* CPV: sci-chemistry/ccp4-apps-6.1.3-r2 * REPO: gentoo * USE: elibc_glibc kernel_linux test userland_GNU x86 * You need one of these Fortran Compilers: g77 gfortran ifc * Installed are: gfortran >>> Unpacking source... >>> Unpacking ccp4-6.1.3-core-src.tar.gz to /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work >>> Unpacking 6.1.3-oasis4.0.patch.bz2 to /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work * Applying patches for selected FORTRAN compiler: gfortran >>> Source unpacked in /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work >>> Preparing source in /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 ... * Applying upstream patches ... * Done. * Applying Gentoo patches ... * 6.1.3-dont-make-dirs-in-configure.patch ... [ ok ] * 6.1.3-dont-build-double-and-make-bindir.patch ... [ ok ] * 6.1.3-dont-build-libs.patch ... [ ok ] * 6.1.3-rename-truncate.patch ... [ ok ] * 6.1.3-rename-rapper.patch ... [ ok ] * 6.1.3-dont-build-molref.patch ... [ ok ] * 6.1.3-dont-build-xia.patch ... [ ok ] * 6.1.3-dont-build-scala.patch ... [ ok ] * 6.1.3-dont-build-imosflm.patch ... [ ok ] * 6.1.3-dont-build-balbes.patch ... [ ok ] * 6.1.3-dont-configure.patch ... [ ok ] * 6.1.3-pythonpath.patch ... [ ok ] * 6.1.3-pisa.patch ... [ ok ] * 6.1.3-clipper-template.patch ... [ ok ] * Applying 6.1.3-oasis4.0.patch ... [ ok ] * Done. /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/rapper /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 * Running eautoreconf in '/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/rapper' ... * Running aclocal ... [ ok ] * Running libtoolize --copy --force --install --automake ... [ ok ] * Running aclocal ... [ ok ] * Running autoconf ... [ ok ] * Running automake --add-missing --copy ... [ ok ] * Running elibtoolize in: ccp4-6.1.3/src/rapper/gc7.0 * Applying install-sh-1.5.patch ... * Applying portage-1.5.10.patch ... * Applying max_cmd_len-1.5.20.patch ... * Applying sed-1.5.6.patch ... * Applying as-needed-1.5.patch ... * Running elibtoolize in: ccp4-6.1.3/src/rapper * Applying portage-2.2.patch ... * Applying sed-1.5.6.patch ... * Applying as-needed-2.2.6.patch ... * Running elibtoolize in: ccp4-6.1.3/src/rapper/libxml2 * Applying install-sh-1.5.patch ... * Applying portage-1.5.10.patch ... * Applying max_cmd_len-1.5.20.patch ... * Applying sed-1.5.6.patch ... * Applying as-needed-1.5.patch ... /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 * Using GNU config files from /usr/share/gnuconfig * Updating x-windows/xdl_view/src/config.sub [ ok ] * Updating x-windows/Mosflm/config.sub [ ok ] * Updating x-windows/Mosflm/jpg/config.sub [ ok ] * Updating x-windows/Mosflm/cbf/config.sub [ ok ] * Updating x-windows/Rotgen/config.sub [ ok ] * Updating x-windows/libjwc/libjwc_f/config.sub [ ok ] * Updating x-windows/libjwc/libjwc_c/config.sub [ ok ] * Updating lib/fftw/config.sub [ ok ] * Updating lib/DiffractionImage/config.sub [ ok ] * Updating lib/rxdispencer/config.sub [ ok ] * Updating lib/ccif/config.sub [ ok ] * Updating lib/clipper/config.sub [ ok ] * Updating lib/ssm/config.sub [ ok ] * Updating src/rapper/gc7.0/config.sub [ ok ] * Updating src/rapper/gc7.0/libatomic_ops-1.2/config.sub [ ok ] * Updating src/rapper/config.sub [ ok ] * Updating src/rapper/libxml2/config.sub [ ok ] * Updating src/clipper_progs/config.sub [ ok ] * Updating src/pointless/config.sub [ ok ] * Updating src/pisa/config.sub [ ok ] * Updating x-windows/xdl_view/src/config.guess [ ok ] * Updating x-windows/Mosflm/jpg/config.guess [ ok ] * Updating x-windows/Mosflm/config.guess [ ok ] * Updating x-windows/Mosflm/cbf/config.guess [ ok ] * Updating x-windows/Rotgen/config.guess [ ok ] * Updating x-windows/libjwc/libjwc_f/config.guess [ ok ] * Updating x-windows/libjwc/libjwc_c/config.guess [ ok ] * Updating lib/fftw/config.guess [ ok ] * Updating lib/DiffractionImage/config.guess [ ok ] * Updating lib/rxdispencer/config.guess [ ok ] * Updating lib/ccif/config.guess [ ok ] * Updating lib/clipper/config.guess [ ok ] * Updating lib/ssm/config.guess [ ok ] * Updating src/rapper/gc7.0/libatomic_ops-1.2/config.guess [ ok ] * Updating src/rapper/gc7.0/config.guess [ ok ] * Updating src/rapper/config.guess [ ok ] * Updating src/rapper/libxml2/config.guess [ ok ] * Updating src/clipper_progs/config.guess [ ok ] * Updating src/pointless/config.guess [ ok ] * Updating src/pisa/config.guess [ ok ] * Converting shebang in 'src/ccp4_pipeline_simple.py' >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 ... with_fftw='/usr' srcdir bindir libdir /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/bin /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib OK, setting up for a system type of `linux'... ! Using gnu fortran compiler. If you have an old fortran compiler, you may be better ! off using f2c, see --with-f2c option. ! The x-windows programs will not be installed. ! If you want the x-windows programs to be installed re-run ! configure with the --enable-x flag. The CCIF library will be built and installed. This has been tested on the most common systems, but if you have problems, use the --disable-ccif flag. Installation of the CCTBX library has been suppressed. Some functionality will be lost. Installation of Phaser has been suppressed. The LAPACK linear algebra package will be included in the installation. Configure will search for existing LAPACK and BLAS libraries on on your system - if a version of LAPACK is not found then the NetLib version will be built for you automatically. If you want NetLib LAPACK and BLAS to be used regardless of system libraries then rerun configure using --with-netlib-lapack To disable inclusion of LAPACK, use the --disable-lapack flag (This is not recommended as some programs will fail to build) Configure will try to set up and build the CCP4i MapSlicer command library, which is required to use the MapSlicer viewer. ***** This may not be possible for some systems! ***** To disable inclusion of the MapSlicer command library, use the --disable-mapslicer flag ! You have specified a non-default Fortran compiler (gfortran). This probably only makes sense if you have made the appropriate changes to the Fortran-C interface routines. testing linux ABI using: i686-pc-linux-gnu-gcc $ 32-bit Testing Fortran90 support. Fortran90 support confirmed (needed for latest Refmac and Molrep) checking for ctime... yes Testing command for running m4 (m4 -D_gfort=1) ... ok Returning to main configure. ********* BLAS AND LAPACK CONFIGURATION *********** Warning: this option has not been extensively tested! Please report problems to ccp4@ccp4.ac.uk Guessing names for native/vendor LAPACK and/or BLAS libraries on this system Possible LAPACK library names for this system: liblapack Searching for libraries with LAPACK and BLAS: ...nothing in /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib ...nothing in /lib ...found LAPACK library: /usr/lib/liblapack.a Testing: try to link library against test program gfortran -O2 -fno-second-underscore -fno-stack-protector -fPIC -o testlink testlink.f -L/usr/lib -llapack