/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708 Tue Nov 8 18:29:07 GMT 2016 . ------------------------------------------------------------------------------ . clipper . ------------------------------------------------------------------------------ CPPFLAGS -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include LDFLAGS -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib PKG_CONFIG_PATH /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/pkgconfig now we have LIBS -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: ./configure --prefix=/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python --enable-mmdb=/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python --enable-ccp4=/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python --enable-shared --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-cns CXXFLAGS=-g -O2 -fno-strict-aliasing checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for ar... ar checking the archiver (ar) interface... ar checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 3458764513820540925 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... 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... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux 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... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether to enable maintainer-specific portions of Makefiles... no checking for library containing cos... -lm checking for prefixed single-precision FFTW2 (sfftw.h)... no checking for not prefixed single-precision FFTW2 (fftw.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... no 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: no make all-recursive make[1]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708' Making all in clipper make[2]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper' Making all in core make[3]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core' /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-cell.lo -MD -MP -MF .deps/libclipper_core_la-cell.Tpo -c cell.cpp -o libclipper_core_la-cell.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-nxmap_operator.lo -MD -MP -MF .deps/libclipper_core_la-nxmap_operator.Tpo -c nxmap_operator.cpp -o libclipper_core_la-nxmap_operator.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-atomsf.lo -MD -MP -MF .deps/libclipper_core_la-atomsf.Tpo -c atomsf.cpp -o libclipper_core_la-atomsf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-coords.lo -MD -MP -MF .deps/libclipper_core_la-coords.Tpo -c coords.cpp -o libclipper_core_la-coords.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-cell.Tpo .deps/libclipper_core_la-cell.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-derivs.lo -MD -MP -MF .deps/libclipper_core_la-derivs.Tpo -c -o libclipper_core_la-derivs.lo `test -f 'derivs.cpp' || echo './'`derivs.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 mv -f .deps/libclipper_core_la-nxmap_operator.Tpo .deps/libclipper_core_la-nxmap_operator.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-ramachandran.lo -MD -MP -MF .deps/libclipper_core_la-ramachandran.Tpo -c -o libclipper_core_la-ramachandran.lo `test -f 'ramachandran.cpp' || echo './'`ramachandran.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-ramachandran.lo -MD -MP -MF .deps/libclipper_core_la-ramachandran.Tpo -c ramachandran.cpp -fPIC -DPIC -o .libs/libclipper_core_la-ramachandran.o mv -f .deps/libclipper_core_la-atomsf.Tpo .deps/libclipper_core_la-atomsf.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-derivs.lo -MD -MP -MF .deps/libclipper_core_la-derivs.Tpo -c derivs.cpp -o libclipper_core_la-derivs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-ramachandran.lo -MD -MP -MF .deps/libclipper_core_la-ramachandran.Tpo -c ramachandran.cpp -o libclipper_core_la-ramachandran.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-derivs.Tpo .deps/libclipper_core_la-derivs.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 mv -f .deps/libclipper_core_la-ramachandran.Tpo .deps/libclipper_core_la-ramachandran.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 mv -f .deps/libclipper_core_la-coords.Tpo .deps/libclipper_core_la-coords.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-fftmap.lo -MD -MP -MF .deps/libclipper_core_la-fftmap.Tpo -c fftmap.cpp -o libclipper_core_la-fftmap.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-resol_basisfn.lo -MD -MP -MF .deps/libclipper_core_la-resol_basisfn.Tpo -c resol_basisfn.cpp -o libclipper_core_la-resol_basisfn.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-clipper_instance.lo -MD -MP -MF .deps/libclipper_core_la-clipper_instance.Tpo -c clipper_instance.cpp -o libclipper_core_la-clipper_instance.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-clipper_memory.lo -MD -MP -MF .deps/libclipper_core_la-clipper_memory.Tpo -c clipper_memory.cpp -o libclipper_core_la-clipper_memory.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-resol_basisfn.Tpo .deps/libclipper_core_la-resol_basisfn.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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-fftmap.Tpo .deps/libclipper_core_la-fftmap.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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-clipper_memory.Tpo .deps/libclipper_core_la-clipper_memory.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-clipper_message.lo -MD -MP -MF .deps/libclipper_core_la-clipper_message.Tpo -c clipper_message.cpp -o libclipper_core_la-clipper_message.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-clipper_message.Tpo .deps/libclipper_core_la-clipper_message.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-fftmap_sparse.lo -MD -MP -MF .deps/libclipper_core_la-fftmap_sparse.Tpo -c fftmap_sparse.cpp -o libclipper_core_la-fftmap_sparse.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-resol_fn.lo -MD -MP -MF .deps/libclipper_core_la-resol_fn.Tpo -c resol_fn.cpp -o libclipper_core_la-resol_fn.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-clipper_instance.Tpo .deps/libclipper_core_la-clipper_instance.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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_sparse.Tpo .deps/libclipper_core_la-fftmap_sparse.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-hkl_compute.lo -MD -MP -MF .deps/libclipper_core_la-hkl_compute.Tpo -c hkl_compute.cpp -o libclipper_core_la-hkl_compute.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-clipper_stats.lo -MD -MP -MF .deps/libclipper_core_la-clipper_stats.Tpo -c clipper_stats.cpp -o libclipper_core_la-clipper_stats.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-resol_fn.Tpo .deps/libclipper_core_la-resol_fn.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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_stats.Tpo .deps/libclipper_core_la-clipper_stats.