=> Bootstrap dependency digest>=20010302: found digest-20121220
WARNING: [license.mk] Every package should define a LICENSE.
===> Skipping vulnerability checks.
WARNING: No /var/db/pkg/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /var/db/pkg fetch-pkg-vulnerabilities'.
=> Checksum SHA1 OK for mpqc-2.3.1.tar.bz2
=> Checksum RMD160 OK for mpqc-2.3.1.tar.bz2
===> Installing dependencies for mpqc-2.3.1nb2
=> Tool dependency libtool-base>=2.2.6bnb3: found libtool-base-2.4.2nb4
=> Tool dependency gmake>=3.81: found gmake-3.82nb7
=> Tool dependency checkperms>=1.1: found checkperms-1.11
=> Build dependency libtool-fortran>=2.2.6bnb3: found libtool-fortran-2.4.2nb3
=> Build dependency libint>=2.0.0: found libint-2.0.0
=> Full dependency perl>=5.0: found perl-5.18.0nb1
=> Full dependency blas>=1.0nb3: found blas-1.1nb2
=> Full dependency lapack>=3.1.1: found lapack-3.1.1nb4
=> Full dependency g95>=0.91: found g95-0.93nb2
===> Overriding tools for mpqc-2.3.1nb2
===> Extracting for mpqc-2.3.1nb2
===> Patching for mpqc-2.3.1nb2
=> Applying pkgsrc patches for mpqc-2.3.1nb2
=> Verifying /data/pkgsrc/biology/mpqc/patches/patch-configure
=> Applying pkgsrc patch /data/pkgsrc/biology/mpqc/patches/patch-configure
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-configure,v 1.1.1.1 2013/03/16 12:43:26 asau Exp $
|
|--- configure.orig	2006-03-22 19:13:52.000000000 +0000
|+++ configure
--------------------------
Patching file configure using Plan A...
Hunk #1 succeeded at 2290.
Hunk #2 succeeded at 5207.
Hunk #3 succeeded at 5265.
Hunk #4 succeeded at 28629.
Hunk #5 succeeded at 28808.
Hunk #6 succeeded at 28846.
done
=> Verifying /data/pkgsrc/biology/mpqc/patches/patch-configure.in
=> Applying pkgsrc patch /data/pkgsrc/biology/mpqc/patches/patch-configure.in
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-configure.in,v 1.1.1.1 2013/03/16 12:43:26 asau Exp $
|
|--- configure.in.orig	2006-03-22 18:04:54.000000000 +0000
|+++ configure.in
--------------------------
Patching file configure.in using Plan A...
Hunk #1 succeeded at 488.
Hunk #2 succeeded at 747.
Hunk #3 succeeded at 759.
Hunk #4 succeeded at 1769.
done
=> Verifying /data/pkgsrc/biology/mpqc/patches/patch-src_bin_mpqc_ccarunproc
=> Applying pkgsrc patch /data/pkgsrc/biology/mpqc/patches/patch-src_bin_mpqc_ccarunproc
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_bin_mpqc_ccarunproc,v 1.1.1.1 2013/03/16 12:43:26 asau Exp $
|
|--- src/bin/mpqc/ccarunproc.orig	2005-07-28 17:52:36.000000000 +0000
|+++ src/bin/mpqc/ccarunproc
--------------------------
Patching file src/bin/mpqc/ccarunproc using Plan A...
Hunk #1 succeeded at 1.
Hunk #2 succeeded at 13.
done
=> Verifying /data/pkgsrc/biology/mpqc/patches/patch-src_bin_mpqc_mpqcrunproc
=> Applying pkgsrc patch /data/pkgsrc/biology/mpqc/patches/patch-src_bin_mpqc_mpqcrunproc
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_bin_mpqc_mpqcrunproc,v 1.1.1.1 2013/03/16 12:43:26 asau Exp $
|
|--- src/bin/mpqc/mpqcrunproc.orig	2005-03-17 05:56:57.000000000 +0000
|+++ src/bin/mpqc/mpqcrunproc
--------------------------
Patching file src/bin/mpqc/mpqcrunproc using Plan A...
Hunk #1 succeeded at 1.
Hunk #2 succeeded at 12.
done
===> Creating toolchain wrappers for mpqc-2.3.1nb2
===> Configuring for mpqc-2.3.1nb2
=> 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 wish interpreter in src/bin/molrender/tkmolrender.in.
=> Replacing Perl interpreter in src/bin/mpqc/ccarun.in src/bin/mpqc/mpqcrun.in.
