Build log

coot-0.6.2:20110808-145204.log (text/plain), 231.43 KB, created by Diego Elio Pettenò (RETIRED) on 2011-08-08 15:30:26 UTC

 * Package:    sci-chemistry/coot-0.6.2
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        elibc_glibc kernel_linux openmp test userland_GNU x86
 * FEATURES:   sandbox test userpriv usersandbox
>>> Unpacking source...
>>> Unpacking coot-0.6.2.tar.gz to /var/tmp/portage/sci-chemistry/coot-0.6.2/work
>>> Unpacking greg-data-0.6.2.tar.gz to /var/tmp/portage/sci-chemistry/coot-0.6.2/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/coot-0.6.2/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2 ...
 * Applying 0.6.2-clipper-config.patch ...
 [ ok ]
 * Applying 0.6.2-mmdb-config.patch ...
 [ ok ]
 * Applying 0.6.2-gl.patch ...
 [ ok ]
 * Applying 0.6.2-test.patch ...
 [ ok ]
 * Applying 0.6.2-ssm.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2' ...
 * Running aclocal -I macros ...
 [ ok ]
 * Running libtoolize --copy --force --install --automake ...
 [ ok ]
 * Running aclocal -I macros ...
 [ ok ]
 * Running autoconf ...
 [ ok ]
 * Running automake --add-missing --copy ...
 [ ok ]
 * Running elibtoolize in: coot-0.6.2/
 *   Applying portage-1.2.0.patch ...
 *   Applying sed-1.5.6.patch ...
 *   Applying as-needed-2.2.6.patch ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2 ...
 * econf: updating coot-0.6.2/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating coot-0.6.2/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --includedir=${prefix}/include/coot --with-gtkcanvas-prefix=/usr --with-gtkgl-prefix=/usr --with-guile --with-python=/usr --with-guile-gtk --with-gtk2 --with-pygtk --enable-openmp
configure: loading site script /usr/share/config.site
configure: loading site script /usr/share/crossdev/include/site/linux
configure: loading site script /usr/share/crossdev/include/site/i686-linux-gnu
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 for style of include used by make... GNU
checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-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 i686-pc-linux-gnu-gcc accepts -g... yes
checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking dependency style of i686-pc-linux-gnu-gcc... gcc3
checking for library containing strerror... none required
checking for i686-pc-linux-gnu-gcc... (cached) i686-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether i686-pc-linux-gnu-gcc accepts -g... (cached) yes
checking for i686-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed
checking dependency style of i686-pc-linux-gnu-gcc... (cached) gcc3
checking for i686-pc-linux-gnu-gcc... (cached) i686-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether i686-pc-linux-gnu-gcc accepts -g... (cached) yes
checking for i686-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed
checking dependency style of i686-pc-linux-gnu-gcc... (cached) gcc3
checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++
checking whether we are using the GNU C++ compiler... yes
checking whether i686-pc-linux-gnu-g++ accepts -g... yes
checking dependency style of i686-pc-linux-gnu-g++... gcc3
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by i686-pc-linux-gnu-gcc... /usr/i686-pc-linux-gnu/bin/ld
checking if the linker (/usr/i686-pc-linux-gnu/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... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop
checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/i686-pc-linux-gnu/bin/ld option to reload object files... -r
checking for i686-pc-linux-gnu-objdump... i686-pc-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for i686-pc-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for i686-pc-linux-gnu-ar... i686-pc-linux-gnu-ar
checking for archiver @FILE support... @
checking for i686-pc-linux-gnu-strip... i686-pc-linux-gnu-strip
checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib
checking command to parse /usr/bin/nm -B output from i686-pc-linux-gnu-gcc object... ok
checking for sysroot... no
checking for i686-pc-linux-gnu-mt... no
checking for mt... mt
checking if mt is a manifest tool... no
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 i686-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
checking for i686-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
checking if i686-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
checking if i686-pc-linux-gnu-gcc static flag -static works... yes
checking if i686-pc-linux-gnu-gcc supports -c -o file.o... yes
checking if i686-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
checking whether the i686-pc-linux-gnu-gcc linker (/usr/i686-pc-linux-gnu/bin/ld) 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... i686-pc-linux-gnu-g++ -E
checking for ld used by i686-pc-linux-gnu-g++... /usr/i686-pc-linux-gnu/bin/ld
checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes
checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
checking for i686-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
checking if i686-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
checking if i686-pc-linux-gnu-g++ static flag -static works... yes
checking if i686-pc-linux-gnu-g++ supports -c -o file.o... yes
checking if i686-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking sys/stdtypes.h usability... no
checking sys/stdtypes.h presence... no
checking for sys/stdtypes.h... no
checking for i686-pc-linux-gnu-gcc option to support OpenMP... -fopenmp
checking if this is MINGW on Windows... no
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 1.3... yes
checking for i686-pc-linux-gnu-pkg-config... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GTK... yes
checking for GNOME_CANVAS... yes
checking for pkg-config... /usr/bin/pkg-config
checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0)
checking for GLUT... yes
checking for MMDB... yes
checking for MMDB... yes
checking for MMDBSSM... yes
checking for Clipper... yes
Congratulations, you are using Guile
checking for guile... /usr/bin/guile
checking for guile-config... /usr/bin/guile-config
checking for guile-tools... /usr/bin/guile-tools
checking libguile compile flags...  -pthread
checking libguile link flags... -pthread  -lguile -lltdl -lgmp -lcrypt -lm -lltdl
checking for Guile-Lib... yes
checking for guile-gui... yes
checking GUILE_VERSION: 1.8
checking for Python... checking Python.h usability... yes
checking Python.h presence... yes
checking for Python.h... yes
Cool, using Python
checking for PYGTK... yes
Good we have pygtk
checking for guile-gtk... 
checking libglade... yes
Not using database
checking for curl >= 7.9.7... 7.21.7
checking build type... error: cannot open Name index using db5 - Permission denied (13)
error: cannot open Name index using db5 - Permission denied (13)
error: cannot open Name index using db5 - Permission denied (13)
Linux-AuthenticAMD---python-gtk2
configure: creating ./config.status
config.status: creating Makefile
config.status: creating macros/Makefile
config.status: creating scheme/Makefile
config.status: creating python/Makefile
config.status: creating compat/Makefile
config.status: creating utils/Makefile
config.status: creating coot-utils/Makefile
config.status: creating ccp4mg-utils/Makefile
config.status: creating coords/Makefile
config.status: creating db-main/Makefile
config.status: creating density-contour/Makefile
config.status: creating surface/Makefile
config.status: creating coot-surface/Makefile
config.status: creating angles/Makefile
config.status: creating mini-mol/Makefile
config.status: creating skeleton/Makefile
config.status: creating ligand/Makefile
config.status: creating geometry/Makefile
config.status: creating ideal/Makefile
config.status: creating build/Makefile
config.status: creating analysis/Makefile
config.status: creating high-res/Makefile
config.status: creating tw/Makefile
config.status: creating cootaneer/Makefile
config.status: creating greg-tests/Makefile
config.status: creating python-tests/Makefile
config.status: creating lidia-core/Makefile
config.status: creating doc/Makefile
config.status: creating src/Makefile
config.status: creating src/coot
config.status: creating python/coot_load_modules.py
config.status: creating data/Makefile
config.status: creating rama-data/Makefile
config.status: creating auxil/Makefile
config.status: creating auxil/catcheck/Makefile
config.status: creating auxil/rama/Makefile
config.status: creating auxil/sec-str/Makefile
config.status: creating auxil/strand-analysis/Makefile
config.status: creating auxil/vectors/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2 ...