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-resol_targetfn.lo -MD -MP -MF .deps/libclipper_core_la-resol_targetfn.Tpo -c resol_targetfn.cpp -o libclipper_core_la-resol_targetfn.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-hkl_compute.Tpo .deps/libclipper_core_la-hkl_compute.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-clipper_test.lo -MD -MP -MF .deps/libclipper_core_la-clipper_test.Tpo -c clipper_test.cpp -o libclipper_core_la-clipper_test.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-clipper_test.Tpo .deps/libclipper_core_la-clipper_test.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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-resol_targetfn.Tpo .deps/libclipper_core_la-resol_targetfn.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-hkl_data.lo -MD -MP -MF .deps/libclipper_core_la-hkl_data.Tpo -c hkl_data.cpp -o libclipper_core_la-hkl_data.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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-hkl_data.Tpo .deps/libclipper_core_la-hkl_data.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-hkl_datatypes.lo -MD -MP -MF .deps/libclipper_core_la-hkl_datatypes.Tpo -c hkl_datatypes.cpp -o libclipper_core_la-hkl_datatypes.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-rotation.lo -MD -MP -MF .deps/libclipper_core_la-rotation.Tpo -c rotation.cpp -o libclipper_core_la-rotation.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-clipper_types.lo -MD -MP -MF .deps/libclipper_core_la-clipper_types.Tpo -c clipper_types.cpp -o libclipper_core_la-clipper_types.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-hkl_datatypes.Tpo .deps/libclipper_core_la-hkl_datatypes.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-spacegroup.lo -MD -MP -MF .deps/libclipper_core_la-spacegroup.Tpo -c spacegroup.cpp -o libclipper_core_la-spacegroup.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-hkl_info.lo -MD -MP -MF .deps/libclipper_core_la-hkl_info.Tpo -c hkl_info.cpp -o libclipper_core_la-hkl_info.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-clipper_types.Tpo .deps/libclipper_core_la-clipper_types.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-spacegroup_data.lo -MD -MP -MF .deps/libclipper_core_la-spacegroup_data.Tpo -c spacegroup_data.cpp -o libclipper_core_la-spacegroup_data.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-spacegroup_data.Tpo .deps/libclipper_core_la-spacegroup_data.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 mv -f .deps/libclipper_core_la-hkl_info.Tpo .deps/libclipper_core_la-hkl_info.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-clipper_util.lo -MD -MP -MF .deps/libclipper_core_la-clipper_util.Tpo -c clipper_util.cpp -o libclipper_core_la-clipper_util.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-clipper_util.Tpo .deps/libclipper_core_la-clipper_util.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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-spacegroup.Tpo .deps/libclipper_core_la-spacegroup.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-symop.lo -MD -MP -MF .deps/libclipper_core_la-symop.Tpo -c symop.cpp -o libclipper_core_la-symop.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-hkl_lookup.lo -MD -MP -MF .deps/libclipper_core_la-hkl_lookup.Tpo -c hkl_lookup.cpp -o libclipper_core_la-hkl_lookup.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-rotation.Tpo .deps/libclipper_core_la-rotation.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-container.lo -MD -MP -MF .deps/libclipper_core_la-container.Tpo -c container.cpp -o libclipper_core_la-container.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-symop.Tpo .deps/libclipper_core_la-symop.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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-container.Tpo .deps/libclipper_core_la-container.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-map_interp.lo -MD -MP -MF .deps/libclipper_core_la-map_interp.Tpo -c map_interp.cpp -o libclipper_core_la-map_interp.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-container_hkl.lo -MD -MP -MF .deps/libclipper_core_la-container_hkl.Tpo -c container_hkl.cpp -o libclipper_core_la-container_hkl.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-container_map.lo -MD -MP -MF .deps/libclipper_core_la-container_map.Tpo -c container_map.cpp -o libclipper_core_la-container_map.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-map_interp.Tpo .deps/libclipper_core_la-map_interp.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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-container_hkl.Tpo .deps/libclipper_core_la-container_hkl.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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_map.Tpo .deps/libclipper_core_la-container_map.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-map_utils.lo -MD -MP -MF .deps/libclipper_core_la-map_utils.Tpo -c map_utils.cpp -o libclipper_core_la-map_utils.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-container_types.lo -MD -MP -MF .deps/libclipper_core_la-container_types.Tpo -c container_types.cpp -o libclipper_core_la-container_types.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-hkl_operators.lo -MD -MP -MF .deps/libclipper_core_la-hkl_operators.Tpo -c hkl_operators.cpp -o libclipper_core_la-hkl_operators.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-map_utils.Tpo .deps/libclipper_core_la-map_utils.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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-container_types.Tpo .deps/libclipper_core_la-container_types.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-nxmap.lo -MD -MP -MF .deps/libclipper_core_la-nxmap.Tpo -c nxmap.cpp -o libclipper_core_la-nxmap.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-clipper_thread.lo -MD -MP -MF .deps/libclipper_core_la-clipper_thread.Tpo -c clipper_thread.cpp -o libclipper_core_la-clipper_thread.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-clipper_thread.Tpo .deps/libclipper_core_la-clipper_thread.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-xmap.lo -MD -MP -MF .deps/libclipper_core_la-xmap.Tpo -c xmap.cpp -o libclipper_core_la-xmap.o >/dev/null 2>&1 /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 mv -f .deps/libclipper_core_la-nxmap.Tpo .deps/libclipper_core_la-nxmap.Plo /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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-hkl_operators.Tpo .deps/libclipper_core_la-hkl_operators.