.o .libs/libclipper_core_la-clipper_memory.o .libs/libclipper_core_la-fftmap_sparse.o .libs/libclipper_core_la-resol_fn.o .libs/libclipper_core_la-clipper_message.o .libs/libclipper_core_la-hkl_compute.o .libs/libclipper_core_la-resol_targetfn.o .libs/libclipper_core_la-clipper_stats.o .libs/libclipper_core_la-hkl_data.o .libs/libclipper_core_la-rotation.o .libs/libclipper_core_la-clipper_test.o .libs/libclipper_core_la-hkl_datatypes.o .libs/libclipper_core_la-spacegroup.o .libs/libclipper_core_la-clipper_types.o .libs/libclipper_core_la-hkl_info.o .libs/libclipper_core_la-spacegroup_data.o .libs/libclipper_core_la-clipper_util.o .libs/libclipper_core_la-hkl_lookup.o .libs/libclipper_core_la-symop.o .libs/libclipper_core_la-container.o .libs/libclipper_core_la-hkl_operators.o .libs/libclipper_core_la-container_hkl.o .libs/libclipper_core_la-map_interp.o .libs/libclipper_core_la-container_map.o .libs/libclipper_core_la-map_utils.o .libs/libclipper_core_la-xmap.o .libs/libclipper_core_la-container_types.o .libs/libclipper_core_la-nxmap.o .libs/libclipper_core_la-clipper_thread.o .libs/libclipper_core_la-test_core.o .libs/libclipper_core_la-test_data.o -Wl,-rpath -Wl,/usr/local/lib -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc8 -L/usr/local/lib /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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-core.so.2 -o .libs/libclipper-core.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) libtool: link: (cd ".libs" && rm -f "libclipper-core.so.2" && ln -s "libclipper-core.so.2.0.1" "libclipper-core.so.2") libtool: link: (cd ".libs" && rm -f "libclipper-core.so" && ln -s "libclipper-core.so.2.0.1" "libclipper-core.so") libtool: link: ( cd ".libs" && rm -f "libclipper-core.la" && ln -s "../libclipper-core.la" "libclipper-core.la" ) gmake[4]: Leaving directory '/construction/science/clipper/clipper-2.1/clipper/core' Making all in contrib gmake[4]: Entering directory '/construction/science/clipper/clipper-2.1/clipper/contrib' depbase=`echo convolution_search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 convolution_search.lo -MD -MP -MF $depbase.Tpo -c -o convolution_search.lo convolution_search.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo sfcalc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 sfcalc.lo -MD -MP -MF $depbase.Tpo -c -o sfcalc.lo sfcalc.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo edcalc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 edcalc.lo -MD -MP -MF $depbase.Tpo -c -o edcalc.lo edcalc.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo sfcalc_obs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 sfcalc_obs.lo -MD -MP -MF $depbase.Tpo -c -o sfcalc_obs.lo sfcalc_obs.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo fffear.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 fffear.lo -MD -MP -MF $depbase.Tpo -c -o fffear.lo fffear.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo sfscale.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 sfscale.lo -MD -MP -MF $depbase.Tpo -c -o sfscale.lo sfscale.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo function_object_bases.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 function_object_bases.lo -MD -MP -MF $depbase.Tpo -c -o function_object_bases.lo function_object_bases.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo sfweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 sfweight.lo -MD -MP -MF $depbase.Tpo -c -o sfweight.lo sfweight.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo mapfilter.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 mapfilter.lo -MD -MP -MF $depbase.Tpo -c -o mapfilter.lo mapfilter.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT edcalc.lo -MD -MP -MF .deps/edcalc.Tpo -c edcalc.cpp -fPIC -DPIC -o .libs/edcalc.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT sfcalc_obs.lo -MD -MP -MF .deps/sfcalc_obs.Tpo -c sfcalc_obs.cpp -fPIC -DPIC -o .libs/sfcalc_obs.o depbase=`echo skeleton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 skeleton.lo -MD -MP -MF $depbase.Tpo -c -o skeleton.lo skeleton.cpp &&\ mv -f $depbase.Tpo $depbase.Plo 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 sfweight.lo -MD -MP -MF .deps/sfweight.Tpo -c sfweight.cpp -fPIC -DPIC -o .libs/sfweight.