=> Checking for portability problems in extracted files
checking build system type... x86_64--netbsd
checking host system type... x86_64--netbsd
checking target system type... x86_64--netbsd
Using extra library directories: -Wl,-R/usr/pkg/lib
checking whether ln -s works... yes
checking for a BSD-compatible install... /usr/bin/install -c -o pbulkXXX -g users
checking for x86_64--netbsd-ranlib... no
checking for ranlib... ranlib
checking for x86_64--netbsd-gcc... 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 ANSI C... none needed
checking for g++... c++
checking for x86_64--netbsd-g++... (cached) c++
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking for x86_64--netbsd-g77... g95
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether g95 accepts -g... yes
checking how to get verbose linking output from g95... -v
checking for Fortran libraries of g95...  -L/usr/pkg/bin/../lib/gcc-lib/x86_64--netbsd/4.1.2/ -L/usr/pkg/bin/../lib/gcc-lib/x86_64--netbsd/4.1.2 -L/usr/pkg/lib/gcc-lib/x86_64--netbsd/4.1.2/ -L/lib// -L/usr/pkg/bin/../lib/gcc-lib/x86_64--netbsd/4.1.2/// -L/usr/pkg/lib/gcc-lib/x86_64--netbsd/4.1.2/// -L/usr/lib// -R/usr/pkg/lib -lf95 -lm
checking how to run the C preprocessor... gcc -E
checking how to run the C++ preprocessor... c++ -E
checking for ar... ar
checking for perl... /usr/pkg/bin/perl
checking for wish... (cached) /usr/pkg/bin/wish
checking for dot... NO
checking for miscellaneous flags... none
checking for special optimization options... "none"
checking for C++ cpu tuning flag... -mtune
checking for C cpu tuning flag... -mtune
checking for special architecture options... "none"
checking "for C++ typename keyword"... "yes"
checking for egrep... 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
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checking for inttypes.h... yes
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checking for unistd.h... yes
checking iostream usability... yes
checking iostream presence... yes
checking for iostream... yes
checking sstream usability... yes
checking sstream presence... yes
checking for sstream... yes
checking iostream name... iostream
checking "for namespace std"... "yes"
checking "for GNU libc++-v3 prerelease bug"... "no"
checking fp.h usability... no
checking fp.h presence... no
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checking endian.h usability... no
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checking machine/endian.h usability... yes
checking machine/endian.h presence... yes
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checking sys/endian.h usability... yes
checking sys/endian.h presence... yes
checking for sys/endian.h... yes
checking sys/machine.h usability... no
checking sys/machine.h presence... no
checking for sys/machine.h... no
checking whether byte ordering is bigendian... no
checking pthreads... yes
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checking perf.h usability... no
checking perf.h presence... no
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checking execinfo.h usability... yes
checking execinfo.h presence... yes
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checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
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checking limits.h usability... yes
checking limits.h presence... yes
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checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
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checking sys/time.h usability... yes
checking sys/time.h presence... yes
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checking for unistd.h... (cached) yes
checking pwd.h usability... yes
checking pwd.h presence... yes
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checking sys/times.h usability... yes
checking sys/times.h presence... yes
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checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
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checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking machine/fpu.h usability... yes
checking machine/fpu.h presence... yes
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checking asm/fpu.h usability... no
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checking termios.h usability... yes
checking termios.h presence... yes
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checking for sys/stat.h... (cached) yes
checking for sys/types.h... (cached) yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for stdint.h... (cached) yes
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 return type of signal handlers... void
checking for vprintf... yes
checking for _doprnt... no
checking for strerror... yes
checking for sigfillset... yes
checking for signal... yes
checking for system... yes
checking for getpwuid... yes
checking for geteuid... yes
checking for gethostname... yes
checking for time... yes
checking for ctime... yes
checking for setrlimit... yes
checking for setenv... yes
checking isnan and iostream... yes
checking fenv.h usability... yes
checking fenv.h presence... yes
checking for fenv.h... yes
checking for feenableexcept... yes
checking for fedisableexcept... yes
checking fchdir... yes
checking ios::fmtflags... yes
checking long long... yes
checking sgetn... yes
checking pubseekoff... yes
checking seekoff... no
checking signal handler needs ellipsis... no