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-test_data.lo -MD -MP -MF .deps/libclipper_core_la-test_data.Tpo -c test_data.cpp -o libclipper_core_la-test_data.o >/dev/null 2>&1 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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT libclipper_core_la-test_core.lo -MD -MP -MF .deps/libclipper_core_la-test_core.Tpo -c test_core.cpp -o libclipper_core_la-test_core.o >/dev/null 2>&1 mv -f .deps/libclipper_core_la-test_core.Tpo .deps/libclipper_core_la-test_core.Plo /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o libclipper-core.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 -lrfftw -lfftw -lpthread -lm -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/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,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/librfftw.so /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libfftw.so -lpthread -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-core.so.2 -o .libs/libclipper-core.so.2.0.1 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: ar cru .libs/libclipper-core.a libclipper_core_la-atomsf.o libclipper_core_la-coords.o libclipper_core_la-nxmap_operator.o libclipper_core_la-cell.o libclipper_core_la-derivs.o libclipper_core_la-ramachandran.o libclipper_core_la-clipper_instance.o libclipper_core_la-fftmap.o libclipper_core_la-resol_basisfn.o libclipper_core_la-clipper_memory.o libclipper_core_la-fftmap_sparse.o libclipper_core_la-resol_fn.o libclipper_core_la-clipper_message.o libclipper_core_la-hkl_compute.o libclipper_core_la-resol_targetfn.o libclipper_core_la-clipper_stats.o libclipper_core_la-hkl_data.o libclipper_core_la-rotation.o libclipper_core_la-clipper_test.o libclipper_core_la-hkl_datatypes.o libclipper_core_la-spacegroup.o libclipper_core_la-clipper_types.o libclipper_core_la-hkl_info.o libclipper_core_la-spacegroup_data.o libclipper_core_la-clipper_util.o libclipper_core_la-hkl_lookup.o libclipper_core_la-symop.o libclipper_core_la-container.o libclipper_core_la-hkl_operators.o libclipper_core_la-container_hkl.o libclipper_core_la-map_interp.o libclipper_core_la-container_map.o libclipper_core_la-map_utils.o libclipper_core_la-xmap.o libclipper_core_la-container_types.o libclipper_core_la-nxmap.o libclipper_core_la-clipper_thread.o libclipper_core_la-test_core.o libclipper_core_la-test_data.o libtool: link: ranlib .libs/libclipper-core.a libtool: link: ( cd ".libs" && rm -f "libclipper-core.la" && ln -s "../libclipper-core.la" "libclipper-core.la" ) make[3]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core' Making all in contrib make[3]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/contrib' depbase=`echo convolution_search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT sfcalc_obs.lo -MD -MP -MF $depbase.Tpo -c -o sfcalc_obs.lo sfcalc_obs.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT convolution_search.lo -MD -MP -MF .deps/convolution_search.Tpo -c convolution_search.cpp -fPIC -DPIC -o .libs/convolution_search.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT edcalc.lo -MD -MP -MF .deps/edcalc.Tpo -c edcalc.cpp -fPIC -DPIC -o .libs/edcalc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT sfcalc.lo -MD -MP -MF .deps/sfcalc.Tpo -c sfcalc.cpp -fPIC -DPIC -o .libs/sfcalc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT sfcalc_obs.lo -MD -MP -MF .deps/sfcalc_obs.Tpo -c sfcalc_obs.cpp -fPIC -DPIC -o .libs/sfcalc_obs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT convolution_search.lo -MD -MP -MF .deps/convolution_search.Tpo -c convolution_search.cpp -o convolution_search.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT edcalc.lo -MD -MP -MF .deps/edcalc.Tpo -c edcalc.cpp -o edcalc.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT sfcalc_obs.lo -MD -MP -MF .deps/sfcalc_obs.Tpo -c sfcalc_obs.cpp -o sfcalc_obs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT sfcalc.lo -MD -MP -MF .deps/sfcalc.Tpo -c sfcalc.cpp -o sfcalc.o >/dev/null 2>&1 depbase=`echo fffear.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT fffear.lo -MD -MP -MF $depbase.Tpo -c -o fffear.lo fffear.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT fffear.lo -MD -MP -MF .deps/fffear.Tpo -c fffear.cpp -fPIC -DPIC -o .libs/fffear.o depbase=`echo sfscale.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT sfscale.lo -MD -MP -MF $depbase.Tpo -c -o sfscale.lo sfscale.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT sfscale.lo -MD -MP -MF .deps/sfscale.Tpo -c sfscale.cpp -fPIC -DPIC -o .libs/sfscale.o depbase=`echo function_object_bases.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT function_object_bases.lo -MD -MP -MF $depbase.Tpo -c -o function_object_bases.lo function_object_bases.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT function_object_bases.lo -MD -MP -MF .deps/function_object_bases.Tpo -c function_object_bases.cpp -fPIC -DPIC -o .libs/function_object_bases.o depbase=`echo sfweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT sfweight.lo -MD -MP -MF $depbase.Tpo -c -o sfweight.lo sfweight.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT sfweight.lo -MD -MP -MF .deps/sfweight.Tpo -c sfweight.cpp -fPIC -DPIC -o .libs/sfweight.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT function_object_bases.lo -MD -MP -MF .deps/function_object_bases.Tpo -c function_object_bases.cpp -o function_object_bases.o >/dev/null 2>&1 depbase=`echo mapfilter.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT mapfilter.lo -MD -MP -MF $depbase.Tpo -c -o mapfilter.lo mapfilter.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT mapfilter.lo -MD -MP -MF .deps/mapfilter.Tpo -c mapfilter.cpp -fPIC -DPIC -o .libs/mapfilter.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT fffear.lo -MD -MP -MF .deps/fffear.Tpo -c fffear.cpp -o fffear.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT mapfilter.lo -MD -MP -MF .deps/mapfilter.Tpo -c mapfilter.cpp -o mapfilter.o >/dev/null 2>&1 depbase=`echo skeleton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT skeleton.lo -MD -MP -MF $depbase.Tpo -c -o skeleton.lo skeleton.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT skeleton.lo -MD -MP -MF .deps/skeleton.Tpo -c skeleton.cpp -fPIC -DPIC -o .libs/skeleton.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT sfscale.lo -MD -MP -MF .deps/sfscale.Tpo -c sfscale.cpp -o sfscale.o >/dev/null 2>&1 depbase=`echo originmatch.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT originmatch.lo -MD -MP -MF $depbase.Tpo -c -o originmatch.lo originmatch.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT originmatch.lo -MD -MP -MF .deps/originmatch.Tpo -c originmatch.cpp -fPIC -DPIC -o .libs/originmatch.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT skeleton.lo -MD -MP -MF .deps/skeleton.Tpo -c skeleton.cpp -o skeleton.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT originmatch.lo -MD -MP -MF .deps/originmatch.Tpo -c originmatch.cpp -o originmatch.o >/dev/null 2>&1 depbase=`echo test_contrib.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT sfweight.lo -MD -MP -MF .deps/sfweight.Tpo -c sfweight.cpp -o sfweight.