make -j14 
Making all in auxil
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil'
Making all in catcheck
make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/catcheck'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/catcheck'
Making all in rama
make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/rama'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/rama'
Making all in sec-str
make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/sec-str'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/sec-str'
Making all in strand-analysis
make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/strand-analysis'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/strand-analysis'
Making all in vectors
make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/vectors'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil/vectors'
make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil'
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/auxil'
Making all in scheme
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/scheme'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/scheme'
Making all in python
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/python'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/python'
Making all in macros
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/macros'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/macros'
Making all in compat
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/compat'
/bin/sh ../libtool --tag=CC   --mode=compile i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.     -O2 -pipe -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c -o getopt.lo getopt.c
/bin/sh ../libtool --tag=CC   --mode=compile i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.     -O2 -pipe -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c -o getopt1.lo getopt1.c
libtool: compile:  i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c  -fPIC -DPIC -o .libs/getopt.o
libtool: compile:  i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c  -fPIC -DPIC -o .libs/getopt1.o
libtool: compile:  i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c -o getopt1.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -o getopt.o >/dev/null 2>&1
mv -f .deps/getopt1.Tpo .deps/getopt1.Plo
mv -f .deps/getopt.Tpo .deps/getopt.Plo
/bin/sh ../libtool --tag=CC   --mode=link i686-pc-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-compat.la -rpath /usr/lib getopt.lo getopt1.lo  
libtool: link: i686-pc-linux-gnu-gcc -shared  -fPIC -DPIC  .libs/getopt.o .libs/getopt1.o   -Wl,--as-needed  -O2 -Wl,-O1 -Wl,--hash-style=gnu   -Wl,-soname -Wl,libcoot-compat.so.0 -o .libs/libcoot-compat.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-compat.so.0" && ln -s "libcoot-compat.so.0.0.0" "libcoot-compat.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-compat.so" && ln -s "libcoot-compat.so.0.0.0" "libcoot-compat.so")
libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-compat.a  getopt.o getopt1.o
libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-compat.a
libtool: link: ( cd ".libs" && rm -f "libcoot-compat.la" && ln -s "../libcoot-compat.la" "libcoot-compat.la" )
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/compat'
Making all in utils
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils'
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat		    -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c -o coot-utils.lo coot-utils.cc
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat		    -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT coot-fasta.lo -MD -MP -MF .deps/coot-fasta.Tpo -c -o coot-fasta.lo coot-fasta.cc
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat		    -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT atomic-numbers.lo -MD -MP -MF .deps/atomic-numbers.Tpo -c -o atomic-numbers.lo atomic-numbers.cc
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libtool: link: (cd ".libs" && rm -f "libcoot-utils.so.0" && ln -s "libcoot-utils.so.0.0.0" "libcoot-utils.so.0")
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libtool: link: ( cd ".libs" && rm -f "libcoot-utils.la" && ln -s "../libcoot-utils.la" "libcoot-utils.la" )
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils'
Making all in geometry
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry'
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libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT read-sbase.lo -MD -MP -MF .deps/read-sbase.Tpo -c read-sbase.cc  -fPIC -DPIC -o .libs/read-sbase.o
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libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT energy-lib.lo -MD -MP -MF .deps/energy-lib.Tpo -c energy-lib.cc  -fPIC -DPIC -o .libs/energy-lib.o
mv -f .deps/test-read-components.Tpo .deps/test-read-components.Po
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT protein-geometry-mmdb.lo -MD -MP -MF .deps/protein-geometry-mmdb.Tpo -c protein-geometry-mmdb.cc -o protein-geometry-mmdb.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT read-sbase.lo -MD -MP -MF .deps/read-sbase.Tpo -c read-sbase.cc -o read-sbase.o >/dev/null 2>&1
mv -f .deps/protein-geometry-mmdb.Tpo .deps/protein-geometry-mmdb.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT energy-lib.lo -MD -MP -MF .deps/energy-lib.Tpo -c energy-lib.cc -o energy-lib.o >/dev/null 2>&1
mv -f .deps/read-sbase.Tpo .deps/read-sbase.Plo
mv -f .deps/test-geometry.Tpo .deps/test-geometry.Po
mv -f .deps/energy-lib.Tpo .deps/energy-lib.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../utils -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT protein-geometry.lo -MD -MP -MF .deps/protein-geometry.Tpo -c protein-geometry.cc -o protein-geometry.o >/dev/null 2>&1
mv -f .deps/protein-geometry.Tpo .deps/protein-geometry.Plo
/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-geometry.la -rpath /usr/lib protein-geometry.lo protein-geometry-mmdb.lo read-sbase.lo energy-lib.lo ../utils/libcoot-utils.la -lmmdb   -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw 
libtool: link: i686-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtbeginS.o  .libs/protein-geometry.o .libs/protein-geometry-mmdb.o .libs/read-sbase.o .libs/energy-lib.o   -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,--as-needed ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-minimol.so -L/usr/lib /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-core.so -lpthread -lccp4c /usr/lib/libmmdb.so /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crtn.o  -O2 -Wl,-O1 -Wl,--hash-style=gnu   -Wl,-soname -Wl,libcoot-geometry.so.0 -o .libs/libcoot-geometry.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so.0" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so")
libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-geometry.a  protein-geometry.o protein-geometry-mmdb.o read-sbase.o energy-lib.o
libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-geometry.a
libtool: link: ( cd ".libs" && rm -f "libcoot-geometry.la" && ln -s "../libcoot-geometry.la" "libcoot-geometry.la" )