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 sfcalc.lo -MD -MP -MF .deps/sfcalc.Tpo -c sfcalc.cpp -fPIC -DPIC -o .libs/sfcalc.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 convolution_search.lo -MD -MP -MF .deps/convolution_search.Tpo -c convolution_search.cpp -fPIC -DPIC -o .libs/convolution_search.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 fffear.lo -MD -MP -MF .deps/fffear.Tpo -c fffear.cpp -fPIC -DPIC -o .libs/fffear.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 skeleton.lo -MD -MP -MF .deps/skeleton.Tpo -c skeleton.cpp -fPIC -DPIC -o .libs/skeleton.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 mapfilter.lo -MD -MP -MF .deps/mapfilter.Tpo -c mapfilter.cpp -fPIC -DPIC -o .libs/mapfilter.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 function_object_bases.lo -MD -MP -MF .deps/function_object_bases.Tpo -c function_object_bases.cpp -fPIC -DPIC -o .libs/function_object_bases.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 sfscale.lo -MD -MP -MF .deps/sfscale.Tpo -c sfscale.cpp -fPIC -DPIC -o .libs/sfscale.o depbase=`echo originmatch.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 originmatch.lo -MD -MP -MF $depbase.Tpo -c -o originmatch.lo originmatch.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT originmatch.lo -MD -MP -MF .deps/originmatch.Tpo -c originmatch.cpp -fPIC -DPIC -o .libs/originmatch.o depbase=`echo test_contrib.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /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 test_contrib.lo -MD -MP -MF $depbase.Tpo -c -o test_contrib.lo test_contrib.cpp &&\ mv -f $depbase.Tpo $depbase.Plo 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 test_contrib.lo -MD -MP -MF .deps/test_contrib.Tpo -c test_contrib.cpp -fPIC -DPIC -o .libs/test_contrib.o /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/gcc8 -L/usr/local/lib/gcc8 -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 libtool: link: 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,/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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-contrib.so.2 -o .libs/libclipper-contrib.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) libtool: link: (cd ".libs" && rm -f "libclipper-contrib.so.2" && ln -s "libclipper-contrib.so.2.0.1" "libclipper-contrib.so.2") libtool: link: (cd ".libs" && rm -f "libclipper-contrib.so" && ln -s "libclipper-contrib.so.2.0.1" "libclipper-contrib.so") libtool: link: ( cd ".libs" && rm -f "libclipper-contrib.la" && ln -s "../libclipper-contrib.la" "libclipper-contrib.la" ) gmake[4]: Leaving directory '/construction/science/clipper/clipper-2.1/clipper/contrib' gmake[4]: Entering directory '/construction/science/clipper/clipper-2.1/clipper' depbase=`echo phs/phs_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT phs/phs_io.lo -MD -MP -MF $depbase.Tpo -c -o phs/phs_io.lo phs/phs_io.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cif/cif_data_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT cif/cif_data_io.lo -MD -MP -MF $depbase.Tpo -c -o cif/cif_data_io.lo cif/cif_data_io.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ccp4/ccp4_mtz_types.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ccp4/ccp4_mtz_types.lo -MD -MP -MF $depbase.Tpo -c -o ccp4/ccp4_mtz_types.lo ccp4/ccp4_mtz_types.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ccp4/ccp4_mtz_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ccp4/ccp4_mtz_io.lo -MD -MP -MF $depbase.Tpo -c -o ccp4/ccp4_mtz_io.lo ccp4/ccp4_mtz_io.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ccp4/ccp4_map_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ccp4/ccp4_map_io.lo -MD -MP -MF $depbase.Tpo -c -o ccp4/ccp4_map_io.lo ccp4/ccp4_map_io.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ccp4/ccp4_utils.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ccp4/ccp4_utils.lo -MD -MP -MF $depbase.Tpo -c -o ccp4/ccp4_utils.lo ccp4/ccp4_utils.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo fortran/f_interface.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT fortran/f_interface.lo -MD -MP -MF $depbase.Tpo -c -o fortran/f_interface.lo fortran/f_interface.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo minimol/minimol.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/minimol.lo -MD -MP -MF $depbase.Tpo -c -o minimol/minimol.lo minimol/minimol.