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT test_contrib.lo -MD -MP -MF .deps/test_contrib.Tpo -c test_contrib.cpp -fPIC -DPIC -o .libs/test_contrib.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT test_contrib.lo -MD -MP -MF .deps/test_contrib.Tpo -c test_contrib.cpp -o test_contrib.o >/dev/null 2>&1 /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o libclipper-contrib.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/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,/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core/.libs -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib ../core/.libs/libclipper-core.so -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-contrib.so.2 -o .libs/libclipper-contrib.so.2.0.1 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: ar cru .libs/libclipper-contrib.a convolution_search.o sfcalc.o edcalc.o sfcalc_obs.o fffear.o sfscale.o function_object_bases.o sfweight.o mapfilter.o skeleton.o originmatch.o test_contrib.o libtool: link: ranlib .libs/libclipper-contrib.a libtool: link: ( cd ".libs" && rm -f "libclipper-contrib.la" && ln -s "../libclipper-contrib.la" "libclipper-contrib.la" ) make[3]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/contrib' make[3]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper' depbase=`echo mmdb/clipper_mmdb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT mmdb/clipper_mmdb.lo -MD -MP -MF $depbase.Tpo -c -o mmdb/clipper_mmdb.lo mmdb/clipper_mmdb.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo minimol/minimol.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_data.lo -MD -MP -MF $depbase.Tpo -c -o minimol/minimol_data.lo minimol/minimol_data.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/container_minimol.lo -MD -MP -MF minimol/.deps/container_minimol.Tpo -c minimol/container_minimol.cpp -fPIC -DPIC -o minimol/.libs/container_minimol.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol.lo -MD -MP -MF minimol/.deps/minimol.Tpo -c minimol/minimol.cpp -fPIC -DPIC -o minimol/.libs/minimol.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_data.lo -MD -MP -MF minimol/.deps/minimol_data.Tpo -c minimol/minimol_data.cpp -fPIC -DPIC -o minimol/.libs/minimol_data.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT mmdb/clipper_mmdb.lo -MD -MP -MF mmdb/.deps/clipper_mmdb.Tpo -c mmdb/clipper_mmdb.cpp -fPIC -DPIC -o mmdb/.libs/clipper_mmdb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_data.lo -MD -MP -MF minimol/.deps/minimol_data.Tpo -c minimol/minimol_data.cpp -o minimol/minimol_data.o >/dev/null 2>&1 depbase=`echo minimol/minimol_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_io.lo -MD -MP -MF $depbase.Tpo -c -o minimol/minimol_io.lo minimol/minimol_io.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/container_minimol.lo -MD -MP -MF minimol/.deps/container_minimol.Tpo -c minimol/container_minimol.cpp -o minimol/container_minimol.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_io.lo -MD -MP -MF minimol/.deps/minimol_io.Tpo -c minimol/minimol_io.cpp -fPIC -DPIC -o minimol/.libs/minimol_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT mmdb/clipper_mmdb.lo -MD -MP -MF mmdb/.deps/clipper_mmdb.Tpo -c mmdb/clipper_mmdb.cpp -o mmdb/clipper_mmdb.o >/dev/null 2>&1 depbase=`echo minimol/minimol_seq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_seq.lo -MD -MP -MF $depbase.Tpo -c -o minimol/minimol_seq.lo minimol/minimol_seq.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_seq.lo -MD -MP -MF minimol/.deps/minimol_seq.Tpo -c minimol/minimol_seq.cpp -fPIC -DPIC -o minimol/.libs/minimol_seq.o depbase=`echo minimol/minimol_utils.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_utils.lo -MD -MP -MF $depbase.Tpo -c -o minimol/minimol_utils.lo minimol/minimol_utils.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_utils.lo -MD -MP -MF minimol/.deps/minimol_utils.Tpo -c minimol/minimol_utils.cpp -fPIC -DPIC -o minimol/.libs/minimol_utils.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_seq.lo -MD -MP -MF minimol/.deps/minimol_seq.Tpo -c minimol/minimol_seq.cpp -o minimol/minimol_seq.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_io.lo -MD -MP -MF minimol/.deps/minimol_io.Tpo -c minimol/minimol_io.cpp -o minimol/minimol_io.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol.lo -MD -MP -MF minimol/.deps/minimol.Tpo -c minimol/minimol.cpp -o minimol/minimol.o >/dev/null 2>&1 depbase=`echo phs/phs_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT phs/phs_io.lo -MD -MP -MF $depbase.Tpo -c -o phs/phs_io.lo phs/phs_io.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT phs/phs_io.lo -MD -MP -MF phs/.deps/phs_io.Tpo -c phs/phs_io.cpp -fPIC -DPIC -o phs/.libs/phs_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT minimol/minimol_utils.lo -MD -MP -MF minimol/.deps/minimol_utils.Tpo -c minimol/minimol_utils.cpp -o minimol/minimol_utils.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT phs/phs_io.lo -MD -MP -MF phs/.deps/phs_io.Tpo -c phs/phs_io.cpp -o phs/phs_io.o >/dev/null 2>&1 depbase=`echo cif/cif_data_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT cif/cif_data_io.lo -MD -MP -MF cif/.deps/cif_data_io.Tpo -c cif/cif_data_io.cpp -fPIC -DPIC -o cif/.libs/cif_data_io.o depbase=`echo ccp4/ccp4_mtz_types.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT ccp4/ccp4_mtz_types.lo -MD -MP -MF ccp4/.deps/ccp4_mtz_types.Tpo -c ccp4/ccp4_mtz_types.cpp -fPIC -DPIC -o ccp4/.libs/ccp4_mtz_types.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT ccp4/ccp4_mtz_types.lo -MD -MP -MF ccp4/.deps/ccp4_mtz_types.Tpo -c ccp4/ccp4_mtz_types.cpp -o ccp4/ccp4_mtz_types.o >/dev/null 2>&1 depbase=`echo ccp4/ccp4_mtz_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT ccp4/ccp4_mtz_io.lo -MD -MP -MF ccp4/.deps/ccp4_mtz_io.Tpo -c ccp4/ccp4_mtz_io.cpp -fPIC -DPIC -o ccp4/.libs/ccp4_mtz_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT ccp4/ccp4_map_io.lo -MD -MP -MF ccp4/.deps/ccp4_map_io.Tpo -c ccp4/ccp4_map_io.cpp -fPIC -DPIC -o ccp4/.libs/ccp4_map_io.o depbase=`echo ccp4/ccp4_utils.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT ccp4/ccp4_utils.lo -MD -MP -MF $depbase.Tpo -c -o ccp4/ccp4_utils.lo ccp4/ccp4_utils.cpp &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT ccp4/ccp4_utils.lo -MD -MP -MF ccp4/.deps/ccp4_utils.Tpo -c ccp4/ccp4_utils.cpp -fPIC -DPIC -o ccp4/.libs/ccp4_utils.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT ccp4/ccp4_utils.lo -MD -MP -MF ccp4/.deps/ccp4_utils.Tpo -c ccp4/ccp4_utils.cpp -o ccp4/ccp4_utils.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT cif/cif_data_io.lo -MD -MP -MF cif/.deps/cif_data_io.Tpo -c cif/cif_data_io.cpp -o cif/cif_data_io.o >/dev/null 2>&1 depbase=`echo cns/cns_hkl_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT cns/cns_hkl_io.lo -MD -MP -MF cns/.deps/cns_hkl_io.Tpo -c cns/cns_hkl_io.cpp -fPIC -DPIC -o cns/.libs/cns_hkl_io.o depbase=`echo cns/cns_map_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT cns/cns_hkl_io.lo -MD -MP -MF cns/.deps/cns_hkl_io.Tpo -c cns/cns_hkl_io.cpp -o cns/cns_hkl_io.