=> Bootstrap dependency digest>=20010302: found digest-20111104 => Bootstrap dependency fetch-[0-9]*: found fetch-1.7 => Checksum SHA1 OK for gromacs-4.5.5.tar.gz => Checksum RMD160 OK for gromacs-4.5.5.tar.gz ===> Installing dependencies for gromacs-4.5.5nb1 ========================================================================== The supported build options for gromacs are: mpi x11 The currently selected options are: mpi x11 You can select which build options to use by setting PKG_DEFAULT_OPTIONS or the following variable. Its current value is shown: PKG_OPTIONS.gromacs (not defined) ========================================================================== => Build dependency libtool-base>=2.2.6bnb3: found libtool-base-2.2.6bnb8 => Build dependency pkg-config>=0.25: found pkg-config-0.25nb1 => Build dependency openpa>=1.0.1: found openpa-1.0.2 => Build dependency kbproto>=1.0.2: found kbproto-1.0.6 => Build dependency xproto>=7.0.9: found xproto-7.0.23 => Build dependency xcb-proto>=1.4: found xcb-proto-1.7.1nb1 => Build dependency checkperms>=1.1: found checkperms-1.11 => Full dependency perl>=5.0: found perl-5.14.2nb5 => Full dependency mpich2>=1.0.7: found mpich2-1.4.1p1 => Full dependency libX11>=1.1: found libX11-1.5.0 => Full dependency libICE>=0.99.1: found libICE-1.0.8 => Full dependency libSM>=0.99.2: found libSM-1.2.1 => Full dependency fftw>=3.1nb1: found fftw-3.3.2 => Full dependency gsl>=1.5nb1: found gsl-1.15 => Full dependency libxml2>=2.8.0nb2: found libxml2-2.8.0nb3 ===> Overriding tools for gromacs-4.5.5nb1 ===> Extracting for gromacs-4.5.5nb1 ===> Patching for gromacs-4.5.5nb1 => Applying pkgsrc patches for gromacs-4.5.5nb1 ===> Creating toolchain wrappers for gromacs-4.5.5nb1 ===> Configuring for gromacs-4.5.5nb1 => Modifying GNU configure scripts to avoid --recheck => Replacing config-guess with pkgsrc versions => Replacing config-sub with pkgsrc versions => Replacing install-sh with pkgsrc version => Replacing Perl interpreter in scripts/demux.pl scripts/xplor2gmx.pl. => Fixing locale directory references. => Checking for portability problems in extracted files checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c -o pbulk -g pbulk checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /tmp/pkgsrc/biology/gromacs/work/.tools/bin/mkdir -p checking for gawk... /usr/bin/awk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for x86_64-unknown-linux-cc... 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking dependency style of gcc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for MPI_IN_PLACE in collective operations... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... (cached) /bin/grep checking for egrep... (cached) /bin/egrep checking whether ln -s works... yes checking whether mpicc accepts -O3... yes checking whether mpicc accepts -msse2... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -std=gnu99... yes checking whether mpicc accepts -fexcess-precision=fast... yes ****************************************** * Using CFLAGS from environment variable * ****************************************** checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /tmp/pkgsrc/biology/gromacs/work/.tools/bin/sed checking for ld used by mpicc... /usr/x86_64-unknown-linux-gnu/bin/ld checking if the linker (/usr/x86_64-unknown-linux-gnu/bin/ld) is GNU ld... yes checking for /usr/x86_64-unknown-linux-gnu/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all 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 mpicc accepts -g... yes checking dependency style of mpicc... gcc3 checking how to run the C++ preprocessor... cpp checking the maximum length of command line arguments... (cached) 2097152 checking command to parse /usr/bin/nm -B output from mpicc object... ok checking for objdir... .libs checking for x86_64-unknown-linux-ar... no checking for ar... ar checking for x86_64-unknown-linux-ranlib... no checking for ranlib... ranlib checking for x86_64-unknown-linux-strip... no checking for strip... strip checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC checking if mpicc PIC flag -fPIC works... yes checking if mpicc static flag -static works... yes checking if mpicc supports -c -o file.o... yes checking whether the mpicc linker (/usr/x86_64-unknown-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no 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 mpicc... /usr/x86_64-unknown-linux-gnu/bin/ld -m elf_x86_64 checking if the linker (/usr/x86_64-unknown-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the mpicc linker (/usr/x86_64-unknown-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking for mpicc option to produce PIC... -fPIC checking if mpicc PIC flag -fPIC works... yes checking if mpicc static flag -static works... yes checking if mpicc supports -c -o file.o... yes checking whether the mpicc linker (/usr/x86_64-unknown-linux-gnu/bin/ld -m elf_x86_64) 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 f77 option to produce PIC... -fPIC checking if f77 PIC flag -fPIC works... no checking if f77 static flag -static works... no checking if f77 supports -c -o file.o... no checking whether the f77 linker (/usr/x86_64-unknown-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... PKGSRC-WARNING: Something is trying to run the fortran compiler, PKGSRC-WARNING: but it is not added to USE_LANGUAGES in the package Makefile. GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3... yes checking rpc/rpc.h usability... yes checking rpc/rpc.h presence... yes checking for rpc/rpc.h... yes checking for rpc/xdr.h... yes checking for xdr_float in -lnsl... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking unistd.h usability... yes checking unistd.h presence... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking direct.h usability... no checking direct.h presence... no checking for direct.h... no checking sys/types.h usability... yes checking sys/types.h presence... yes checking for sys/types.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking dirent.h usability... yes checking dirent.h presence... yes checking for dirent.h... yes checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for working memcmp... yes checking return type of signal handlers... void checking for off_t... yes checking for vprintf... yes checking for _doprnt... no checking if malloc debugging is wanted... no checking for strcasecmp... yes checking for strdup... yes checking for gettimeofday... yes checking for cbrt... yes checking for isnan... yes checking for _isnan... no checking for isfinite... no checking for _isfinite... no checking for fsync... yes checking for fileno... yes checking for bool... no checking for library containing posix_memalign... none required checking for library containing memalign... none required checking for _aligned_malloc... no checking size of int... 4 checking size of long int... 8 checking size of long long int... 8 checking size of off_t... 8 checking size of void*... 8 checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking gsl/gsl_version.h usability... yes checking gsl/gsl_version.h presence... yes checking for gsl/gsl_version.h... yes checking for main in -lgslcblas... yes checking for main in -lgsl... yes checking libxml/parser.h usability... no checking libxml/parser.h presence... no checking for libxml/parser.h... no checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for inline... inline checking for C/C++ restrict keyword... __restrict checking for uid_t... yes checking for gid_t... yes checking for sig_atomic_t... yes checking whether your compiler can handle assembly files (*.s)... yes checking whether as fully supports X86_64 SSE2... yes checking whether byte ordering is bigendian... (cached) no checking if dlopen supported... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/gmxlib/Makefile config.status: creating src/gmxlib/libgmx_mpi_d.pc config.status: creating src/gmxlib/gmx_blas/Makefile config.status: creating src/gmxlib/gmx_lapack/Makefile config.status: creating src/gmxlib/selection/Makefile config.status: creating src/gmxlib/statistics/Makefile config.status: creating src/gmxlib/trajana/Makefile config.status: creating src/gmxlib/thread_mpi/Makefile config.status: creating src/gmxlib/nonbonded/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_c/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_bluegene/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_power6/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_single/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_double/Makefile config.status: creating include/Makefile config.status: creating include/types/Makefile config.status: creating include/thread_mpi/Makefile config.status: creating include/thread_mpi/atomic/Makefile config.status: creating src/mdlib/Makefile config.status: creating src/mdlib/libmd_mpi_d.pc config.status: creating src/kernel/Makefile config.status: creating src/kernel/libgmxpreprocess_mpi_d.pc config.status: creating src/tools/Makefile config.status: creating src/tools/libgmxana_mpi_d.pc config.status: creating src/ngmx/Makefile config.status: creating src/contrib/Makefile config.status: creating scripts/Makefile config.status: creating admin/Makefile config.status: creating share/Makefile config.status: creating share/tutor/Makefile config.status: creating share/tutor/gmxdemo/Makefile config.status: creating share/tutor/nmr1/Makefile config.status: creating share/tutor/nmr2/Makefile config.status: creating share/tutor/water/Makefile config.status: creating share/tutor/mixed/Makefile config.status: creating share/tutor/methanol/Makefile config.status: creating share/tutor/speptide/Makefile config.status: creating share/template/Makefile config.status: creating share/top/Makefile config.status: creating share/top/gmx.ff/Makefile config.status: creating share/top/gmx2.ff/Makefile config.status: creating share/top/encadv.ff/Makefile config.status: creating share/top/encads.ff/Makefile config.status: creating share/top/oplsaa.ff/Makefile config.status: creating share/top/gromos43a1.ff/Makefile config.status: creating share/top/gromos43a2.ff/Makefile config.status: creating share/top/gromos45a3.ff/Makefile config.status: creating share/top/gromos53a5.ff/Makefile config.status: creating share/top/gromos53a6.ff/Makefile config.status: creating share/top/charmm27.ff/Makefile config.status: creating share/top/amber94.ff/Makefile config.status: creating share/top/amber96.ff/Makefile config.status: creating share/top/amberGS.ff/Makefile config.status: creating share/top/amber99.ff/Makefile config.status: creating share/top/amber99sb.ff/Makefile config.status: creating share/top/amber99sb-ildn.ff/Makefile config.status: creating share/top/amber03.ff/Makefile config.status: creating share/html/Makefile config.status: creating share/html/images/Makefile config.status: creating share/html/online/Makefile config.status: creating man/Makefile config.status: creating man/man1/Makefile config.status: creating man/man7/Makefile config.status: creating Doxyfile config.status: creating src/config.h config.status: executing depfiles commands => Modifying libtool scripts to use pkgsrc libtool WARNING: *** Please consider adding fortran to USE_LANGUAGES in the package Makefile.