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo minimol/container_minimol.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/container_minimol.lo -MD -MP -MF $depbase.Tpo -c -o minimol/container_minimol.lo minimol/container_minimol.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo minimol/minimol_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/minimol_data.lo -MD -MP -MF $depbase.Tpo -c -o minimol/minimol_data.lo minimol/minimol_data.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ccp4/ccp4_mtz_io.lo -MD -MP -MF ccp4/.deps/ccp4_mtz_io.Tpo -c ccp4/ccp4_mtz_io.cpp -fPIC -DPIC -o ccp4/.libs/ccp4_mtz_io.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT phs/phs_io.lo -MD -MP -MF phs/.deps/phs_io.Tpo -c phs/phs_io.cpp -fPIC -DPIC -o phs/.libs/phs_io.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ccp4/ccp4_utils.lo -MD -MP -MF ccp4/.deps/ccp4_utils.Tpo -c ccp4/ccp4_utils.cpp -fPIC -DPIC -o ccp4/.libs/ccp4_utils.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ccp4/ccp4_mtz_types.lo -MD -MP -MF ccp4/.deps/ccp4_mtz_types.Tpo -c ccp4/ccp4_mtz_types.cpp -fPIC -DPIC -o ccp4/.libs/ccp4_mtz_types.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT fortran/f_interface.lo -MD -MP -MF fortran/.deps/f_interface.Tpo -c fortran/f_interface.cpp -fPIC -DPIC -o fortran/.libs/f_interface.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/minimol.lo -MD -MP -MF minimol/.deps/minimol.Tpo -c minimol/minimol.cpp -fPIC -DPIC -o minimol/.libs/minimol.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/minimol_data.lo -MD -MP -MF minimol/.deps/minimol_data.Tpo -c minimol/minimol_data.cpp -fPIC -DPIC -o minimol/.libs/minimol_data.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ccp4/ccp4_map_io.lo -MD -MP -MF ccp4/.deps/ccp4_map_io.Tpo -c ccp4/ccp4_map_io.cpp -fPIC -DPIC -o ccp4/.libs/ccp4_map_io.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/container_minimol.lo -MD -MP -MF minimol/.deps/container_minimol.Tpo -c minimol/container_minimol.cpp -fPIC -DPIC -o minimol/.libs/container_minimol.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT cif/cif_data_io.lo -MD -MP -MF cif/.deps/cif_data_io.Tpo -c cif/cif_data_io.cpp -fPIC -DPIC -o cif/.libs/cif_data_io.o depbase=`echo minimol/minimol_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/minimol_io.lo -MD -MP -MF $depbase.Tpo -c -o minimol/minimol_io.lo minimol/minimol_io.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/minimol_io.lo -MD -MP -MF minimol/.deps/minimol_io.Tpo -c minimol/minimol_io.cpp -fPIC -DPIC -o minimol/.libs/minimol_io.o depbase=`echo minimol/minimol_seq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/minimol_seq.lo -MD -MP -MF $depbase.Tpo -c -o minimol/minimol_seq.lo minimol/minimol_seq.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/minimol_seq.lo -MD -MP -MF minimol/.deps/minimol_seq.Tpo -c minimol/minimol_seq.cpp -fPIC -DPIC -o minimol/.libs/minimol_seq.o depbase=`echo minimol/minimol_utils.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/minimol_utils.lo -MD -MP -MF $depbase.Tpo -c -o minimol/minimol_utils.lo minimol/minimol_utils.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT minimol/minimol_utils.lo -MD -MP -MF minimol/.deps/minimol_utils.Tpo -c minimol/minimol_utils.cpp -fPIC -DPIC -o minimol/.libs/minimol_utils.o /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -version-info 2:1 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -B/usr/local/bin -L/usr/local/lib -o phs/libclipper-phs.la -rpath /usr/local/lib phs/phs_io.lo core/libclipper-core.la -lm depbase=`echo cns/cns_hkl_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT cns/cns_hkl_io.lo -MD -MP -MF $depbase.Tpo -c -o cns/cns_hkl_io.lo cns/cns_hkl_io.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o phs/.libs/phs_io.o -Wl,-rpath -Wl,/construction/science/clipper/clipper-2.1/clipper/core/.libs -Wl,-rpath -Wl,/usr/local/lib -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc8 -L/usr/local/lib core/.libs/libclipper-core.