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT ccp4/ccp4_map_io.lo -MD -MP -MF ccp4/.deps/ccp4_map_io.Tpo -c ccp4/ccp4_map_io.cpp -o ccp4/ccp4_map_io.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o mmdb/libclipper-mmdb.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib mmdb/clipper_mmdb.lo core/libclipper-core.la -lmmdb2 -lm -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbeginS.o mmdb/.libs/clipper_mmdb.o -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core/.libs -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib core/.libs/libclipper-core.so /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libmmdb2.so -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-mmdb.so.2 -o mmdb/.libs/libclipper-mmdb.so.2.0.1 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: ar cru mmdb/.libs/libclipper-mmdb.a mmdb/clipper_mmdb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT ccp4/ccp4_mtz_io.lo -MD -MP -MF ccp4/.deps/ccp4_mtz_io.Tpo -c ccp4/ccp4_mtz_io.cpp -o ccp4/ccp4_mtz_io.o >/dev/null 2>&1 libtool: link: ranlib mmdb/.libs/libclipper-mmdb.a 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 g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o phs/libclipper-phs.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib phs/phs_io.lo core/libclipper-core.la -lm -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbeginS.o phs/.libs/phs_io.o -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core/.libs -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib core/.libs/libclipper-core.so -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-phs.so.2 -o phs/.libs/libclipper-phs.so.2.0.1 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: ar cru phs/.libs/libclipper-phs.a phs/phs_io.o libtool: link: ranlib phs/.libs/libclipper-phs.a libtool: link: ( cd "phs/.libs" && rm -f "libclipper-phs.la" && ln -s "../libclipper-phs.la" "libclipper-phs.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o cif/libclipper-cif.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib cif/cif_data_io.lo core/libclipper-core.la -lmmdb2 -lm -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbeginS.o cif/.libs/cif_data_io.o -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core/.libs -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib core/.libs/libclipper-core.so /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libmmdb2.so -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-cif.so.2 -o cif/.libs/libclipper-cif.so.2.0.1 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: ar cru cif/.libs/libclipper-cif.a cif/cif_data_io.o libtool: link: ranlib cif/.libs/libclipper-cif.a 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 g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o minimol/libclipper-minimol.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/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,/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core/.libs -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/mmdb/.libs -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib core/.libs/libclipper-core.so mmdb/.libs/libclipper-mmdb.so /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libmmdb2.so -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-minimol.so.2 -o minimol/.libs/libclipper-minimol.so.2.0.1 libtool: link: (cd "minimol/.libs" && rm -f "libclipper-minimol.so.2" && ln -s "libclipper-minimol.so.2.0.1" "libclipper-minimol.so.2") libtool: link: (cd "minimol/.libs" && rm -f "libclipper-minimol.so" && ln -s "libclipper-minimol.so.2.0.1" "libclipper-minimol.so") libtool: link: ar cru minimol/.libs/libclipper-minimol.a minimol/minimol.o minimol/container_minimol.o minimol/minimol_data.o minimol/minimol_io.o minimol/minimol_seq.o minimol/minimol_utils.o libtool: link: ranlib minimol/.libs/libclipper-minimol.a libtool: link: ( cd "minimol/.libs" && rm -f "libclipper-minimol.la" && ln -s "../libclipper-minimol.la" "libclipper-minimol.la" ) libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include -g -O2 -fno-strict-aliasing -MT cns/cns_map_io.lo -MD -MP -MF cns/.deps/cns_map_io.Tpo -c cns/cns_map_io.cpp -o cns/cns_map_io.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o ccp4/libclipper-ccp4.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/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,/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core/.libs -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib core/.libs/libclipper-core.so /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libccp4c.so -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-ccp4.so.2 -o ccp4/.libs/libclipper-ccp4.so.2.0.1 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: ar cru ccp4/.libs/libclipper-ccp4.a ccp4/ccp4_mtz_types.o ccp4/ccp4_mtz_io.o ccp4/ccp4_map_io.o ccp4/ccp4_utils.o libtool: link: ranlib ccp4/.libs/libclipper-ccp4.a 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 g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o cns/libclipper-cns.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib cns/cns_hkl_io.lo cns/cns_map_io.lo core/libclipper-core.la -lm -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbeginS.o cns/.libs/cns_hkl_io.o cns/.libs/cns_map_io.o -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core/.libs -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib core/.libs/libclipper-core.so -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-cns.so.2 -o cns/.libs/libclipper-cns.so.2.0.1 libtool: link: (cd "cns/.libs" && rm -f "libclipper-cns.so.2" && ln -s "libclipper-cns.so.2.0.1" "libclipper-cns.so.2") libtool: link: (cd "cns/.libs" && rm -f "libclipper-cns.so" && ln -s "libclipper-cns.so.2.0.1" "libclipper-cns.so") libtool: link: ar cru cns/.libs/libclipper-cns.a cns/cns_hkl_io.o cns/cns_map_io.o libtool: link: ranlib cns/.libs/libclipper-cns.a libtool: link: ( cd "cns/.libs" && rm -f "libclipper-cns.la" && ln -s "../libclipper-cns.la" "libclipper-cns.la" ) make[3]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper' make[2]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper' Making all in examples make[2]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/examples' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/examples' make[2]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708' make[2]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708' make[1]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708' Making install in clipper make[1]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper' Making install in core