/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o test-geometry test-geometry.o ./libcoot-geometry.la ../utils/libcoot-utils.la -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb   
/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"'  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o test-read-components test-read-components.o ./libcoot-geometry.la ../utils/libcoot-utils.la -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb   
libtool: link: i686-pc-linux-gnu-g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -Wl,--hash-style=gnu -o .libs/test-geometry test-geometry.o  -Wl,--as-needed ./.libs/libcoot-geometry.so -L/usr/lib /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-core.so -lpthread -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lm /usr/lib/libmmdb.so
libtool: link: i686-pc-linux-gnu-g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -Wl,-O1 -Wl,--hash-style=gnu -o .libs/test-read-components test-read-components.o  -Wl,--as-needed ./.libs/libcoot-geometry.so -L/usr/lib /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-core.so -lpthread -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lm /usr/lib/libmmdb.so
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry'
Making all in mini-mol
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol'
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -O2 -pipe -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c -o mini-mol.lo mini-mol.cc
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -O2 -pipe -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c -o mini-mol-utils.lo mini-mol-utils.cc
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -O2 -pipe -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c -o atom-quads.lo atom-quads.cc
i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP    -O2 -pipe -MT testminimol.o -MD -MP -MF .deps/testminimol.Tpo -c -o testminimol.o testminimol.cc
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c mini-mol.cc  -fPIC -DPIC -o .libs/mini-mol.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c atom-quads.cc  -fPIC -DPIC -o .libs/atom-quads.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c mini-mol-utils.cc  -fPIC -DPIC -o .libs/mini-mol-utils.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c atom-quads.cc -o atom-quads.o >/dev/null 2>&1
mv -f .deps/testminimol.Tpo .deps/testminimol.Po
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c mini-mol-utils.cc -o mini-mol-utils.o >/dev/null 2>&1
mv -f .deps/atom-quads.Tpo .deps/atom-quads.Plo
mv -f .deps/mini-mol-utils.Tpo .deps/mini-mol-utils.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c mini-mol.cc -o mini-mol.o >/dev/null 2>&1
mv -f .deps/mini-mol.Tpo .deps/mini-mol.Plo
/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-mini-mol.la -rpath /usr/lib mini-mol.lo mini-mol-utils.lo atom-quads.lo -lmmdb   -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw  
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Making all in coot-utils
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libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-utils-nucleotides.lo -MD -MP -MF .deps/coot-coord-utils-nucleotides.Tpo -c coot-coord-utils-nucleotides.cc  -fPIC -DPIC -o .libs/coot-coord-utils-nucleotides.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT water-coordination.lo -MD -MP -MF .deps/water-coordination.Tpo -c water-coordination.cc  -fPIC -DPIC -o .libs/water-coordination.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-rama.lo -MD -MP -MF .deps/coot-rama.Tpo -c coot-rama.cc  -fPIC -DPIC -o .libs/coot-rama.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-extras.lo -MD -MP -MF .deps/coot-coord-extras.Tpo -c coot-coord-extras.cc  -fPIC -DPIC -o .libs/coot-coord-extras.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-h-bonds.lo -MD -MP -MF .deps/coot-h-bonds.Tpo -c coot-h-bonds.cc  -fPIC -DPIC -o .libs/coot-h-bonds.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT peak-search.lo -MD -MP -MF .deps/peak-search.Tpo -c peak-search.cc  -fPIC -DPIC -o .libs/peak-search.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT xmap-stats.lo -MD -MP -MF .deps/xmap-stats.Tpo -c xmap-stats.cc  -fPIC -DPIC -o .libs/xmap-stats.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-lsq.lo -MD -MP -MF .deps/coot-coord-lsq.Tpo -c coot-coord-lsq.cc  -fPIC -DPIC -o .libs/coot-coord-lsq.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-map-utils.lo -MD -MP -MF .deps/coot-map-utils.Tpo -c coot-map-utils.cc  -fPIC -DPIC -o .libs/coot-map-utils.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT trim.lo -MD -MP -MF .deps/trim.Tpo -c trim.cc  -fPIC -DPIC -o .libs/trim.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT peak-search-from-list.lo -MD -MP -MF .deps/peak-search-from-list.Tpo -c peak-search-from-list.cc  -fPIC -DPIC -o .libs/peak-search-from-list.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT trim.lo -MD -MP -MF .deps/trim.Tpo -c trim.cc -o trim.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT xmap-stats.lo -MD -MP -MF .deps/xmap-stats.Tpo -c xmap-stats.cc -o xmap-stats.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-rama.lo -MD -MP -MF .deps/coot-rama.Tpo -c coot-rama.cc -o coot-rama.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT peak-search-from-list.lo -MD -MP -MF .deps/peak-search-from-list.Tpo -c peak-search-from-list.cc -o peak-search-from-list.o >/dev/null 2>&1
mv -f .deps/trim.Tpo .deps/trim.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON   -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT coot-map-heavy.lo -MD -MP -MF .deps/coot-map-heavy.Tpo -c -o coot-map-heavy.lo coot-map-heavy.cc
mv -f .deps/xmap-stats.Tpo .deps/xmap-stats.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON   -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT coot-fffear.lo -MD -MP -MF .deps/coot-fffear.Tpo -c -o coot-fffear.lo coot-fffear.cc
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-map-heavy.lo -MD -MP -MF .deps/coot-map-heavy.Tpo -c coot-map-heavy.cc  -fPIC -DPIC -o .libs/coot-map-heavy.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-fffear.lo -MD -MP -MF .deps/coot-fffear.Tpo -c coot-fffear.cc  -fPIC -DPIC -o .libs/coot-fffear.o
mv -f .deps/peak-search-from-list.Tpo .deps/peak-search-from-list.Plo
i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON   -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT test-h-bonds.o -MD -MP -MF .deps/test-h-bonds.Tpo -c -o test-h-bonds.o test-h-bonds.cc
mv -f .deps/coot-rama.Tpo .deps/coot-rama.Plo
i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON   -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT test-shelx-reader.o -MD -MP -MF .deps/test-shelx-reader.Tpo -c -o test-shelx-reader.o test-shelx-reader.cc
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT water-coordination.lo -MD -MP -MF .deps/water-coordination.Tpo -c water-coordination.cc -o water-coordination.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-lsq.lo -MD -MP -MF .deps/coot-coord-lsq.Tpo -c coot-coord-lsq.cc -o coot-coord-lsq.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-utils-nucleotides.lo -MD -MP -MF .deps/coot-coord-utils-nucleotides.Tpo -c coot-coord-utils-nucleotides.cc -o coot-coord-utils-nucleotides.o >/dev/null 2>&1