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lpthread -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -O2 -Wl,-rpath=/usr/local/lib/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-phs.so.2 -o phs/.libs/libclipper-phs.so.2.0.1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT cns/cns_hkl_io.lo -MD -MP -MF cns/.deps/cns_hkl_io.Tpo -c cns/cns_hkl_io.cpp -fPIC -DPIC -o cns/.libs/cns_hkl_io.o /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) libtool: link: (cd "phs/.libs" && rm -f "libclipper-phs.so.2" && ln -s "libclipper-phs.so.2.0.1" "libclipper-phs.so.2") libtool: link: (cd "phs/.libs" && rm -f "libclipper-phs.so" && ln -s "libclipper-phs.so.2.0.1" "libclipper-phs.so") libtool: link: ( cd "phs/.libs" && rm -f "libclipper-phs.la" && ln -s "../libclipper-phs.la" "libclipper-phs.la" ) depbase=`echo cns/cns_map_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT cns/cns_map_io.lo -MD -MP -MF $depbase.Tpo -c -o cns/cns_map_io.lo cns/cns_map_io.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT cns/cns_map_io.lo -MD -MP -MF cns/.deps/cns_map_io.Tpo -c cns/cns_map_io.cpp -fPIC -DPIC -o cns/.libs/cns_map_io.o depbase=`echo mmdb/clipper_mmdb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT mmdb/clipper_mmdb.lo -MD -MP -MF $depbase.Tpo -c -o mmdb/clipper_mmdb.lo mmdb/clipper_mmdb.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT mmdb/clipper_mmdb.lo -MD -MP -MF mmdb/.deps/clipper_mmdb.Tpo -c mmdb/clipper_mmdb.cpp -fPIC -DPIC -o mmdb/.libs/clipper_mmdb.o /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/gcc8 -L/usr/local/lib/gcc8 -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 libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o fortran/.libs/f_interface.o -Wl,-rpath -Wl,/construction/science/clipper/clipper-2.1/clipper/core/.libs -Wl,-rpath -Wl,/construction/science/clipper/clipper-2.1/clipper/contrib/.libs -Wl,-rpath -Wl,/usr/local/lib -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-fortran.so.2 -o fortran/.libs/libclipper-fortran.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) 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/gcc8 -L/usr/local/lib/gcc8 -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 libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o cif/.libs/cif_data_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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-cif.so.2 -o cif/.libs/libclipper-cif.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) libtool: link: (cd "cif/.libs" && rm -f "libclipper-cif.so.2" && ln -s "libclipper-cif.so.2.0.1" "libclipper-cif.so.2") libtool: link: (cd "cif/.libs" && rm -f "libclipper-cif.so" && ln -s "libclipper-cif.so.2.0.1" "libclipper-cif.so") libtool: link: ( cd "cif/.libs" && rm -f "libclipper-cif.la" && ln -s "../libclipper-cif.la" "libclipper-cif.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/gcc8 -L/usr/local/lib/gcc8 -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 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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-mmdb.so.2 -o mmdb/.libs/libclipper-mmdb.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) libtool: link: (cd "mmdb/.libs" && rm -f "libclipper-mmdb.so.2" && ln -s "libclipper-mmdb.so.2.0.1" "libclipper-mmdb.so.2") libtool: link: (cd "mmdb/.libs" && rm -f "libclipper-mmdb.so" && ln -s "libclipper-mmdb.so.2.0.1" "libclipper-mmdb.so") libtool: link: ( cd "mmdb/.libs" && rm -f "libclipper-mmdb.la" && ln -s "../libclipper-mmdb.la" "libclipper-mmdb.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/gcc8 -L/usr/local/lib/gcc8 -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: 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,/construction/science/clipper/clipper-2.1/clipper/core/.libs -Wl,-rpath -Wl,/construction/science/clipper/clipper-2.1/clipper/mmdb/.libs -Wl,-rpath -Wl,/usr/local/lib -Wl,-rpath -Wl,/usr/local/lib -L/usr/local/lib/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-minimol.so.2 -o minimol/.libs/libclipper-minimol.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) 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/gcc8 -L/usr/local/lib/gcc8 -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 ccp4/.libs/ccp4_mtz_io.o ccp4/.libs/ccp4_map_io.o ccp4/.libs/ccp4_utils.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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-ccp4.so.2 -o ccp4/.libs/libclipper-ccp4.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) libtool: link: (cd "ccp4/.libs" && rm -f "libclipper-ccp4.so.2" && ln -s "libclipper-ccp4.so.2.0.1" "libclipper-ccp4.so.2") libtool: link: (cd "ccp4/.libs" && rm -f "libclipper-ccp4.so" && ln -s "libclipper-ccp4.so.2.0.1" "libclipper-ccp4.so") libtool: link: ( cd "ccp4/.libs" && rm -f "libclipper-ccp4.la" && ln -s "../libclipper-ccp4.la" "libclipper-ccp4.