Link ok - using liblapack from /usr/lib * Checking whether we need a separate BLAS library * Testing: try linking library against test program gfortran -O2 -fno-second-underscore -fno-stack-protector -fPIC -o testlsame lsametst.f -L/usr/lib -llapack /usr/lib/liblapack.so: undefined reference to `clapack_ilaenv' collect2: ld returned 1 exit status gfortran -O2 -fno-second-underscore -fno-stack-protector -fPIC -o testlsame lsametst.f -L/usr/lib -llapack -Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm /usr/lib/liblapack.so: undefined reference to `clapack_ilaenv' collect2: ld returned 1 exit status Test program failed - need a separate BLAS library Possible BLAS library names for this system: libblas Searching for libraries with BLAS: ...nothing in /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib ...nothing in /lib ...found BLAS library: /usr/lib/libblas.a Testing: try to link library against test program gfortran -O2 -fno-second-underscore -fno-stack-protector -fPIC -o testlink testlink.f -L/usr/lib -lblas Link ok - using libblas from /usr/lib Test C linking for lapack library i686-pc-linux-gnu-gcc -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -o testlink testlink.c -L/usr/lib -llapack -L/usr/lib -lblas /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/temp/ccuxUVsJ.o: In function `main': testlink.c:(.text+0x9c): undefined reference to `dsyev' collect2: ld returned 1 exit status Linking in LAPACK/BLAS using XLAPACK_LIB="-L/usr/lib -llapack -L/usr/lib -lblas" ***** BLAS AND LAPACK CONFIGURATION FINISHED ******* ********* SSM CONFIGURATION *********** Updating modification times for configuration files Please wait... ...done. configure --enable-shared=yes --with-mmdb=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --with-ccp4=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --exec_prefix=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --prefix=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --bindir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/bin --libdir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for style of include used by make... GNU checking for gcc... i686-pc-linux-gnu-gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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 a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for 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 /usr/i686-pc-linux-gnu/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking whether ln -s works... yes checking how to recognize dependent libraries... pass_all checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes 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 how to run the C++ preprocessor... i686-pc-linux-gnu-g++ -E checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking the maximum length of command line arguments... 1572864 checking command to parse /usr/bin/nm -B output from i686-pc-linux-gnu-gcc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip 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 checking if i686-pc-linux-gnu-gcc PIC flag -fPIC 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 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 configure: creating libtool appending configuration tag "CXX" to libtool 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 checking if i686-pc-linux-gnu-g++ PIC flag -fPIC 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 whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate appending configuration tag "F77" to libtool checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... yes checking if gfortran supports -c -o file.o... yes checking whether the gfortran linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether to enable maintainer-specific portions of Makefiles... no checking whether we are using the GNU C++ compiler... (cached) yes checking whether i686-pc-linux-gnu-g++ accepts -g... (cached) yes checking dependency style of i686-pc-linux-gnu-g++... (cached) gcc3 checking for ANSI C header files... (cached) yes checking for a BSD-compatible install... /usr/bin/install -c checking for CMMDBManager in MMDB... no configure: WARNING: assuming library -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lmmdb headers -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for sqrt in -lm... yes configure: creating ./config.status config.status: creating Makefile config.status: executing depfiles commands ***** SSM CONFIGURATION FINISHED ******* ********* RAPPER CONFIGURATION *********** Updating modification times for configuration files Please wait... ...done. configure --enable-shared=yes --exec_prefix=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --prefix=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --bindir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/bin --libdir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib --disable-shared checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether 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-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-g++... gcc3 checking for gcc... i686-pc-linux-gnu-gcc 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 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 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 bstring.h usability... no checking bstring.h presence... no checking for bstring.h... no checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu 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 for /usr/i686-pc-linux-gnu/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from i686-pc-linux-gnu-gcc object... ok checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... (cached) yes checking whether i686-pc-linux-gnu-g++ accepts -g... (cached) yes checking dependency style of i686-pc-linux-gnu-g++... (cached) gcc3 checking how to run the C++ preprocessor... i686-pc-linux-gnu-g++ -E 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 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... no checking whether to build static libraries... yes 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... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate configure: creating ./config.status config.status: creating Makefile config.status: creating LOOP/Makefile config.status: creating data/Makefile config.status: executing depfiles commands config.status: executing libtool commands ***** RAPPER CONFIGURATION FINISHED ******* ********* PISA CONFIGURATION *********** Updating modification times for configuration files Please wait... ...done. configure --enable-shared=yes --exec_prefix=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --prefix=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --bindir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/bin --libdir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib --with-mmdb=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --with-ssm=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether i686-pc-linux-gnu-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-g++... gcc3 checking how to run the C++ preprocessor... i686-pc-linux-gnu-g++ -E checking for egrep... grep -E checking for ANSI C header files... yes checking for a BSD-compatible install... /usr/bin/install -c checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for sqrt in -lm... yes checking for CMMDBManager in MMDB... no configure: WARNING: assuming library -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lmmdb headers -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb checking for CSSMAlign in SSM... no configure: WARNING: assuming library -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lssm headers -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/ssm configure: creating ./config.status config.status: creating Makefile config.status: creating pisastore/Makefile config.status: creating molref/Makefile config.status: creating sbase/Makefile config.status: creating doc/Makefile config.status: creating pisa.cfg config.status: executing depfiles commands ***** PISA CONFIGURATION FINISHED ******* ********* MAPSLICER CONFIGURATION *********** Please check the output below and report any problems to ccp4@ccp4.ac.uk Searching for tclConfig.sh and/or tkConfig.sh... ...found tclConfig.sh in /usr/bin/../lib TCL major version is 8.5 - OK Found tcl.h in /usr/bin/../include ...found tkConfig.sh in /usr/bin/../lib TK major version is 8.5 - OK Found tk.h in /usr/bin/../include WARNING: the TCL_CONFIG environment variable was not detected. configure has searched and guessed that your tclConfig.sh installation is: /usr/bin/../lib/tclConfig.sh If you think that this not the correct version to use then please set the correct version using the environment variable TCL_CONFIG before running configure. WARNING: the TK_CONFIG environment variable was not detected. configure has searched and guessed that your tkConfig.sh installation is: /usr/bin/../lib/tkConfig.sh If you think that this not the correct version to use then please set the correct version using the environment variable TK_CONFIG before running configure. Options acquired from tclConfig.sh: ...to link to Tcl library : -L/usr/lib -ltcl8.5 Options acquired from tkConfig.sh: ...to link to Tk library : -L/usr/lib -ltk8.5 ...other libraries for Tk : -lX11 -lXss -lXext -lpthread -ldl -lpthread -lieee -lm ...switch to make X11 includes accessible: Checking: try to compile test program using these settings... i686-pc-linux-gnu-gcc -I/usr/bin/../include -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -o testcomp testcomp.c -L/usr/lib -ltk8.5 -L/usr/lib -ltcl8.5 -lX11 -lXss -lXext -lpthread -ldl -lpthread -lieee -lm Test compilation successful - using these settings to build ccp4mapwish Also configured to build the command library as a loadable package ***** MAPSLICER CONFIGURATION FINISHED ******* Building of the RCSB PDB_EXTRACT suite has been suppressed. As a result you will not be able to use the PDB_EXTRACT programs. The configuration can be re-built by executing config.status : #!/bin/sh # (Generated automatically by configure) # CCP4 was configured as follows: libdir="/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib" RANLIB="ranlib" \ FC="gfortran" FOPTIM=" -O2" \ COPTIM="-O2 -pipe" XFFLAGS="-fno-second-underscore -fno-stack-protector -fPIC" \ XCFLAGS="-DGFORTRAN -DPROTOTYPE -fPIC" CC="i686-pc-linux-gnu-gcc" \ LNS="ln -s" M4="m4 -D_gfort=1" \ XCXXFLAGS=" -fPIC" CXX="i686-pc-linux-gnu-g++" \ CXXOPTIM="-O2 -pipe" \ M4FLAGS="" SETFLAGS="lgglib_FLAGS='-fno-second-underscore -fno-stack-protector -fPIC -O0' arp_waters_FLAGS='-fno-second-underscore -fno-stack-protector -fPIC -O2 -fforce-mem' " \ MAKE="make" F="f" \ INSTALL_PROGRAM="cp -p" INSTALL_DATA="cp -p" \ XLDFLAGS="-Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm" \ SHARE_LIB="ld -shared -soname libmmdb.so -o libmmdb.so ${MMDBOBJS}; ld -shared -soname libccp4c.so -o libccp4c.so ${CORELIBOBJS} ${CGENERALOBJS} ${CUCOBJS} ${CMTZOBJS} ${CMAPOBJS} ${CSYMOBJS}; ld -shared -soname libccp4f.so -o libccp4f.so $(FORTRANLOBJS) $(FINTERFACEOBJS)" \ SHARED_LIB_CFLAGS='' \ SHARED_LIB_FFLAGS="" \ SHARE_INST="$(INSTALL_DATA) `pwd`/libmmdb.so $(libdir)/libmmdb.so; $(INSTALL_DATA) `pwd`/libccp4c.so $(libdir)/libccp4c.so; $(INSTALL_DATA) `pwd`/libccp4f.so $(libdir)/libccp4f.so; " \ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/configure --prefix=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --srcdir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --bindir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/bin --libdir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib --with-shared-libs --tmpdir=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/temp --disable-x --disable-cctbx --disable-phaser --enable-ssm --disable-clipper --disable-fftw --with-fftw=/usr --with-warnings --disable-pdb_extract --disable-diffractionImg linux -hush /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 * econf: updating ccp4-6.1.3/x-windows/xdl_view/src/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/x-windows/xdl_view/src/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/x-windows/Mosflm/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/x-windows/Mosflm/jpg/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/x-windows/Mosflm/jpg/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/x-windows/Mosflm/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/x-windows/Mosflm/cbf/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/x-windows/Mosflm/cbf/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/x-windows/Rotgen/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/x-windows/Rotgen/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/x-windows/libjwc/libjwc_f/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/x-windows/libjwc/libjwc_f/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/x-windows/libjwc/libjwc_c/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/x-windows/libjwc/libjwc_c/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/lib/fftw/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/lib/fftw/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/lib/DiffractionImage/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/lib/DiffractionImage/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/lib/rxdispencer/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/lib/rxdispencer/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/lib/ccif/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/lib/ccif/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/lib/clipper/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/lib/clipper/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/lib/ssm/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/lib/ssm/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/src/rapper/gc7.0/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/src/rapper/gc7.0/libatomic_ops-1.2/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/src/rapper/gc7.0/libatomic_ops-1.2/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/src/rapper/gc7.0/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/src/rapper/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/src/rapper/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/src/rapper/libxml2/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/src/rapper/libxml2/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/src/clipper_progs/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/src/clipper_progs/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/src/pointless/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/src/pointless/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ccp4-6.1.3/src/pisa/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ccp4-6.1.3/src/pisa/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 --prefix=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --with-ccp4=/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 --with-clipper=/usr --with-fftw=/usr --with-mmdb=/usr CXX=i686-pc-linux-gnu-g++ checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for i686-pc-linux-gnu-xlc++... i686-pc-linux-gnu-g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether i686-pc-linux-gnu-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-g++... gcc3 checking for i686-pc-linux-gnu-xlc... i686-pc-linux-gnu-gcc 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 ANSI C... none needed checking dependency style of i686-pc-linux-gnu-gcc... gcc3 checking for i686-pc-linux-gnu-g77... no checking for i686-pc-linux-gnu-f77... no checking for i686-pc-linux-gnu-xlf... no checking for i686-pc-linux-gnu-frt... no checking for i686-pc-linux-gnu-pgf77... no checking for i686-pc-linux-gnu-fort77... no checking for i686-pc-linux-gnu-fl32... no checking for i686-pc-linux-gnu-af77... no checking for i686-pc-linux-gnu-f90... no checking for i686-pc-linux-gnu-xlf90... no checking for i686-pc-linux-gnu-pgf90... no checking for i686-pc-linux-gnu-epcf90... no checking for i686-pc-linux-gnu-f95... no checking for i686-pc-linux-gnu-fort... no checking for i686-pc-linux-gnu-xlf95... no checking for i686-pc-linux-gnu-ifc... no checking for i686-pc-linux-gnu-efc... no checking for i686-pc-linux-gnu-pgf95... no checking for i686-pc-linux-gnu-lf95... no checking for i686-pc-linux-gnu-gfortran... i686-pc-linux-gnu-gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether i686-pc-linux-gnu-gfortran accepts -g... yes checking how to run the C++ preprocessor... i686-pc-linux-gnu-g++ -E checking for egrep... grep -E checking for ANSI C header files... yes checking for a BSD-compatible install... /usr/bin/install -c checking for fftw_print_max_memory_usage in fftw... no checking for fftw_print_max_memory_usage in sfftw... yes checking for CMMDBManager in MMDB... yes checking for ccp4_errno in CCP4... no configure: WARNING: assuming library -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c headers -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src checking for clipper_errno in CLIPPER... yes checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for sqrt in -lm... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/pirate/Makefile config.status: creating src/parrot/Makefile config.status: creating src/buccaneer/Makefile config.status: creating html/Makefile config.status: executing depfiles commands /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 ... /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 make -j14 fsplit -j1 test ! -x /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/fsplit && i686-pc-linux-gnu-gcc -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/fsplit fsplit.c || true /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 make -j14 Making all in src make[1]: Entering directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs/src' Making all in pirate make[2]: Entering directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs/src/pirate' source='cpirate.cpp' object='cpirate.o' libtool=no \ depfile='.deps/cpirate.Po' tmpdepfile='.deps/cpirate.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cpirate.o `test -f 'cpirate.cpp' || echo './'`cpirate.cpp source='simulate-lib.cpp' object='simulate-lib.o' libtool=no \ depfile='.deps/simulate-lib.Po' tmpdepfile='.deps/simulate-lib.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o simulate-lib.o `test -f 'simulate-lib.cpp' || echo './'`simulate-lib.cpp source='pirate-lib.cpp' object='pirate-lib.o' libtool=no \ depfile='.deps/pirate-lib.Po' tmpdepfile='.deps/pirate-lib.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o pirate-lib.o `test -f 'pirate-lib.cpp' || echo './'`pirate-lib.cpp source='pirate-ncsaver.cpp' object='pirate-ncsaver.o' libtool=no \ depfile='.deps/pirate-ncsaver.Po' tmpdepfile='.deps/pirate-ncsaver.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o pirate-ncsaver.o `test -f 'pirate-ncsaver.cpp' || echo './'`pirate-ncsaver.cpp source='pirate-ncsfind.cpp' object='pirate-ncsfind.o' libtool=no \ depfile='.deps/pirate-ncsfind.Po' tmpdepfile='.deps/pirate-ncsfind.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o pirate-ncsfind.o `test -f 'pirate-ncsfind.cpp' || echo './'`pirate-ncsfind.cpp source='simplex-lib.cpp' object='simplex-lib.o' libtool=no \ depfile='.deps/simplex-lib.Po' tmpdepfile='.deps/simplex-lib.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o simplex-lib.o `test -f 'simplex-lib.cpp' || echo './'`simplex-lib.cpp source='cmakereference.cpp' object='cmakereference.o' libtool=no \ depfile='.deps/cmakereference.Po' tmpdepfile='.deps/cmakereference.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cmakereference.o `test -f 'cmakereference.cpp' || echo './'`cmakereference.cpp source='ftplib.c' object='ftplib.o' libtool=no \ depfile='.deps/ftplib.Po' tmpdepfile='.deps/ftplib.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c `test -f 'ftplib.c' || echo './'`ftplib.c source='compress42.c' object='compress42.o' libtool=no \ depfile='.deps/compress42.Po' tmpdepfile='.deps/compress42.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c `test -f 'compress42.c' || echo './'`compress42.c i686-pc-linux-gnu-g++ -O2 -pipe -o cmakereference cmakereference.o ftplib.o compress42.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o cpirate cpirate.o simulate-lib.o pirate-lib.o pirate-ncsaver.o pirate-ncsfind.o simplex-lib.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs/src/pirate' Making all in buccaneer make[2]: Entering directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs/src/buccaneer' source='buccaneer-build.cpp' object='buccaneer-build.o' libtool=no \ depfile='.deps/buccaneer-build.Po' tmpdepfile='.deps/buccaneer-build.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-build.o `test -f 'buccaneer-build.cpp' || echo './'`buccaneer-build.cpp source='buccaneer-prune.cpp' object='buccaneer-prune.o' libtool=no \ depfile='.deps/buccaneer-prune.Po' tmpdepfile='.deps/buccaneer-prune.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-prune.o `test -f 'buccaneer-prune.cpp' || echo './'`buccaneer-prune.cpp source='buccaneer-lib.cpp' object='buccaneer-lib.o' libtool=no \ depfile='.deps/buccaneer-lib.Po' tmpdepfile='.deps/buccaneer-lib.