mv -f .deps/test-shelx-reader.Tpo .deps/test-shelx-reader.Po
i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON   -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -MT test-utils.o -MD -MP -MF .deps/test-utils.Tpo -c -o test-utils.o test-utils.cc
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-map-heavy.lo -MD -MP -MF .deps/coot-map-heavy.Tpo -c coot-map-heavy.cc -o coot-map-heavy.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-tree-extras.lo -MD -MP -MF .deps/coot-tree-extras.Tpo -c coot-tree-extras.cc -o coot-tree-extras.o >/dev/null 2>&1
mv -f .deps/test-utils.Tpo .deps/test-utils.Po
mv -f .deps/coot-coord-lsq.Tpo .deps/coot-coord-lsq.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT peak-search.lo -MD -MP -MF .deps/peak-search.Tpo -c peak-search.cc -o peak-search.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-h-bonds.lo -MD -MP -MF .deps/coot-h-bonds.Tpo -c coot-h-bonds.cc -o coot-h-bonds.o >/dev/null 2>&1
mv -f .deps/water-coordination.Tpo .deps/water-coordination.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-fffear.lo -MD -MP -MF .deps/coot-fffear.Tpo -c coot-fffear.cc -o coot-fffear.o >/dev/null 2>&1
mv -f .deps/test-h-bonds.Tpo .deps/test-h-bonds.Po
mv -f .deps/coot-map-heavy.Tpo .deps/coot-map-heavy.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-shelx-ins.lo -MD -MP -MF .deps/coot-shelx-ins.Tpo -c coot-shelx-ins.cc -o coot-shelx-ins.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-extras.lo -MD -MP -MF .deps/coot-coord-extras.Tpo -c coot-coord-extras.cc -o coot-coord-extras.o >/dev/null 2>&1
mv -f .deps/coot-coord-utils-nucleotides.Tpo .deps/coot-coord-utils-nucleotides.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-map-utils.lo -MD -MP -MF .deps/coot-map-utils.Tpo -c coot-map-utils.cc -o coot-map-utils.o >/dev/null 2>&1
mv -f .deps/coot-tree-extras.Tpo .deps/coot-tree-extras.Plo
mv -f .deps/coot-fffear.Tpo .deps/coot-fffear.Plo
mv -f .deps/peak-search.Tpo .deps/peak-search.Plo
mv -f .deps/coot-h-bonds.Tpo .deps/coot-h-bonds.Plo
mv -f .deps/coot-shelx-ins.Tpo .deps/coot-shelx-ins.Plo
mv -f .deps/coot-coord-extras.Tpo .deps/coot-coord-extras.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../utils -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -MT coot-coord-utils.lo -MD -MP -MF .deps/coot-coord-utils.Tpo -c coot-coord-utils.cc -o coot-coord-utils.o >/dev/null 2>&1
mv -f .deps/coot-map-utils.Tpo .deps/coot-map-utils.Plo
mv -f .deps/coot-coord-utils.Tpo .deps/coot-coord-utils.Plo
/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-coord-utils.la -rpath /usr/lib coot-coord-utils.lo coot-coord-utils-nucleotides.lo coot-rama.lo coot-h-bonds.lo ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb   
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/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-shelx.la -rpath /usr/lib coot-shelx-ins.lo libcoot-coord-utils.la ../utils/libcoot-utils.la 
/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL  -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-coord-extras.la -rpath /usr/lib coot-coord-extras.lo coot-coord-lsq.lo coot-tree-extras.lo water-coordination.lo libcoot-coord-utils.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la 
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Making all in surface
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface'
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libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXSurface.lo -MD -MP -MF .deps/CXXSurface.Tpo -c CXXSurface.cpp  -fPIC -DPIC -o .libs/CXXSurface.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXTorusElement.lo -MD -MP -MF .deps/CXXTorusElement.Tpo -c CXXTorusElement.cpp  -fPIC -DPIC -o .libs/CXXTorusElement.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXSphereTriangle.lo -MD -MP -MF .deps/CXXSphereTriangle.Tpo -c CXXSphereTriangle.cpp  -fPIC -DPIC -o .libs/CXXSphereTriangle.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXCoord.lo -MD -MP -MF .deps/CXXCoord.Tpo -c CXXCoord.cpp  -fPIC -DPIC -o .libs/CXXCoord.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXException.lo -MD -MP -MF .deps/CXXException.Tpo -c CXXException.cpp -o CXXException.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXCoord.lo -MD -MP -MF .deps/CXXCoord.Tpo -c CXXCoord.cpp -o CXXCoord.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXSphereTriangleEdge.lo -MD -MP -MF .deps/CXXSphereTriangleEdge.Tpo -c CXXSphereTriangleEdge.cpp -o CXXSphereTriangleEdge.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXSphereNode.lo -MD -MP -MF .deps/CXXSphereNode.Tpo -c CXXSphereNode.cpp -o CXXSphereNode.o >/dev/null 2>&1
mv -f .deps/CXXException.Tpo .deps/CXXException.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include    -fopenmp -O2 -pipe -MT CXXTorusNode.lo -MD -MP -MF .deps/CXXTorusNode.Tpo -c -o CXXTorusNode.lo CXXTorusNode.cpp
mv -f .deps/CXXCoord.Tpo .deps/CXXCoord.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include    -fopenmp -O2 -pipe -MT CXXFortranFile.lo -MD -MP -MF .deps/CXXFortranFile.Tpo -c -o CXXFortranFile.lo CXXFortranFile.cpp
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXSurfaceVertex.lo -MD -MP -MF .deps/CXXSurfaceVertex.Tpo -c CXXSurfaceVertex.cpp -o CXXSurfaceVertex.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXSphereTriangle.lo -MD -MP -MF .deps/CXXSphereTriangle.Tpo -c CXXSphereTriangle.cpp -o CXXSphereTriangle.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXTorusNode.lo -MD -MP -MF .deps/CXXTorusNode.Tpo -c CXXTorusNode.cpp  -fPIC -DPIC -o .libs/CXXTorusNode.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXFortranFile.lo -MD -MP -MF .deps/CXXFortranFile.Tpo -c CXXFortranFile.cpp  -fPIC -DPIC -o .libs/CXXFortranFile.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXFFTSolventMap.lo -MD -MP -MF .deps/CXXFFTSolventMap.Tpo -c CXXFFTSolventMap.cpp -o CXXFFTSolventMap.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXChargeTable.lo -MD -MP -MF .deps/CXXChargeTable.Tpo -c CXXChargeTable.cpp -o CXXChargeTable.o >/dev/null 2>&1
mv -f .deps/CXXSphereTriangleEdge.Tpo .deps/CXXSphereTriangleEdge.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include    -fopenmp -O2 -pipe -MT CXXNewHood.lo -MD -MP -MF .deps/CXXNewHood.Tpo -c -o CXXNewHood.lo CXXNewHood.cpp
mv -f .deps/CXXSphereNode.Tpo .deps/CXXSphereNode.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include    -fopenmp -O2 -pipe -MT CXXTriangle.lo -MD -MP -MF .deps/CXXTriangle.Tpo -c -o CXXTriangle.lo CXXTriangle.cpp
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXTorusNode.lo -MD -MP -MF .deps/CXXTorusNode.Tpo -c CXXTorusNode.cpp -o CXXTorusNode.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXCircle.lo -MD -MP -MF .deps/CXXCircle.Tpo -c CXXCircle.cpp -o CXXCircle.o >/dev/null 2>&1