make[2]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core' make[3]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/core' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib' /bin/sh ../../libtool --mode=install /usr/bin/install -c libclipper-core.la '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib' /usr/bin/install -c -m 644 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 '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/core' libtool: install: /usr/bin/install -c .libs/libclipper-core.so.2.0.1 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-core.so.2.0.1 /usr/bin/install -c -m 644 test_data.h '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/core' libtool: install: (cd /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-core.la libtool: install: /usr/bin/install -c .libs/libclipper-core.a /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-core.a libtool: install: chmod 644 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-core.a libtool: install: ranlib /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-core.a libtool: finish: PATH="/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/bin:/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2/bin:/lmb/home/pemsley/bin:/lmb/home/sharp/buster_snapshot_200616/scripts:/lmb/home/sharp/buster_snapshot_200616/MakeTNT/bin:/lmb/home/sharp/buster_snapshot_200616/autoBUSTER/bin/linux64:/lmb/home/sharp/buster_snapshot_200616/scripts:/lmb/home/sharp/sharp-2.8/scripts:/public/xtal/CCP4/ccp4-64/Prerelease/bin:/public/xtal/linux-bin:/public/xtal/bin:/lmb/home/public/xtal/dials/dials-dev20160923/build/bin:/public/xtal/Coot:/lmb/home/public/xtal/autoPROC-1.0/autoPROC/bin/linux64:/lmb/home/public/xtal/Phenix/Phenix64/phenix-1.11.1-2575/build/bin:/public/xtal/cns/cns_solve_1.3_mp/intel-x86_64bit-linux/bin:/public/xtal/cns/cns_solve_1.3_mp/intel-x86_64bit-linux/utils:.:/lmb/home/public/xtal/main2015/:/lmb/home/public/xtal/main2015//prog:/lmb/home/public/xtal/main2015//config:/lmb/home/public/xtal/CCP4/ccp4-64/arp_warp_7.6/bin/bin-x86_64-Linux:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-7.0/etc:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-7.0/bin:/public/ImageMagick/latest/bin:/gridware/sge/bin/lx24-amd64:/bin:/usr/bin:/usr/local/bin:/public/com:/public/bin/noarch:/public/bin/i686:/lmb/home/pemsley/bzr:/lmb/home/pemsley/scsh/bin:/lmb/home/pemsley/bin:/lmb/home/flong/workplace/LIBG/bin:/lmb/home/pemsley/glade/bin:/lmb/home/pemsley/vim/bin:/lmb/home/pemsley/gqview/bin:/lmb/home/pemsley/bin.Linux:/lmb/home/pemsley/x86_64-linux/bin:/lmb/home/pemsley/build/bin:/lmb/home/pemsley/build/Linux/bin:/usr/sbin:/usr/X11R6/bin:/usr/bin/X11:/lmb/home/public/CSD/bin:/public/xtal/vmd:/public/xtal/Raster3D/Raster3D_2.5f/bin:/public/xtal/situs/Situs_2.6.3/bin:/public/xtal/mafft/mafft-6.240/scripts:/public/xtal/mafft/mafft-6.240/binaries:/public/xtal/script:/public/xtal/imosflm/src:/lmb/home/public/xtal/CCP4/clustalw-2.0.9/bin:/lmb/home/public/xtal/CCP4/fasta-35.4.1/bin:/lmb/home/public/xtal/CCP4/graphviz-2.20.2/bin:/public/xtal/HKL:/public/xtal/XDS-versions/current:/public/xtal/XDS-versions/share:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the 'LD_RUN_PATH' environment variable during linking - use the '-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to '/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[3]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core' make[2]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/core' Making install in contrib make[2]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/contrib' make[3]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/contrib' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/contrib' /bin/sh ../../libtool --mode=install /usr/bin/install -c libclipper-contrib.la '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib' /usr/bin/install -c -m 644 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 '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/contrib' libtool: warning: relinking 'libclipper-contrib.la' libtool: install: (cd /lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/contrib; /bin/sh "/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/libtool" --tag CXX --mode=relink g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o libclipper-contrib.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: ) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/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,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -lclipper-core -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-contrib.so.2 -o .libs/libclipper-contrib.so.2.0.1 libtool: install: /usr/bin/install -c .libs/libclipper-contrib.so.2.0.1T /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-contrib.so.2.0.1 libtool: install: (cd /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-contrib.la libtool: install: /usr/bin/install -c .libs/libclipper-contrib.a /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-contrib.a libtool: install: chmod 644 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-contrib.a libtool: install: ranlib /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-contrib.a libtool: finish: PATH="/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/bin:/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2/bin:/lmb/home/pemsley/bin:/lmb/home/sharp/buster_snapshot_200616/scripts:/lmb/home/sharp/buster_snapshot_200616/MakeTNT/bin:/lmb/home/sharp/buster_snapshot_200616/autoBUSTER/bin/linux64:/lmb/home/sharp/buster_snapshot_200616/scripts:/lmb/home/sharp/sharp-2.8/scripts:/public/xtal/CCP4/ccp4-64/Prerelease/bin:/public/xtal/linux-bin:/public/xtal/bin:/lmb/home/public/xtal/dials/dials-dev20160923/build/bin:/public/xtal/Coot:/lmb/home/public/xtal/autoPROC-1.0/autoPROC/bin/linux64:/lmb/home/public/xtal/Phenix/Phenix64/phenix-1.11.1-2575/build/bin:/public/xtal/cns/cns_solve_1.3_mp/intel-x86_64bit-linux/bin:/public/xtal/cns/cns_solve_1.3_mp/intel-x86_64bit-linux/utils:.:/lmb/home/public/xtal/main2015/:/lmb/home/public/xtal/main2015//prog:/lmb/home/public/xtal/main2015//config:/lmb/home/public/xtal/CCP4/ccp4-64/arp_warp_7.6/bin/bin-x86_64-Linux:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-7.0/etc:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-7.0/bin:/public/ImageMagick/latest/bin:/gridware/sge/bin/lx24-amd64:/bin:/usr/bin:/usr/local/bin:/public/com:/public/bin/noarch:/public/bin/i686:/lmb/home/pemsley/bzr:/lmb/home/pemsley/scsh/bin:/lmb/home/pemsley/bin:/lmb/home/flong/workplace/LIBG/bin:/lmb/home/pemsley/glade/bin:/lmb/home/pemsley/vim/bin:/lmb/home/pemsley/gqview/bin:/lmb/home/pemsley/bin.Linux:/lmb/home/pemsley/x86_64-linux/bin:/lmb/home/pemsley/build/bin:/lmb/home/pemsley/build/Linux/bin:/usr/sbin:/usr/X11R6/bin:/usr/bin/X11:/lmb/home/public/CSD/bin:/public/xtal/vmd:/public/xtal/Raster3D/Raster3D_2.5f/bin:/public/xtal/situs/Situs_2.6.3/bin:/public/xtal/mafft/mafft-6.240/scripts:/public/xtal/mafft/mafft-6.240/binaries:/public/xtal/script:/public/xtal/imosflm/src:/lmb/home/public/xtal/CCP4/clustalw-2.0.9/bin:/lmb/home/public/xtal/CCP4/fasta-35.4.1/bin:/lmb/home/public/xtal/CCP4/graphviz-2.20.2/bin:/public/xtal/HKL:/public/xtal/XDS-versions/current:/public/xtal/XDS-versions/share:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the 