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/gcc8 -L/usr/local/lib/gcc8 -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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-cns.so.2 -o cns/.libs/libclipper-cns.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) 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]: 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' SUCCEEDED 00:00:58 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> clipper-2.1.20180802_3 depends on executable: gfortran8 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for clipper-2.1.20180802_3 ===> clipper-2.1.20180802_3 depends on executable: gfortran8 - found ===> 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/gcc8 -L/usr/local/lib/gcc8 -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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-contrib.so.2 -o .libs/libclipper-contrib.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) 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/gcc8 -L/usr/local/lib/gcc8 -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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-mmdb.so.2 -o mmdb/.libs/libclipper-mmdb.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) 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/gcc8 -L/usr/local/lib/gcc8 -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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-minimol.so.2 -o minimol/.libs/libclipper-minimol.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) 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/gcc8 -L/usr/local/lib/gcc8 -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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-phs.so.2 -o phs/.libs/libclipper-phs.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) 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/gcc8 -L/usr/local/lib/gcc8 -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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-cif.so.2 -o cif/.libs/libclipper-cif.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) 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/gcc8 -L/usr/local/lib/gcc8 -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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-ccp4.so.2 -o ccp4/.libs/libclipper-ccp4.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) 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/gcc8 -L/usr/local/lib/gcc8 -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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-cns.so.2 -o cns/.libs/libclipper-cns.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) 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/gcc8 -L/usr/local/lib/gcc8 -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/gcc8 -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/gcc8 -B/usr/local/bin -Wl,-soname -Wl,libclipper-fortran.so.2 -o fortran/.libs/libclipper-fortran.so.2.0.1 /usr/local/bin/ld: /usr/lib/libc.so: .dynsym local symbol at index 8 (>= sh_info of 6) 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) ====> Running Q/A tests (stage-qa) Warning: 'lib/libclipper-core.so.2.0.1' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/libclipper-cns.so.2.0.1' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/libclipper-minimol.so.2.0.1' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/libclipper-phs.so.2.0.1' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/libclipper-cif.so.2.0.1' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/libclipper-fortran.so.2.0.1' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/libclipper-mmdb.so.2.0.1' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/libclipper-ccp4.so.2.0.1' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/libclipper-contrib.so.2.0.1' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:05 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for clipper-2.1.20180802_3 file sizes/checksums [107]: 0% file sizes/checksums [107]: 93% file sizes/checksums [107]: 100% packing files [107]: 0% packing files [107]: 93% packing files [107]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:05 TOTAL TIME 00:01:39