mv -f .deps/CXXSurfaceVertex.Tpo .deps/CXXSurfaceVertex.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include    -fopenmp -O2 -pipe -MT CXXNode.lo -MD -MP -MF .deps/CXXNode.Tpo -c -o CXXNode.lo CXXNode.cpp
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXTorusElement.lo -MD -MP -MF .deps/CXXTorusElement.Tpo -c CXXTorusElement.cpp -o CXXTorusElement.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXNewHood.lo -MD -MP -MF .deps/CXXNewHood.Tpo -c CXXNewHood.cpp  -fPIC -DPIC -o .libs/CXXNewHood.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXTriangle.lo -MD -MP -MF .deps/CXXTriangle.Tpo -c CXXTriangle.cpp  -fPIC -DPIC -o .libs/CXXTriangle.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXFortranFile.lo -MD -MP -MF .deps/CXXFortranFile.Tpo -c CXXFortranFile.cpp -o CXXFortranFile.o >/dev/null 2>&1
mv -f .deps/CXXSphereTriangle.Tpo .deps/CXXSphereTriangle.Plo
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mv -f .deps/CXXTorusNode.Tpo .deps/CXXTorusNode.Plo
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libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXNode.lo -MD -MP -MF .deps/CXXNode.Tpo -c CXXNode.cpp  -fPIC -DPIC -o .libs/CXXNode.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXNode.lo -MD -MP -MF .deps/CXXNode.Tpo -c CXXNode.cpp -o CXXNode.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXCreator.lo -MD -MP -MF .deps/CXXCreator.Tpo -c CXXCreator.cpp -o CXXCreator.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXBall.lo -MD -MP -MF .deps/CXXBall.Tpo -c CXXBall.cpp  -fPIC -DPIC -o .libs/CXXBall.o
mv -f .deps/CXXNode.Tpo .deps/CXXNode.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include    -fopenmp -O2 -pipe -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c -o CXXQADSurfaceStaticData.lo CXXQADSurfaceStaticData.cpp
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXQADSurface.lo -MD -MP -MF .deps/CXXQADSurface.Tpo -c CXXQADSurface.cpp  -fPIC -DPIC -o .libs/CXXQADSurface.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXTriangle.lo -MD -MP -MF .deps/CXXTriangle.Tpo -c CXXTriangle.cpp -o CXXTriangle.o >/dev/null 2>&1
mv -f .deps/CXXFortranFile.Tpo .deps/CXXFortranFile.Plo
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libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c CXXQADSurfaceStaticData.cpp  -fPIC -DPIC -o .libs/CXXQADSurfaceStaticData.o
mv -f .deps/CXXFFTSolventMap.Tpo .deps/CXXFFTSolventMap.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include    -fopenmp -O2 -pipe -MT CXXUtils.lo -MD -MP -MF .deps/CXXUtils.Tpo -c -o CXXUtils.lo CXXUtils.cpp
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c CXXSpace.cpp  -fPIC -DPIC -o .libs/CXXSpace.o
mv -f .deps/CXXTriangle.Tpo .deps/CXXTriangle.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXUtils.lo -MD -MP -MF .deps/CXXUtils.Tpo -c CXXUtils.cpp  -fPIC -DPIC -o .libs/CXXUtils.o
mv -f .deps/CXXChargeTable.Tpo .deps/CXXChargeTable.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXNewHood.lo -MD -MP -MF .deps/CXXNewHood.Tpo -c CXXNewHood.cpp -o CXXNewHood.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXCircleNode.lo -MD -MP -MF .deps/CXXCircleNode.Tpo -c CXXCircleNode.cpp -o CXXCircleNode.o >/dev/null 2>&1
mv -f .deps/CXXCircle.Tpo .deps/CXXCircle.Plo
mv -f .deps/CXXTorusElement.Tpo .deps/CXXTorusElement.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c CXXSpace.cpp -o CXXSpace.o >/dev/null 2>&1
mv -f .deps/CXXCreator.Tpo .deps/CXXCreator.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c CXXQADSurfaceStaticData.cpp -o CXXQADSurfaceStaticData.o >/dev/null 2>&1
mv -f .deps/CXXSpace.Tpo .deps/CXXSpace.Plo
mv -f .deps/CXXNewHood.Tpo .deps/CXXNewHood.Plo
mv -f .deps/CXXQADSurfaceStaticData.Tpo .deps/CXXQADSurfaceStaticData.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXSurface.lo -MD -MP -MF .deps/CXXSurface.Tpo -c CXXSurface.cpp -o CXXSurface.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXSphereElement.lo -MD -MP -MF .deps/CXXSphereElement.Tpo -c CXXSphereElement.cpp -o CXXSphereElement.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXBall.lo -MD -MP -MF .deps/CXXBall.Tpo -c CXXBall.cpp -o CXXBall.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXQADSurface.lo -MD -MP -MF .deps/CXXQADSurface.Tpo -c CXXQADSurface.cpp -o CXXQADSurface.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -fopenmp -O2 -pipe -MT CXXUtils.lo -MD -MP -MF .deps/CXXUtils.Tpo -c CXXUtils.cpp -o CXXUtils.o >/dev/null 2>&1
mv -f .deps/CXXCircleNode.Tpo .deps/CXXCircleNode.Plo
mv -f .deps/CXXBall.Tpo .deps/CXXBall.Plo
mv -f .deps/CXXUtils.Tpo .deps/CXXUtils.Plo
mv -f .deps/CXXSphereElement.Tpo .deps/CXXSphereElement.Plo
mv -f .deps/CXXQADSurface.Tpo .deps/CXXQADSurface.Plo
mv -f .deps/CXXSurface.Tpo .deps/CXXSurface.Plo
/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++ -fopenmp -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libccp4mg-surface.la -rpath /usr/lib CXXSphereElement.lo CXXChargeTable.lo CXXSphereNode.lo CXXCircle.lo CXXSphereTriangle.lo CXXCircleNode.lo CXXSphereTriangleEdge.lo CXXCoord.lo CXXSurface.lo CXXCreator.lo CXXSurfaceVertex.lo CXXException.lo CXXTorusElement.lo CXXFFTSolventMap.lo CXXTorusNode.lo CXXFortranFile.lo CXXNewHood.lo CXXTriangle.lo CXXNode.lo CXXQADSurface.lo CXXBall.lo CXXQADSurfaceStaticData.lo CXXSpace.lo CXXUtils.lo -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb   
libtool: link: i686-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtbeginS.o  .libs/CXXSphereElement.o .libs/CXXChargeTable.o .libs/CXXSphereNode.o .libs/CXXCircle.o .libs/CXXSphereTriangle.o .libs/CXXCircleNode.o .libs/CXXSphereTriangleEdge.o .libs/CXXCoord.o .libs/CXXSurface.o .libs/CXXCreator.o .libs/CXXSurfaceVertex.o .libs/CXXException.o .libs/CXXTorusElement.o .libs/CXXFFTSolventMap.o .libs/CXXTorusNode.o .libs/CXXFortranFile.o .libs/CXXNewHood.o .libs/CXXTriangle.o .libs/CXXNode.o .libs/CXXQADSurface.o .libs/CXXBall.o .libs/CXXQADSurfaceStaticData.o .libs/CXXSpace.o .libs/CXXUtils.o   -Wl,--as-needed /usr/lib/libclipper-minimol.so -L/usr/lib /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-core.so -lpthread -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crtn.o  -O2 -Wl,-O1 -Wl,--hash-style=gnu   -Wl,-soname -Wl,libccp4mg-surface.so.0 -o .libs/libccp4mg-surface.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libccp4mg-surface.so.0" && ln -s "libccp4mg-surface.so.0.0.0" "libccp4mg-surface.so.0")
libtool: link: (cd ".libs" && rm -f "libccp4mg-surface.so" && ln -s "libccp4mg-surface.so.0.0.0" "libccp4mg-surface.so")
libtool: link: i686-pc-linux-gnu-ar cru .libs/libccp4mg-surface.a  CXXSphereElement.o CXXChargeTable.o CXXSphereNode.o CXXCircle.o CXXSphereTriangle.o CXXCircleNode.o CXXSphereTriangleEdge.o CXXCoord.o CXXSurface.o CXXCreator.o CXXSurfaceVertex.o CXXException.o CXXTorusElement.o CXXFFTSolventMap.o CXXTorusNode.o CXXFortranFile.o CXXNewHood.o CXXTriangle.o CXXNode.o CXXQADSurface.o CXXBall.o CXXQADSurfaceStaticData.o CXXSpace.o CXXUtils.o
libtool: link: i686-pc-linux-gnu-ranlib .libs/libccp4mg-surface.a
libtool: link: ( cd ".libs" && rm -f "libccp4mg-surface.la" && ln -s "../libccp4mg-surface.la" "libccp4mg-surface.la" )