'LD_RUN_PATH' environment variable during linking - use the '-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to '/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[3]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/contrib' make[2]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper/contrib' make[2]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper' make[3]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/ccp4' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/cif' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib' /usr/bin/install -c -m 644 cif/cif_data_io.h '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/cif' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/cns' /usr/bin/install -c -m 644 ccp4/ccp4_map_io.h ccp4/ccp4_mtz_io.h ccp4/ccp4_mtz_types.h ccp4/ccp4_utils.h '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/ccp4' /usr/bin/install -c -m 644 cns/cns_hkl_io.h cns/cns_map_io.h '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/cns' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/minimol' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/mmdb' /usr/bin/install -c -m 644 minimol/container_minimol.h minimol/minimol_data.h minimol/minimol_seq.h minimol/minimol.h minimol/minimol_io.h minimol/minimol_utils.h '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/minimol' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/phs' /usr/bin/install -c -m 644 mmdb/clipper_mmdb.h '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/mmdb' /usr/bin/install -c -m 644 phs/phs_io.h '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper/phs' /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper' /usr/bin/install -c -m 644 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 '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/include/clipper' libtool: warning: relinking 'mmdb/libclipper-mmdb.la' libtool: install: (cd /lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper; /bin/sh "/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/libtool" --tag CXX --mode=relink g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o mmdb/libclipper-mmdb.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib mmdb/clipper_mmdb.lo core/libclipper-core.la -lmmdb2 -lm -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: ) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbeginS.o mmdb/.libs/clipper_mmdb.o -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -lclipper-core -lmmdb2 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-mmdb.so.2 -o mmdb/.libs/libclipper-mmdb.so.2.0.1 libtool: install: /usr/bin/install -c mmdb/.libs/libclipper-mmdb.so.2.0.1T /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-mmdb.so.2.0.1 libtool: install: (cd /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-mmdb.la libtool: warning: relinking 'minimol/libclipper-minimol.la' libtool: install: (cd /lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper; /bin/sh "/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/libtool" --tag CXX --mode=relink g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o minimol/libclipper-minimol.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: ) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/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,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -lclipper-core -lclipper-mmdb -lmmdb2 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-minimol.so.2 -o minimol/.libs/libclipper-minimol.so.2.0.1 libtool: install: /usr/bin/install -c minimol/.libs/libclipper-minimol.so.2.0.1T /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-minimol.so.2.0.1 libtool: install: (cd /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-minimol.la libtool: warning: relinking 'phs/libclipper-phs.la' libtool: install: (cd /lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper; /bin/sh "/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/libtool" --tag CXX --mode=relink g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o phs/libclipper-phs.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib phs/phs_io.lo core/libclipper-core.la -lm -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: ) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbeginS.o phs/.libs/phs_io.o -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -lclipper-core -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-phs.so.2 -o phs/.libs/libclipper-phs.so.2.0.1 libtool: install: /usr/bin/install -c phs/.libs/libclipper-phs.so.2.0.1T /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-phs.so.2.0.1 libtool: install: (cd /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-phs.la libtool: warning: relinking 'cif/libclipper-cif.la' libtool: install: (cd /lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper; /bin/sh "/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/libtool" --tag CXX --mode=relink g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o cif/libclipper-cif.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib cif/cif_data_io.lo core/libclipper-core.la -lmmdb2 -lm -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: ) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbeginS.o cif/.libs/cif_data_io.o -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -lclipper-core -lmmdb2 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-cif.so.2 -o cif/.libs/libclipper-cif.so.2.0.1 libtool: install: /usr/bin/install -c cif/.libs/libclipper-cif.so.2.0.1T /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-cif.so.2.0.1 libtool: install: (cd /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-cif.la libtool: warning: relinking 'ccp4/libclipper-ccp4.la' libtool: install: (cd /lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper; /bin/sh "/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/libtool" --tag CXX --mode=relink g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o ccp4/libclipper-ccp4.