checking for drand48... yes
checking for shmget... yes
checking for semget... yes
checking sys/ipc.h usability... yes
checking sys/ipc.h presence... yes
checking for sys/ipc.h... yes
checking sys/sem.h usability... yes
checking sys/sem.h presence... yes
checking for sys/sem.h... yes
checking sys/shm.h usability... yes
checking sys/shm.h presence... yes
checking for sys/shm.h... yes
checking for SYSV IPC... yes
checking if semctl requires semun... no
checking if fortran compiler works... yes
checking fortran symbols... lowercase with underscore
checking for daxpy_... no
checking for daxpy_ in -lessl... no
checking for daxpy_ in -lblas... yes
checking for dgesvd_... no
checking for dgesvd_ in -llapack... yes
checking for sB_init... no
checking for sB_init in -lsB_BLAS... no
checking for niama-config... no
checking libint/libint.h usability... no
checking libint/libint.h presence... no
checking for libint/libint.h... no
checking libr12/libr12.h usability... no
checking libr12/libr12.h presence... no
checking for libr12/libr12.h... no
checking libderiv/libderiv.h usability... no
checking libderiv/libderiv.h presence... no
checking for libderiv/libderiv.h... no
checking template instantiation flags... none
checking for special flags that must be set last... none
checking for a sed that does not truncate output... /scratch/biology/mpqc/work/.tools/bin/sed
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... match_pattern /lib[^/]+(\.so|_pic\.a)$
checking for dlfcn.h... (cached) yes
checking how to run the C++ preprocessor... c++ -E
checking the maximum length of command line arguments... (cached) 262144
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for x86_64--netbsd-ar... (cached) ar
checking for x86_64--netbsd-ranlib... ranlib
checking for x86_64--netbsd-strip... no
checking for strip... strip
checking for correct ltmain.sh version... yes
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... NetBSD ld.elf_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
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by c++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking for c++ option to produce PIC... -fPIC
checking if c++ PIC flag -fPIC works... yes
checking if c++ static flag -static works... yes
checking if c++ supports -c -o file.o... yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... NetBSD ld.elf_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... no
checking whether to build static libraries... yes
checking for g95 option to produce PIC... -fPIC
checking if g95 PIC flag -fPIC works... yes
checking if g95 static flag -static works... no
checking if g95 supports -c -o file.o... yes
checking whether the g95 linker (/usr/bin/ld) supports shared libraries... Warning (116): Reading file <stdin> as free form
yes
checking dynamic linker characteristics... Warning (116): Reading file <stdin> as free form
NetBSD (a.out) ld.so
checking how to hardcode library paths into programs... immediate
Skipping ./Makefile
Skipping ./bin/Makefile
Skipping ./doc/Makefile
Skipping ./lib/basis/Makefile
Skipping ./lib/cca/Makefile
Skipping ./lib/Makefile
Skipping ./lib/elisp/Makefile
Skipping ./lib/perl/Makefile
Skipping ./src/bin/molrender/Makefile
Skipping ./src/bin/mpqc/Makefile
Skipping ./src/bin/mpqc/validate/Makefile
Skipping ./src/bin/Makefile
Skipping ./src/bin/scls/Makefile
Skipping ./src/bin/scpr/Makefile
Skipping ./src/lib/chemistry/cca/Makefile
Skipping ./src/lib/chemistry/qc/basis/Makefile
Skipping ./src/lib/chemistry/qc/cints/Makefile
Skipping ./src/lib/chemistry/qc/Makefile
Skipping ./src/lib/chemistry/qc/dft/Makefile
Skipping ./src/lib/chemistry/qc/intcca/Makefile
Skipping ./src/lib/chemistry/qc/intv3/Makefile
Skipping ./src/lib/chemistry/qc/mbpt/Makefile
Skipping ./src/lib/chemistry/qc/mbptr12/Makefile
Skipping ./src/lib/chemistry/qc/oint3/Makefile
Skipping ./src/lib/chemistry/qc/psi/Makefile
Skipping ./src/lib/chemistry/qc/scf/Makefile
Skipping ./src/lib/chemistry/qc/wfn/Makefile
Skipping ./src/lib/chemistry/molecule/Makefile
Skipping ./src/lib/chemistry/Makefile
Skipping ./src/lib/chemistry/solvent/Makefile
Skipping ./src/lib/Makefile
Skipping ./src/lib/math/isosurf/Makefile
Skipping ./src/lib/math/optimize/Makefile
Skipping ./src/lib/math/Makefile
Skipping ./src/lib/math/scmat/Makefile
Skipping ./src/lib/math/symmetry/Makefile
Skipping ./src/lib/util/class/Makefile
Skipping ./src/lib/util/container/Makefile
Skipping ./src/lib/util/Makefile
Skipping ./src/lib/util/group/Makefile
Skipping ./src/lib/util/keyval/Makefile
Skipping ./src/lib/util/misc/Makefile
Skipping ./src/lib/util/options/Makefile
Skipping ./src/lib/util/psi3/libpsio/Makefile
Skipping ./src/lib/util/psi3/Makefile
Skipping ./src/lib/util/ref/Makefile
Skipping ./src/lib/util/render/Makefile
Skipping ./src/lib/util/state/Makefile
Skipping ./src/Makefile
configure: creating ./config.status
config.status: creating lib/LocalMakefile
config.status: creating lib/cca/components.cca
config.status: creating bin/sc-config
config.status: creating bin/mkf77sym.pl
config.status: creating src/bin/mpqc/mpqcrun
config.status: creating src/bin/mpqc/ccarun
config.status: creating src/bin/mpqc/validate/makeccain.pl
config.status: creating doc/doxygen.cfg
config.status: creating doc/doxygen.man1.cfg
config.status: creating doc/doxygen.man3.cfg
config.status: creating src/lib/scconfig.h
=> Modifying libtool scripts to use pkgsrc libtool