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface'
Making all in coot-surface
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-surface'
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include      -O2 -pipe -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c -o coot-surface.lo coot-surface.cc
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include      -O2 -pipe -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c -o rgbreps.lo rgbreps.cc
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -O2 -pipe -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c rgbreps.cc  -fPIC -DPIC -o .libs/rgbreps.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -O2 -pipe -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c coot-surface.cc  -fPIC -DPIC -o .libs/coot-surface.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -O2 -pipe -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c rgbreps.cc -o rgbreps.o >/dev/null 2>&1
mv -f .deps/rgbreps.Tpo .deps/rgbreps.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -O2 -pipe -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c coot-surface.cc -o coot-surface.o >/dev/null 2>&1
mv -f .deps/coot-surface.Tpo .deps/coot-surface.Plo
/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-surface.la -rpath /usr/lib coot-surface.lo rgbreps.lo ../surface/libccp4mg-surface.la -lglut  -lXmu -pthread -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lm -lcairo -lpng15 -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0   -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb   -lGL 
libtool: link: i686-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtbeginS.o  .libs/coot-surface.o .libs/rgbreps.o   -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/surface/.libs -Wl,--as-needed ../surface/.libs/libccp4mg-surface.so -L/usr/lib -lglut -lXmu /usr/lib/libgtk-x11-2.0.so /usr/lib/libgdk-x11-2.0.so /usr/lib/libatk-1.0.so /usr/lib/libgio-2.0.so -lresolv -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpng15 -lpango-1.0 /usr/lib/libfontconfig.so -lfreetype -lz -lbz2 -lexpat /usr/lib/libgobject-2.0.so /usr/lib/libgmodule-2.0.so -ldl /usr/lib/libgthread-2.0.so /usr/lib/libglib-2.0.so -lrt /usr/lib/libclipper-minimol.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-core.so -lpthread -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so /usr/lib/libmmdb.so -lGL -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crtn.o  -O2 -Wl,-O1 -Wl,--hash-style=gnu -pthread   -pthread -Wl,-soname -Wl,libcoot-surface.so.0 -o .libs/libcoot-surface.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-surface.so.0" && ln -s "libcoot-surface.so.0.0.0" "libcoot-surface.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-surface.so" && ln -s "libcoot-surface.so.0.0.0" "libcoot-surface.so")
libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-surface.a  coot-surface.o rgbreps.o
libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-surface.a
libtool: link: ( cd ".libs" && rm -f "libcoot-surface.la" && ln -s "../libcoot-surface.la" "libcoot-surface.la" )
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-surface'
Making all in lidia-core
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core'
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include    -O2 -pipe -MT lbg-molfile.lo -MD -MP -MF .deps/lbg-molfile.Tpo -c -o lbg-molfile.lo lbg-molfile.cc
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include    -O2 -pipe -MT lig-build.lo -MD -MP -MF .deps/lig-build.Tpo -c -o lig-build.lo lig-build.cc
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -O2 -pipe -MT lbg-molfile.lo -MD -MP -MF .deps/lbg-molfile.Tpo -c lbg-molfile.cc  -fPIC -DPIC -o .libs/lbg-molfile.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -O2 -pipe -MT lig-build.lo -MD -MP -MF .deps/lig-build.Tpo -c lig-build.cc  -fPIC -DPIC -o .libs/lig-build.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -O2 -pipe -MT lig-build.lo -MD -MP -MF .deps/lig-build.Tpo -c lig-build.cc -o lig-build.o >/dev/null 2>&1
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libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -O2 -pipe -MT lbg-molfile.lo -MD -MP -MF .deps/lbg-molfile.Tpo -c lbg-molfile.cc -o lbg-molfile.o >/dev/null 2>&1
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/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-lidia-core.la -rpath /usr/lib lbg-molfile.lo lig-build.lo  
libtool: link: i686-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtbeginS.o  .libs/lbg-molfile.o .libs/lig-build.o   -Wl,--as-needed -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crtn.o  -O2 -Wl,-O1 -Wl,--hash-style=gnu   -Wl,-soname -Wl,libcoot-lidia-core.so.0 -o .libs/libcoot-lidia-core.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-lidia-core.so.0" && ln -s "libcoot-lidia-core.so.0.0.0" "libcoot-lidia-core.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-lidia-core.so" && ln -s "libcoot-lidia-core.so.0.0.0" "libcoot-lidia-core.so")
libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-lidia-core.a  lbg-molfile.o lig-build.o
libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-lidia-core.a
libtool: link: ( cd ".libs" && rm -f "libcoot-lidia-core.la" && ln -s "../libcoot-lidia-core.la" "libcoot-lidia-core.la" )
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core'
Making all in coords
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords'
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libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT Bond_lines.lo -MD -MP -MF .deps/Bond_lines.Tpo -c Bond_lines.cc  -fPIC -DPIC -o .libs/Bond_lines.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT mmdb-crystal.lo -MD -MP -MF .deps/mmdb-crystal.Tpo -c mmdb-crystal.cc  -fPIC -DPIC -o .libs/mmdb-crystal.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c utils.cc  -fPIC -DPIC -o .libs/utils.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT mmdb.lo -MD -MP -MF .deps/mmdb.Tpo -c mmdb.cc  -fPIC -DPIC -o .libs/mmdb.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c utils.cc -o utils.o >/dev/null 2>&1
mv -f .deps/utils.Tpo .deps/utils.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT cos-sin.lo -MD -MP -MF .deps/cos-sin.Tpo -c cos-sin.cc -o cos-sin.o >/dev/null 2>&1
mv -f .deps/cos-sin.Tpo .deps/cos-sin.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT Cartesian.lo -MD -MP -MF .deps/Cartesian.Tpo -c Cartesian.cc -o Cartesian.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT coot-close.lo -MD -MP -MF .deps/coot-close.Tpo -c coot-close.cc -o coot-close.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT Bond_lines_ext.lo -MD -MP -MF .deps/Bond_lines_ext.Tpo -c Bond_lines_ext.cc -o Bond_lines_ext.o >/dev/null 2>&1
mv -f .deps/Cartesian.Tpo .deps/Cartesian.Plo
mv -f .deps/coot-close.Tpo .deps/coot-close.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT mmdb.lo -MD -MP -MF .deps/mmdb.Tpo -c mmdb.cc -o mmdb.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT mmdb-crystal.lo -MD -MP -MF .deps/mmdb-crystal.Tpo -c mmdb-crystal.cc -o mmdb-crystal.o >/dev/null 2>&1