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-lib.o `test -f 'buccaneer-lib.cpp' || echo './'`buccaneer-lib.cpp source='buccaneer-correct.cpp' object='buccaneer-correct.o' libtool=no \ depfile='.deps/buccaneer-correct.Po' tmpdepfile='.deps/buccaneer-correct.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-correct.o `test -f 'buccaneer-correct.cpp' || echo './'`buccaneer-correct.cpp source='buccaneer-sequence.cpp' object='buccaneer-sequence.o' libtool=no \ depfile='.deps/buccaneer-sequence.Po' tmpdepfile='.deps/buccaneer-sequence.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-sequence.o `test -f 'buccaneer-sequence.cpp' || echo './'`buccaneer-sequence.cpp source='buccaneer-link.cpp' object='buccaneer-link.o' libtool=no \ depfile='.deps/buccaneer-link.Po' tmpdepfile='.deps/buccaneer-link.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-link.o `test -f 'buccaneer-link.cpp' || echo './'`buccaneer-link.cpp source='buccaneer-filter.cpp' object='buccaneer-filter.o' libtool=no \ depfile='.deps/buccaneer-filter.Po' tmpdepfile='.deps/buccaneer-filter.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-filter.o `test -f 'buccaneer-filter.cpp' || echo './'`buccaneer-filter.cpp source='buccaneer-util.cpp' object='buccaneer-util.o' libtool=no \ depfile='.deps/buccaneer-util.Po' tmpdepfile='.deps/buccaneer-util.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-util.o `test -f 'buccaneer-util.cpp' || echo './'`buccaneer-util.cpp source='buccaneer-ncsbuild.cpp' object='buccaneer-ncsbuild.o' libtool=no \ depfile='.deps/buccaneer-ncsbuild.Po' tmpdepfile='.deps/buccaneer-ncsbuild.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-ncsbuild.o `test -f 'buccaneer-ncsbuild.cpp' || echo './'`buccaneer-ncsbuild.cpp source='buccaneer-find.cpp' object='buccaneer-find.o' libtool=no \ depfile='.deps/buccaneer-find.Po' tmpdepfile='.deps/buccaneer-find.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-find.o `test -f 'buccaneer-find.cpp' || echo './'`buccaneer-find.cpp source='cbuccaneer.cpp' object='cbuccaneer.o' libtool=no \ depfile='.deps/cbuccaneer.Po' tmpdepfile='.deps/cbuccaneer.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cbuccaneer.o `test -f 'cbuccaneer.cpp' || echo './'`cbuccaneer.cpp source='buccaneer-prep.cpp' object='buccaneer-prep.o' libtool=no \ depfile='.deps/buccaneer-prep.Po' tmpdepfile='.deps/buccaneer-prep.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-prep.o `test -f 'buccaneer-prep.cpp' || echo './'`buccaneer-prep.cpp source='simplex-lib.cpp' object='simplex-lib.o' libtool=no \ depfile='.deps/simplex-lib.Po' tmpdepfile='.deps/simplex-lib.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o simplex-lib.o `test -f 'simplex-lib.cpp' || echo './'`simplex-lib.cpp source='buccaneer-grow.cpp' object='buccaneer-grow.o' libtool=no \ depfile='.deps/buccaneer-grow.Po' tmpdepfile='.deps/buccaneer-grow.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-grow.o `test -f 'buccaneer-grow.cpp' || echo './'`buccaneer-grow.cpp source='buccaneer-prot.cpp' object='buccaneer-prot.o' libtool=no \ depfile='.deps/buccaneer-prot.Po' tmpdepfile='.deps/buccaneer-prot.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-prot.o `test -f 'buccaneer-prot.cpp' || echo './'`buccaneer-prot.cpp source='simulate-lib.cpp' object='simulate-lib.o' libtool=no \ depfile='.deps/simulate-lib.Po' tmpdepfile='.deps/simulate-lib.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o simulate-lib.o `test -f 'simulate-lib.cpp' || echo './'`simulate-lib.cpp source='buccaneer-join.cpp' object='buccaneer-join.o' libtool=no \ depfile='.deps/buccaneer-join.Po' tmpdepfile='.deps/buccaneer-join.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o buccaneer-join.o `test -f 'buccaneer-join.cpp' || echo './'`buccaneer-join.cpp source='csequins.cpp' object='csequins.o' libtool=no \ depfile='.deps/csequins.Po' tmpdepfile='.deps/csequins.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o csequins.o `test -f 'csequins.cpp' || echo './'`csequins.cpp i686-pc-linux-gnu-g++ -O2 -pipe -o csequins csequins.o buccaneer-sequence.o simulate-lib.o buccaneer-prot.o buccaneer-lib.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o cbuccaneer buccaneer-build.o buccaneer-prune.o buccaneer-lib.o buccaneer-correct.o buccaneer-sequence.o buccaneer-link.o buccaneer-filter.o buccaneer-util.o buccaneer-ncsbuild.o buccaneer-find.o cbuccaneer.o buccaneer-prep.o simplex-lib.o buccaneer-grow.o buccaneer-prot.o simulate-lib.o buccaneer-join.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs/src/buccaneer' Making all in parrot make[2]: Entering directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs/src/parrot' source='cparrot.cpp' object='cparrot.o' libtool=no \ depfile='.deps/cparrot.Po' tmpdepfile='.deps/cparrot.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cparrot.o `test -f 'cparrot.cpp' || echo './'`cparrot.cpp source='parrot-lib.cpp' object='parrot-lib.o' libtool=no \ depfile='.deps/parrot-lib.Po' tmpdepfile='.deps/parrot-lib.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o parrot-lib.o `test -f 'parrot-lib.cpp' || echo './'`parrot-lib.cpp source='parrot-ncs.cpp' object='parrot-ncs.o' libtool=no \ depfile='.deps/parrot-ncs.Po' tmpdepfile='.deps/parrot-ncs.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o parrot-ncs.o `test -f 'parrot-ncs.cpp' || echo './'`parrot-ncs.cpp source='simplex-lib.cpp' object='simplex-lib.o' libtool=no \ depfile='.deps/simplex-lib.Po' tmpdepfile='.deps/simplex-lib.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o simplex-lib.o `test -f 'simplex-lib.cpp' || echo './'`simplex-lib.cpp source='parrot-ncsfind.cpp' object='parrot-ncsfind.o' libtool=no \ depfile='.deps/parrot-ncsfind.Po' tmpdepfile='.deps/parrot-ncsfind.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o parrot-ncsfind.o `test -f 'parrot-ncsfind.cpp' || echo './'`parrot-ncsfind.cpp source='parrot-ncsaver.cpp' object='parrot-ncsaver.o' libtool=no \ depfile='.deps/parrot-ncsaver.Po' tmpdepfile='.deps/parrot-ncsaver.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o parrot-ncsaver.o `test -f 'parrot-ncsaver.cpp' || echo './'`parrot-ncsaver.cpp source='simulate-lib.cpp' object='simulate-lib.o' libtool=no \ depfile='.deps/simulate-lib.Po' tmpdepfile='.deps/simulate-lib.TPo' \ depmode=gcc3 /bin/sh ../../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o simulate-lib.o `test -f 'simulate-lib.cpp' || echo './'`simulate-lib.cpp i686-pc-linux-gnu-g++ -O2 -pipe -o cparrot cparrot.o parrot-lib.o parrot-ncs.o simplex-lib.o parrot-ncsfind.o parrot-ncsaver.o simulate-lib.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs/src/parrot' make[2]: Entering directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs/src' source='chltofom.cpp' object='chltofom.o' libtool=no \ depfile='.deps/chltofom.Po' tmpdepfile='.deps/chltofom.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o chltofom.o `test -f 'chltofom.cpp' || echo './'`chltofom.cpp source='cphasematch.cpp' object='cphasematch.o' libtool=no \ depfile='.deps/cphasematch.Po' tmpdepfile='.deps/cphasematch.