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: ) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/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,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -lclipper-core -lccp4c -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-ccp4.so.2 -o ccp4/.libs/libclipper-ccp4.so.2.0.1 libtool: install: /usr/bin/install -c ccp4/.libs/libclipper-ccp4.so.2.0.1T /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-ccp4.so.2.0.1 libtool: install: (cd /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-ccp4.la libtool: warning: relinking 'cns/libclipper-cns.la' libtool: install: (cd /lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper; /bin/sh "/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/libtool" --tag CXX --mode=relink g++ -g -O2 -fno-strict-aliasing -version-info 2:1 -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -o cns/libclipper-cns.la -rpath /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib cns/cns_hkl_io.lo cns/cns_map_io.lo core/libclipper-core.la -lm -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: ) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbeginS.o cns/.libs/cns_hkl_io.o cns/.libs/cns_map_io.o -Wl,-rpath -Wl,/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib -lclipper-core -L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib:-L/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib: -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o -g -O2 -Wl,-soname -Wl,libclipper-cns.so.2 -o cns/.libs/libclipper-cns.so.2.0.1 libtool: install: /usr/bin/install -c cns/.libs/libclipper-cns.so.2.0.1T /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-cns.so.2.0.1 libtool: install: (cd /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/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 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-cns.la libtool: install: /usr/bin/install -c mmdb/.libs/libclipper-mmdb.a /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-mmdb.a libtool: install: chmod 644 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-mmdb.a libtool: install: ranlib /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-mmdb.a libtool: install: /usr/bin/install -c minimol/.libs/libclipper-minimol.a /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-minimol.a libtool: install: chmod 644 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-minimol.a libtool: install: ranlib /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-minimol.a libtool: install: /usr/bin/install -c phs/.libs/libclipper-phs.a /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-phs.a libtool: install: chmod 644 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-phs.a libtool: install: ranlib /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-phs.a libtool: install: /usr/bin/install -c cif/.libs/libclipper-cif.a /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-cif.a libtool: install: chmod 644 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-cif.a libtool: install: ranlib /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-cif.a libtool: install: /usr/bin/install -c ccp4/.libs/libclipper-ccp4.a /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-ccp4.a libtool: install: chmod 644 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-ccp4.a libtool: install: ranlib /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-ccp4.a libtool: install: /usr/bin/install -c cns/.libs/libclipper-cns.a /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-cns.a libtool: install: chmod 644 /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-cns.a libtool: install: ranlib /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/libclipper-cns.a libtool: finish: PATH="/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/bin:/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2/bin:/lmb/home/pemsley/bin:/lmb/home/sharp/buster_snapshot_200616/scripts:/lmb/home/sharp/buster_snapshot_200616/MakeTNT/bin:/lmb/home/sharp/buster_snapshot_200616/autoBUSTER/bin/linux64:/lmb/home/sharp/buster_snapshot_200616/scripts:/lmb/home/sharp/sharp-2.8/scripts:/public/xtal/CCP4/ccp4-64/Prerelease/bin:/public/xtal/linux-bin:/public/xtal/bin:/lmb/home/public/xtal/dials/dials-dev20160923/build/bin:/public/xtal/Coot:/lmb/home/public/xtal/autoPROC-1.0/autoPROC/bin/linux64:/lmb/home/public/xtal/Phenix/Phenix64/phenix-1.11.1-2575/build/bin:/public/xtal/cns/cns_solve_1.3_mp/intel-x86_64bit-linux/bin:/public/xtal/cns/cns_solve_1.3_mp/intel-x86_64bit-linux/utils:.:/lmb/home/public/xtal/main2015/:/lmb/home/public/xtal/main2015//prog:/lmb/home/public/xtal/main2015//config:/lmb/home/public/xtal/CCP4/ccp4-64/arp_warp_7.6/bin/bin-x86_64-Linux:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-7.0/etc:/lmb/home/public/xtal/CCP4/ccp4-64/ccp4-7.0/bin:/public/ImageMagick/latest/bin:/gridware/sge/bin/lx24-amd64:/bin:/usr/bin:/usr/local/bin:/public/com:/public/bin/noarch:/public/bin/i686:/lmb/home/pemsley/bzr:/lmb/home/pemsley/scsh/bin:/lmb/home/pemsley/bin:/lmb/home/flong/workplace/LIBG/bin:/lmb/home/pemsley/glade/bin:/lmb/home/pemsley/vim/bin:/lmb/home/pemsley/gqview/bin:/lmb/home/pemsley/bin.Linux:/lmb/home/pemsley/x86_64-linux/bin:/lmb/home/pemsley/build/bin:/lmb/home/pemsley/build/Linux/bin:/usr/sbin:/usr/X11R6/bin:/usr/bin/X11:/lmb/home/public/CSD/bin:/public/xtal/vmd:/public/xtal/Raster3D/Raster3D_2.5f/bin:/public/xtal/situs/Situs_2.6.3/bin:/public/xtal/mafft/mafft-6.240/scripts:/public/xtal/mafft/mafft-6.240/binaries:/public/xtal/script:/public/xtal/imosflm/src:/lmb/home/public/xtal/CCP4/clustalw-2.0.9/bin:/lmb/home/public/xtal/CCP4/fasta-35.4.1/bin:/lmb/home/public/xtal/CCP4/graphviz-2.20.2/bin:/public/xtal/HKL:/public/xtal/XDS-versions/current:/public/xtal/XDS-versions/share:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc:/sbin" ldconfig -n /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib ---------------------------------------------------------------------- Libraries have been installed in: /lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the 'LD_RUN_PATH' environment variable during linking - use the '-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to '/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[3]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper' make[2]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper' make[1]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/clipper' Making install in examples make[1]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/examples' make[2]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/examples' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/examples' make[1]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708/examples' make[1]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708' make[2]: Entering directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708' make[2]: Nothing to be done for `install-exec-am'. /bin/mkdir -p '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/pkgconfig' /usr/bin/install -c -m 644 clipper.pc '/lmb/home/pemsley/autobuild/Linux-hal-scientific-linux-6.8-el-gtk2-python/lib/pkgconfig' make[2]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708' make[1]: Leaving directory `/lmb/home/pemsley/autobuild/building/hal.lmb.internal_2016-11-08__T18_28_04/clipper-2.1.20160708'