mv -f .deps/Bond_lines_ext.Tpo .deps/Bond_lines_ext.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT mmdb-extras.lo -MD -MP -MF .deps/mmdb-extras.Tpo -c mmdb-extras.cc -o mmdb-extras.o >/dev/null 2>&1
mv -f .deps/mmdb.Tpo .deps/mmdb.Plo
mv -f .deps/mmdb-crystal.Tpo .deps/mmdb-crystal.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../skeleton -I../utils -I../coot-utils -I../geometry -I../mini-mol -I../compat -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -MT Bond_lines.lo -MD -MP -MF .deps/Bond_lines.Tpo -c Bond_lines.cc -o Bond_lines.o >/dev/null 2>&1
mv -f .deps/mmdb-extras.Tpo .deps/mmdb-extras.Plo
mv -f .deps/Bond_lines.Tpo .deps/Bond_lines.Plo
/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"'  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-coords.la -rpath /usr/lib Bond_lines.lo Cartesian.lo cos-sin.lo mmdb-extras.lo utils.lo mmdb.lo mmdb-crystal.lo Bond_lines_ext.lo coot-close.lo ../lidia-core/libcoot-lidia-core.la ../geometry/libcoot-geometry.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la -lmmdb   
libtool: link: i686-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtbeginS.o  .libs/Bond_lines.o .libs/Cartesian.o .libs/cos-sin.o .libs/mmdb-extras.o .libs/utils.o .libs/mmdb.o .libs/mmdb-crystal.o .libs/Bond_lines_ext.o .libs/coot-close.o   -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,--as-needed ../lidia-core/.libs/libcoot-lidia-core.so ../geometry/.libs/libcoot-geometry.so -L/usr/lib ../coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-core.so -lpthread -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crtn.o  -O2 -Wl,-O1 -Wl,--hash-style=gnu   -Wl,-soname -Wl,libcoot-coords.so.0 -o .libs/libcoot-coords.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-coords.so.0" && ln -s "libcoot-coords.so.0.0.0" "libcoot-coords.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-coords.so" && ln -s "libcoot-coords.so.0.0.0" "libcoot-coords.so")
libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-coords.a  Bond_lines.o Cartesian.o cos-sin.o mmdb-extras.o utils.o mmdb.o mmdb-crystal.o Bond_lines_ext.o coot-close.o
libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-coords.a
libtool: link: ( cd ".libs" && rm -f "libcoot-coords.la" && ln -s "../libcoot-coords.la" "libcoot-coords.la" )
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords'
Making all in angles
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/angles'
/bin/sh ../libtool  --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include   -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo.Tpo -c -o libcoot_AngleInfo_la-AngleInfo.lo `test -f 'AngleInfo.cc' || echo './'`AngleInfo.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include   -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c -o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo `test -f 'AngleInfo-angle-torsions-autogen.cc' || echo './'`AngleInfo-angle-torsions-autogen.cc
/bin/sh ../libtool  --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include   -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c -o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo `test -f 'AngleInfo-theta_2-autogen.cc' || echo './'`AngleInfo-theta_2-autogen.cc
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo.Tpo -c AngleInfo.cc  -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c AngleInfo-angle-torsions-autogen.cc  -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c AngleInfo-theta_2-autogen.cc  -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c AngleInfo-theta_2-autogen.cc -o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o >/dev/null 2>&1
mv -f .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo.Tpo -c AngleInfo.cc -o libcoot_AngleInfo_la-AngleInfo.o >/dev/null 2>&1
mv -f .deps/libcoot_AngleInfo_la-AngleInfo.Tpo .deps/libcoot_AngleInfo_la-AngleInfo.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include -g -O1 -O2 -pipe -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c AngleInfo-angle-torsions-autogen.cc -o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o >/dev/null 2>&1
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/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++ -g -O1 -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-AngleInfo.la -rpath /usr/lib libcoot_AngleInfo_la-AngleInfo.lo libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo  
libtool: link: i686-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtbeginS.o  .libs/libcoot_AngleInfo_la-AngleInfo.o .libs/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o .libs/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o   -Wl,--as-needed -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crtn.o  -O1 -O2 -Wl,-O1 -Wl,--hash-style=gnu   -Wl,-soname -Wl,libcoot-AngleInfo.so.0 -o .libs/libcoot-AngleInfo.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-AngleInfo.so.0" && ln -s "libcoot-AngleInfo.so.0.0.0" "libcoot-AngleInfo.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-AngleInfo.so" && ln -s "libcoot-AngleInfo.so.0.0.0" "libcoot-AngleInfo.so")
libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-AngleInfo.a  libcoot_AngleInfo_la-AngleInfo.o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o
libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-AngleInfo.a
libtool: link: ( cd ".libs" && rm -f "libcoot-AngleInfo.la" && ln -s "../libcoot-AngleInfo.la" "libcoot-AngleInfo.la" )
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/angles'
Making all in skeleton
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/skeleton'
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include     -O2 -pipe -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c -o dm-utils.lo dm-utils.cc
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/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include     -O2 -pipe -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c -o BuildCas.lo BuildCas.cc
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -O2 -pipe -MT graphical_skel.lo -MD -MP -MF .deps/graphical_skel.Tpo -c graphical_skel.cc  -fPIC -DPIC -o .libs/graphical_skel.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -O2 -pipe -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c dm-utils.cc  -fPIC -DPIC -o .libs/dm-utils.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -O2 -pipe -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c BuildCas.cc  -fPIC -DPIC -o .libs/BuildCas.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -O2 -pipe -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c dm-utils.cc -o dm-utils.o >/dev/null 2>&1
mv -f .deps/dm-utils.Tpo .deps/dm-utils.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -O2 -pipe -MT graphical_skel.lo -MD -MP -MF .deps/graphical_skel.Tpo -c graphical_skel.cc -o graphical_skel.o >/dev/null 2>&1
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libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../angles -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -O2 -pipe -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c BuildCas.cc -o BuildCas.o >/dev/null 2>&1