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cphasematch.o `test -f 'cphasematch.cpp' || echo './'`cphasematch.cpp source='csfcalc.cpp' object='csfcalc.o' libtool=no \ depfile='.deps/csfcalc.Po' tmpdepfile='.deps/csfcalc.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o csfcalc.o `test -f 'csfcalc.cpp' || echo './'`csfcalc.cpp source='cfft.cpp' object='cfft.o' libtool=no \ depfile='.deps/cfft.Po' tmpdepfile='.deps/cfft.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cfft.o `test -f 'cfft.cpp' || echo './'`cfft.cpp source='cinvfft.cpp' object='cinvfft.o' libtool=no \ depfile='.deps/cinvfft.Po' tmpdepfile='.deps/cinvfft.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cinvfft.o `test -f 'cinvfft.cpp' || echo './'`cinvfft.cpp source='csigmaa.cpp' object='csigmaa.o' libtool=no \ depfile='.deps/csigmaa.Po' tmpdepfile='.deps/csigmaa.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o csigmaa.o `test -f 'csigmaa.cpp' || echo './'`csigmaa.cpp source='cecalc.cpp' object='cecalc.o' libtool=no \ depfile='.deps/cecalc.Po' tmpdepfile='.deps/cecalc.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cecalc.o `test -f 'cecalc.cpp' || echo './'`cecalc.cpp source='cphasecombine.cpp' object='cphasecombine.o' libtool=no \ depfile='.deps/cphasecombine.Po' tmpdepfile='.deps/cphasecombine.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cphasecombine.o `test -f 'cphasecombine.cpp' || echo './'`cphasecombine.cpp source='cpatterson.cpp' object='cpatterson.o' libtool=no \ depfile='.deps/cpatterson.Po' tmpdepfile='.deps/cpatterson.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cpatterson.o `test -f 'cpatterson.cpp' || echo './'`cpatterson.cpp source='caniso.cpp' object='caniso.o' libtool=no \ depfile='.deps/caniso.Po' tmpdepfile='.deps/caniso.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o caniso.o `test -f 'caniso.cpp' || echo './'`caniso.cpp source='convert2mtz.cpp' object='convert2mtz.o' libtool=no \ depfile='.deps/convert2mtz.Po' tmpdepfile='.deps/convert2mtz.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o convert2mtz.o `test -f 'convert2mtz.cpp' || echo './'`convert2mtz.cpp source='ctruncate.cpp' object='ctruncate.o' libtool=no \ depfile='.deps/ctruncate.Po' tmpdepfile='.deps/ctruncate.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o ctruncate.o `test -f 'ctruncate.cpp' || echo './'`ctruncate.cpp source='ctruncate_utils.cpp' object='ctruncate_utils.o' libtool=no \ depfile='.deps/ctruncate_utils.Po' tmpdepfile='.deps/ctruncate_utils.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o ctruncate_utils.o `test -f 'ctruncate_utils.cpp' || echo './'`ctruncate_utils.cpp source='cpsf_utils.cpp' object='cpsf_utils.o' libtool=no \ depfile='.deps/cpsf_utils.Po' tmpdepfile='.deps/cpsf_utils.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cpsf_utils.o `test -f 'cpsf_utils.cpp' || echo './'`cpsf_utils.cpp i686-pc-linux-gnu-gfortran -c -o twinlaws.o `test -f 'twinlaws.f' || echo './'`twinlaws.f source='csymmatch.cpp' object='csymmatch.o' libtool=no \ depfile='.deps/csymmatch.Po' tmpdepfile='.deps/csymmatch.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o csymmatch.o `test -f 'csymmatch.cpp' || echo './'`csymmatch.cpp source='cmaplocal.cpp' object='cmaplocal.o' libtool=no \ depfile='.deps/cmaplocal.Po' tmpdepfile='.deps/cmaplocal.TPo' \ depmode=gcc3 /bin/sh ../depcomp \ i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"clipper_progs\" -DPACKAGE_TARNAME=\"clipper_progs\" -DPACKAGE_VERSION=\"0.1.0\" -DPACKAGE_STRING=\"clipper_progs\ 0.1.0\" -DPACKAGE_BUGREPORT=\"ccb@dl.ac.uk\" -DPACKAGE=\"clipper_progs\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_FLOOR=1 -DHAVE_POW=1 -DHAVE_RINT=1 -DHAVE_SQRT=1 -DHAVE_LIBM=1 -I. -I. -I/usr/include -I/usr/include -I/usr/include -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/include -O2 -pipe -c -o cmaplocal.o `test -f 'cmaplocal.cpp' || echo './'`cmaplocal.cpp i686-pc-linux-gnu-g++ -O2 -pipe -o cphasecombine cphasecombine.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o caniso caniso.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o chltofom chltofom.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o cinvfft cinvfft.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o cecalc cecalc.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o cpatterson cpatterson.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o cmaplocal cmaplocal.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o csigmaa csigmaa.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o csfcalc csfcalc.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o csymmatch csymmatch.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o cfft cfft.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o cphasematch cphasematch.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o convert2mtz convert2mtz.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm i686-pc-linux-gnu-g++ -O2 -pipe -o ctruncate ctruncate.o ctruncate_utils.o cpsf_utils.o twinlaws.o -L/usr/lib -lclipper-cif -lclipper-ccp4 -lclipper-contrib -lclipper-minimol -lclipper-mmdb -lclipper-core -L/usr/lib -lsrfftw -lsfftw -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -lccp4c -L/usr/lib -lmmdb -lm make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs/src' make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs/src' make[1]: Entering directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs' make[1]: Nothing to be done for `all-am'. make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/clipper_progs' /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3 make -j14 -j1 if test -d src; then cd src; make ; else true; fi make[1]: Entering directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src' i686-pc-linux-gnu-gcc -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/../lib/src -o pltdev /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/pltdev.c -lm -Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/pltdev.c: In function ‘finish’: /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/pltdev.c:1206: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result i686-pc-linux-gnu-gcc -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/../lib/src -o binsort /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/binsort.c -lm -Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm i686-pc-linux-gnu-gcc -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -c -o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/pdbhtf.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/topp_/pdbhtf.c eval i686-pc-linux-gnu-gcc ${pdbhtf_FLAGS-"-O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC"} -o pdbhtf pdbhtf.o -Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm && rm -f pdbhtf.o i686-pc-linux-gnu-gcc -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -c -o cmap_io.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/cmap_io.c /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/cmap_io.c: In function ‘WriteMap’: /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/cmap_io.c:357: warning: passing argument 3 of ‘mat4_to_symop’ from incompatible pointer type /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/ccp4_parser.h:290: note: expected ‘const float (*)[4]’ but argument is of type ‘float (*)[4]’ i686-pc-linux-gnu-gcc -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -c -o solomon.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/solomon.c /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/solomon.c: In function ‘ParseInput’: /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/solomon.c:709: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/solomon.c:714: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result i686-pc-linux-gnu-gcc -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -c -o matrix.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/matrix.c i686-pc-linux-gnu-gcc -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -c -o cmap_calc.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/cmap_calc.c i686-pc-linux-gnu-gcc -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -c -o cmsk_io.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/cmsk_io.c /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/cmsk_io.c: In function ‘ReadOMask’: /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/cmsk_io.c:116: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/cmsk_io.c: In function ‘DumpMask’: /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/solomon_/cmsk_io.c:844: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result i686-pc-linux-gnu-gcc -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -o solomon cmap_io.o solomon.o matrix.o cmap_calc.o cmsk_io.o -L../lib/src -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lccp4c -lmmdb -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/ccif -lccif -L/usr/lib -llapack -L/usr/lib -lblas -lstdc++ -Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm -lgfortran i686-pc-linux-gnu-gcc -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -o mtzdiff /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/dev_tools_/mtzdiff.c -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -L../lib/src -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lccp4c -lmmdb -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/ccif -lccif -L/usr/lib -llapack -L/usr/lib -lblas -lstdc++ -Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm -lgfortran i686-pc-linux-gnu-gcc -O2 -pipe -DGFORTRAN -DPROTOTYPE -fPIC -o mapdiff /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/dev_tools_/mapdiff.c -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -L../lib/src -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lccp4c -lmmdb -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/ccif -lccif -L/usr/lib -llapack -L/usr/lib -lblas -lstdc++ -Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm -lgfortran /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mtz2cif_/mtz2cif.c: In function ‘main’: /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mtz2cif_/mtz2cif.c:516: warning: passing argument 2 of ‘MtzParseLabin’ from incompatible pointer type /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/cmtzlib.h:718: note: expected ‘const char (*)[31]’ but argument is of type ‘char *’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mtz2cif_/mtz2cif_lib.c: In function ‘GetSymopString’: /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mtz2cif_/mtz2cif_lib.c:104: warning: passing argument 3 of ‘mat4_to_symop’ from incompatible pointer type /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/ccp4_parser.h:290: note: expected ‘const float (*)[4]’ but argument is of type ‘float (*)[4]’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/symconv_/symconv.c: In function ‘ApplyCellToSymmat’: /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/symconv_/symconv.c:443: warning: passing argument 2 of ‘ccp4_3matmul’ from incompatible pointer type /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/cvecmat.h:28: note: expected ‘const double (*)[3]’ but argument is of type ‘double (*)[3]’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/symconv_/symconv.c:443: warning: passing argument 3 of ‘ccp4_3matmul’ from incompatible pointer type /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/cvecmat.h:28: note: expected ‘const double (*)[3]’ but argument is of type ‘double (*)[3]’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/symconv_/symconv.c:444: warning: passing argument 2 of ‘ccp4_3matmul’ from incompatible pointer type /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/cvecmat.h:28: note: expected ‘const double (*)[3]’ but argument is of type ‘double (*)[3]’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/symconv_/symconv.c:444: warning: passing argument 3 of ‘ccp4_3matmul’ from incompatible pointer type /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/cvecmat.h:28: note: expected ‘const double (*)[3]’ but argument is of type ‘double (*)[3]’ i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o pdbcur.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/pdbcur.cpp eval i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb ${mmdb_app_FLAGS-"-O2 -pipe -fPIC"} -c -o pdbcur.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/`basename pdbcur.o .o`.cpp i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o pcur_funcs.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/pcur_funcs.cpp eval i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb ${mmdb_app_FLAGS-"-O2 -pipe -fPIC"} -c -o pcur_funcs.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/`basename pcur_funcs.o .o`.cpp /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/pcur_funcs.cpp: In function ‘void delhydrogen(CCP4::CCP4PARSERTOKEN*, int, CMMDBManager&, int&)’: /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/pcur_funcs.cpp:58: warning: deprecated conversion from string constant to ‘char*’ i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o ncont.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/ncont.cpp eval i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb ${mmdb_app_FLAGS-"-O2 -pipe -fPIC"} -c -o ncont.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/`basename ncont.o .o`.cpp i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o coord_format.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/coord_format.cpp eval i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb ${mmdb_app_FLAGS-"-O2 -pipe -fPIC"} -c -o coord_format.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/`basename coord_format.o .o`.cpp i686-pc-linux-gnu-g++ -O2 -pipe -fPIC -o coord_format coord_format.o -L../lib/src -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lccp4c -lmmdb -Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/ccif -lccif -L/usr/lib -llapack -L/usr/lib -lblas -lgfortran i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o pdb_merge.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/pdb_merge.cpp eval i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb ${mmdb_app_FLAGS-"-O2 -pipe -fPIC"} -c -o pdb_merge.