mv -f .deps/BuildCas.Tpo .deps/BuildCas.Plo
/bin/sh ../libtool --tag=CXX   --mode=link i686-pc-linux-gnu-g++  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o libcoot-skeleton.la -rpath /usr/lib dm-utils.lo graphical_skel.lo BuildCas.lo ../angles/libcoot-AngleInfo.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-cif -lclipper-contrib -lclipper-ccp4 -lclipper-phs -lclipper-core -lccp4c -L/usr/lib -lmmdb -lsrfftw -lsfftw -lmmdb   
libtool: link: warning: `/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../libmmdb.la' seems to be moved
libtool: link: i686-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtbeginS.o  .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o   -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/angles/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coords/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs -L/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs -Wl,--as-needed ../angles/.libs/libcoot-AngleInfo.so ../geometry/.libs/libcoot-geometry.so -L/usr/lib ../coords/.libs/libcoot-coords.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../.. /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/lidia-core/.libs/libcoot-lidia-core.so /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/utils/.libs/libcoot-utils.so /var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/mini-mol/.libs/libcoot-mini-mol.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-core.so -lpthread -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so /usr/lib/libmmdb.so -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0 -L/usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../../i686-pc-linux-gnu/lib -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/../../../crtn.o  -O2 -Wl,-O1 -Wl,--hash-style=gnu   -Wl,-soname -Wl,libcoot-skeleton.so.0 -o .libs/libcoot-skeleton.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so.0" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so.0")
libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so")
libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-skeleton.a  dm-utils.o graphical_skel.o BuildCas.o
libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-skeleton.a
libtool: link: ( cd ".libs" && rm -f "libcoot-skeleton.la" && ln -s "../libcoot-skeleton.la" "libcoot-skeleton.la" )
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/skeleton'
Making all in ccp4mg-utils
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ccp4mg-utils'
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG    -O2 -pipe -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c -o geomutil.lo geomutil.cc
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG    -O2 -pipe -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c -o mgtree.lo mgtree.cc
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG    -O2 -pipe -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c -o cartesian.lo cartesian.cc
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG    -O2 -pipe -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c -o matrix.lo matrix.cc
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG    -O2 -pipe -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c -o quat.lo quat.cc
/bin/sh ../libtool --tag=CXX   --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb   -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG    -O2 -pipe -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c -o ppmutil.lo ppmutil.cc
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -O2 -pipe -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c geomutil.cc  -fPIC -DPIC -o .libs/geomutil.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -O2 -pipe -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c mgtree.cc  -fPIC -DPIC -o .libs/mgtree.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -O2 -pipe -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cc  -fPIC -DPIC -o .libs/matrix.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -O2 -pipe -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c cartesian.cc  -fPIC -DPIC -o .libs/cartesian.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -O2 -pipe -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c ppmutil.cc  -fPIC -DPIC -o .libs/ppmutil.o
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -O2 -pipe -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c quat.cc  -fPIC -DPIC -o .libs/quat.o
ppmutil.cc: In member function 'void image_info::readpng(const char*)':
ppmutil.cc:2500:60: error: invalid use of incomplete type 'png_struct'
/usr/include/png.h:827:16: error: forward declaration of 'png_struct'
ppmutil.cc:2501:62: error: invalid use of incomplete type 'png_struct'
/usr/include/png.h:827:16: error: forward declaration of 'png_struct'
ppmutil.cc:2502:62: error: invalid use of incomplete type 'png_struct'
/usr/include/png.h:827:16: error: forward declaration of 'png_struct'
ppmutil.cc:2503:38: error: invalid use of incomplete type 'png_struct'
/usr/include/png.h:827:16: error: forward declaration of 'png_struct'
ppmutil.cc:2505:63: error: invalid use of incomplete type 'png_struct'
/usr/include/png.h:827:16: error: forward declaration of 'png_struct'
make[1]: *** [ppmutil.lo] Error 1
make[1]: *** Waiting for unfinished jobs....
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -O2 -pipe -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c quat.cc -o quat.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -O2 -pipe -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c cartesian.cc -o cartesian.o >/dev/null 2>&1
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -O2 -pipe -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c geomutil.cc -o geomutil.o >/dev/null 2>&1
mv -f .deps/quat.Tpo .deps/quat.Plo
mv -f .deps/cartesian.Tpo .deps/cartesian.Plo
mv -f .deps/geomutil.Tpo .deps/geomutil.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -O2 -pipe -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cc -o matrix.o >/dev/null 2>&1
mv -f .deps/matrix.Tpo .deps/matrix.Plo
libtool: compile:  i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DUSE_LIBPNG -O2 -pipe -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c mgtree.cc -o mgtree.o >/dev/null 2>&1
mv -f .deps/mgtree.Tpo .deps/mgtree.Plo
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2/ccp4mg-utils'
make: *** [all-recursive] Error 1
emake failed
 * ERROR: sci-chemistry/coot-0.6.2 failed (compile phase):
 *   emake failed
 * 
 * Call stack:
 *     ebuild.sh, line  56:  Called src_compile
 *   environment, line 5988:  Called die
 * The specific snippet of code:
 *       emake || die "emake failed";
 * 
 * If you need support, post the output of 'emerge --info =sci-chemistry/coot-0.6.2',
 * the complete build log and the output of 'emerge -pqv =sci-chemistry/coot-0.6.2'.
 * The complete build log is located at '/var/log/portage/build/sci-chemistry/coot-0.6.2:20110808-145204.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/coot-0.6.2/temp/environment'.
 * S: '/var/tmp/portage/sci-chemistry/coot-0.6.2/work/coot-0.6.2'