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/mmdb_app_/`basename pdb_merge.o .o`.cpp i686-pc-linux-gnu-g++ -O2 -pipe -fPIC -o pdb_merge pdb_merge.o -L../lib/src -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lccp4c -lmmdb -Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/ccif -lccif -L/usr/lib -llapack -L/usr/lib -lblas -lgfortran /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp: In function ‘int main(int, char**, char**)’: /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:152: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:152: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:152: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:152: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:152: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:152: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:152: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:152: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:152: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:152: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:251: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:256: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:257: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:258: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:259: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:260: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:261: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:267: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:276: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:283: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:296: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:298: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:300: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:301: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:317: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:318: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:319: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:320: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:321: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:322: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:323: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:324: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:329: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:338: warning: deprecated conversion from string constant to ‘char*’ /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/harvest_app_/cross_validate.cpp:339: warning: deprecated conversion from string constant to ‘char*’ i686-pc-linux-gnu-g++ -O2 -pipe -fPIC -o pdbdiff /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/dev_tools_/pdbdiff.cpp -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -L../lib/src -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lccp4c -lmmdb -Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/ccif -lccif -L/usr/lib -llapack -L/usr/lib -lblas -lgfortran i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o crystal.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/crystal.C /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/crystal.C: In member function ‘Crystal& Crystal::setwithmanysca(std::string)’: /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/crystal.C:926: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/crystal.C:927: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/crystal.C:928: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/crystal.C:959: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/crystal.C:1015: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/crystal.C:1016: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/crystal.C:1017: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o gauss.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/gauss.C i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o input.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/input.C i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o likelihood.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/likelihood.C i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o minimizer.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/minimizer.C i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o misc.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/misc.C i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o model.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/model.C i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o sfdata.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/sfdata.C ar r libbp3.a crystal.o gauss.o input.o likelihood.o minimizer.o misc.o model.o sfdata.o ar: creating libbp3.a ranlib libbp3.a i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o bp3input.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/bp3input.C i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o bp3likelihood.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/bp3likelihood.C i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o bp3main.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/bp3main.C i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o mir.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/mir.C i686-pc-linux-gnu-g++ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_ -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src -I/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/src/mmdb -O2 -pipe -fPIC -c -o sad.o /var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src/bp3_/sad.C i686-pc-linux-gnu-g++ -O2 -pipe -fPIC -o bp3 bp3input.o bp3likelihood.o bp3main.o mir.o sad.o crystal.o gauss.o input.o likelihood.o minimizer.o misc.o model.o sfdata.o -L../lib/src -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lccp4c -lmmdb -Wl,-rpath,/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib -lm -L/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/lib/ccif -lccif -L/usr/lib -llapack -L/usr/lib -lblas -lgfortran -L/usr/lib -llapack -L/usr/lib -lblas /usr/lib/liblapack.so: undefined reference to `clapack_ilaenv' collect2: ld returned 1 exit status make[1]: *** [bp3] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3/src' make: *** [srcdir] Error 2 * ERROR: sci-chemistry/ccp4-apps-6.1.3-r2 failed: * emake failed * * Call stack: * ebuild.sh, line 54: Called src_compile * environment, line 5547: Called die * The specific snippet of code: * emake -j1 || die "emake failed" * * If you need support, post the output of 'emerge --info =sci-chemistry/ccp4-apps-6.1.3-r2', * the complete build log and the output of 'emerge -pqv =sci-chemistry/ccp4-apps-6.1.3-r2'. Merge of sci-chemistry/ccp4-apps-6.1.3-r2 at 2010-04-07T04:43:11+00:00 failed * The complete build log is located at '/var/log/portage/build/sci-chemistry/ccp4-apps-6.1.3-r2:20100407-044311.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/temp/environment'. * S: '/var/tmp/portage/sci-chemistry/ccp4-apps-6.1.3-r2/work/ccp4-6.1.3'