------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/dsr-pdb XDG_CONFIG_HOME=/construction/biology/dsr-pdb HOME=/construction/biology/dsr-pdb TMPDIR="/tmp" PATH=/construction/biology/dsr-pdb/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/dsr-pdb XDG_CONFIG_HOME=/construction/biology/dsr-pdb HOME=/construction/biology/dsr-pdb TMPDIR="/tmp" PATH=/construction/biology/dsr-pdb/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/dsr-pdb/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/dsr-pdb" EXAMPLESDIR="share/examples/dsr-pdb" DATADIR="share/dsr-pdb" WWWDIR="www/dsr-pdb" ETCDIR="etc/dsr-pdb" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/dsr-pdb DOCSDIR=/usr/local/share/doc/dsr-pdb EXAMPLESDIR=/usr/local/share/examples/dsr-pdb WWWDIR=/usr/local/www/dsr-pdb ETCDIR=/usr/local/etc/dsr-pdb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600106 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=12 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gettext-runtime-0.21.pkg Installing /packages/All/gmake-4.3_2.pkg Installing /packages/All/icu-69.1,1.pkg Installing /packages/All/boost-libs-1.72.0_5.pkg ===== Message from boost-libs-1.72.0_5: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. SUCCEEDED 00:00:06 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> dsr-pdb-1.0.3_5 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> dsr-pdb-1.0.3_5 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by dsr-pdb-1.0.3_5 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> dsr-pdb-1.0.3_5 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by dsr-pdb-1.0.3_5 for building => SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> dsr-pdb-1.0.3_5 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by dsr-pdb-1.0.3_5 for building ===> Extracting for dsr-pdb-1.0.3_5 => SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz. Extracted Memory Use: 4.53M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for dsr-pdb-1.0.3_5 ===> Applying ports patches for dsr-pdb-1.0.3_5 from /xports/biology/dsr-pdb/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> dsr-pdb-1.0.3_5 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> dsr-pdb-1.0.3_5 depends on shared library: libboost_program_options.so - found (/usr/local/lib/libboost_program_options.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> dsr-pdb-1.0.3_5 depends on package: gmake>=4.3 - found ===> dsr-pdb-1.0.3_5 depends on shared library: libboost_program_options.so - found (/usr/local/lib/libboost_program_options.so) ===> Configuring for dsr-pdb-1.0.3_5 configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes 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 c++ accepts -g... yes checking for style of include used by gmake... GNU checking dependency style of c++... gcc3 checking for gcc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ANSI C... none needed checking dependency style of cc... gcc3 checking how to run the C preprocessor... cpp checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking whether gmake sets $(MAKE)... (cached) yes checking build system type... x86_64-portbld-dragonfly6.1 checking host system type... x86_64-portbld-dragonfly6.1 checking for a sed that does not truncate output... /usr/bin/sed checking for egrep... grep -E checking for ld used by cc... /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... pass_all checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking how to run the C++ preprocessor... c++ -E checking for g77... no checking for f77... no checking for xlf... no checking for frt... no checking for pgf77... no checking for fort77... no checking for fl32... no checking for af77... no checking for f90... no checking for xlf90... no checking for pgf90... no checking for epcf90... no checking for f95... no checking for fort... no checking for xlf95... no checking for ifc... no checking for efc... no checking for pgf95... no checking for lf95... no checking for gfortran... no checking whether we are using the GNU Fortran 77 compiler... no checking whether accepts -g... no checking the maximum length of command line arguments... (cached) 262144 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc static flag works... yes checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... dragonfly6.1 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 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++ supports -c -o file.o... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... dragonfly6.1 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes appending configuration tag "F77" to libtool checking CGAL_MAKEFILE... no checking CGAL/Exact_predicates_inexact_constructions_kernel.h usability... no checking CGAL/Exact_predicates_inexact_constructions_kernel.h presence... no checking for CGAL/Exact_predicates_inexact_constructions_kernel.h... no checking CGAL... no checking boost/program_options.hpp usability... yes checking boost/program_options.hpp presence... yes checking for boost/program_options.hpp... yes checking for main in -lboost_program_options... yes checking for main in -lMagick++... no checking Magick++.h usability... no checking Magick++.h presence... no checking for Magick++.h... no configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating include/Makefile config.status: creating include/dsrpdb/Makefile config.status: creating include/dsrpdb_internal/Makefile config.status: creating include/tnt/Makefile config.status: creating lib/Makefile config.status: creating test/Makefile config.status: creating tools/Makefile config.status: creating config.h config.status: executing depfiles commands ImageMagick++ not found, writing of images will be disabled. SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for dsr-pdb-1.0.3_5 gmake[1]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' gmake all-recursive gmake[2]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' Making all in lib gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/lib' if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue.lo -MD -MP -MF ".deps/Residue.Tpo" -c -o Residue.lo Residue.cc; \ then mv -f ".deps/Residue.Tpo" ".deps/Residue.Plo"; else rm -f ".deps/Residue.Tpo"; exit 1; fi if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein.lo -MD -MP -MF ".deps/Protein.Tpo" -c -o Protein.lo Protein.cc; \ then mv -f ".deps/Protein.Tpo" ".deps/Protein.Plo"; else rm -f ".deps/Protein.Tpo"; exit 1; fi if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue_data.lo -MD -MP -MF ".deps/Residue_data.Tpo" -c -o Residue_data.lo Residue_data.cc; \ then mv -f ".deps/Residue_data.Tpo" ".deps/Residue_data.Plo"; else rm -f ".deps/Residue_data.Tpo"; exit 1; fi if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein_pdb.lo -MD -MP -MF ".deps/Protein_pdb.Tpo" -c -o Protein_pdb.lo Protein_pdb.cc; \ then mv -f ".deps/Protein_pdb.Tpo" ".deps/Protein_pdb.Plo"; else rm -f ".deps/Protein_pdb.Tpo"; exit 1; fi if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_utils.lo -MD -MP -MF ".deps/pdb_utils.Tpo" -c -o pdb_utils.lo pdb_utils.cc; \ then mv -f ".deps/pdb_utils.Tpo" ".deps/pdb_utils.Plo"; else rm -f ".deps/pdb_utils.Tpo"; exit 1; fi if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Model.lo -MD -MP -MF ".deps/Model.Tpo" -c -o Model.lo Model.cc; \ then mv -f ".deps/Model.Tpo" ".deps/Model.Plo"; else rm -f ".deps/Model.Tpo"; exit 1; fi if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT PDB.lo -MD -MP -MF ".deps/PDB.Tpo" -c -o PDB.lo PDB.cc; \ then mv -f ".deps/PDB.Tpo" ".deps/PDB.Plo"; else rm -f ".deps/PDB.Tpo"; exit 1; fi if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT align.lo -MD -MP -MF ".deps/align.Tpo" -c -o align.lo align.cc; \ then mv -f ".deps/align.Tpo" ".deps/align.Plo"; else rm -f ".deps/align.Tpo"; exit 1; fi if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT distance.lo -MD -MP -MF ".deps/distance.Tpo" -c -o distance.lo distance.cc; \ then mv -f ".deps/distance.Tpo" ".deps/distance.Plo"; else rm -f ".deps/distance.Tpo"; exit 1; fi if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Error_logger.lo -MD -MP -MF ".deps/Error_logger.Tpo" -c -o Error_logger.lo Error_logger.cc; \ then mv -f ".deps/Error_logger.Tpo" ".deps/Error_logger.Plo"; else rm -f ".deps/Error_logger.Tpo"; exit 1; fi mkdir .libs c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT PDB.lo -MD -MP -MF .deps/PDB.Tpo -c PDB.cc -fPIC -DPIC -o .libs/PDB.o c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue.lo -MD -MP -MF .deps/Residue.Tpo -c Residue.cc -fPIC -DPIC -o .libs/Residue.o c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein_pdb.lo -MD -MP -MF .deps/Protein_pdb.Tpo -c Protein_pdb.cc -fPIC -DPIC -o .libs/Protein_pdb.o c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Model.lo -MD -MP -MF .deps/Model.Tpo -c Model.cc -fPIC -DPIC -o .libs/Model.o c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT align.lo -MD -MP -MF .deps/align.Tpo -c align.cc -fPIC -DPIC -o .libs/align.o c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_utils.lo -MD -MP -MF .deps/pdb_utils.Tpo -c pdb_utils.cc -fPIC -DPIC -o .libs/pdb_utils.o c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Error_logger.lo -MD -MP -MF .deps/Error_logger.Tpo -c Error_logger.cc -fPIC -DPIC -o .libs/Error_logger.o c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein.lo -MD -MP -MF .deps/Protein.Tpo -c Protein.cc -fPIC -DPIC -o .libs/Protein.o c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue_data.lo -MD -MP -MF .deps/Residue_data.Tpo -c Residue_data.cc -fPIC -DPIC -o .libs/Residue_data.o c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT distance.lo -MD -MP -MF .deps/distance.Tpo -c distance.cc -fPIC -DPIC -o .libs/distance.o c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_utils.lo -MD -MP -MF .deps/pdb_utils.Tpo -c pdb_utils.cc -o pdb_utils.o >/dev/null 2>&1 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Error_logger.lo -MD -MP -MF .deps/Error_logger.Tpo -c Error_logger.cc -o Error_logger.o >/dev/null 2>&1 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Model.lo -MD -MP -MF .deps/Model.Tpo -c Model.cc -o Model.o >/dev/null 2>&1 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein.lo -MD -MP -MF .deps/Protein.Tpo -c Protein.cc -o Protein.o >/dev/null 2>&1 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue_data.lo -MD -MP -MF .deps/Residue_data.Tpo -c Residue_data.cc -o Residue_data.o >/dev/null 2>&1 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein_pdb.lo -MD -MP -MF .deps/Protein_pdb.Tpo -c Protein_pdb.cc -o Protein_pdb.o >/dev/null 2>&1 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT PDB.lo -MD -MP -MF .deps/PDB.Tpo -c PDB.cc -o PDB.o >/dev/null 2>&1 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT align.lo -MD -MP -MF .deps/align.Tpo -c align.cc -o align.o >/dev/null 2>&1 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue.lo -MD -MP -MF .deps/Residue.Tpo -c Residue.cc -o Residue.o >/dev/null 2>&1 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT distance.lo -MD -MP -MF .deps/distance.Tpo -c distance.cc -o distance.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o libdsrpdb.la -rpath /usr/local/lib -static Residue.lo Protein.lo Residue_data.lo Protein_pdb.lo pdb_utils.lo Model.lo PDB.lo align.lo distance.lo Error_logger.lo ar cru .libs/libdsrpdb.a Residue.o Protein.o Residue_data.o Protein_pdb.o pdb_utils.o Model.o PDB.o align.o distance.o Error_logger.o /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib .libs/libdsrpdb.a creating libdsrpdb.la (cd .libs && rm -f libdsrpdb.la && ln -s ../libdsrpdb.la libdsrpdb.la) gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/lib' Making all in tools gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/tools' if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_stats.o -MD -MP -MF ".deps/pdb_stats.Tpo" -c -o pdb_stats.o pdb_stats.cc; \ then mv -f ".deps/pdb_stats.Tpo" ".deps/pdb_stats.Po"; else rm -f ".deps/pdb_stats.Tpo"; exit 1; fi if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_split.o -MD -MP -MF ".deps/pdb_split.Tpo" -c -o pdb_split.o pdb_split.cc; \ then mv -f ".deps/pdb_split.Tpo" ".deps/pdb_split.Po"; else rm -f ".deps/pdb_split.Tpo"; exit 1; fi if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_transform.o -MD -MP -MF ".deps/pdb_transform.Tpo" -c -o pdb_transform.o pdb_transform.cc; \ then mv -f ".deps/pdb_transform.Tpo" ".deps/pdb_transform.Po"; else rm -f ".deps/pdb_transform.Tpo"; exit 1; fi if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_cat.o -MD -MP -MF ".deps/pdb_cat.Tpo" -c -o pdb_cat.o pdb_cat.cc; \ then mv -f ".deps/pdb_cat.Tpo" ".deps/pdb_cat.Po"; else rm -f ".deps/pdb_cat.Tpo"; exit 1; fi if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_align.o -MD -MP -MF ".deps/pdb_align.Tpo" -c -o pdb_align.o pdb_align.cc; \ then mv -f ".deps/pdb_align.Tpo" ".deps/pdb_align.Po"; else rm -f ".deps/pdb_align.Tpo"; exit 1; fi if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_align_points.o -MD -MP -MF ".deps/pdb_align_points.Tpo" -c -o pdb_align_points.o pdb_align_points.cc; \ then mv -f ".deps/pdb_align_points.Tpo" ".deps/pdb_align_points.Po"; else rm -f ".deps/pdb_align_points.Tpo"; exit 1; fi if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_distance_matrix.o -MD -MP -MF ".deps/pdb_distance_matrix.Tpo" -c -o pdb_distance_matrix.o pdb_distance_matrix.cc; \ then mv -f ".deps/pdb_distance_matrix.Tpo" ".deps/pdb_distance_matrix.Po"; else rm -f ".deps/pdb_distance_matrix.Tpo"; exit 1; fi if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_distance.o -MD -MP -MF ".deps/pdb_distance.Tpo" -c -o pdb_distance.o pdb_distance.cc; \ then mv -f ".deps/pdb_distance.Tpo" ".deps/pdb_distance.Po"; else rm -f ".deps/pdb_distance.Tpo"; exit 1; fi /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o pdb_distance_matrix pdb_distance_matrix.o ../lib/libdsrpdb.la /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o pdb_transform pdb_transform.o ../lib/libdsrpdb.la mkdir .libs c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o pdb_distance_matrix pdb_distance_matrix.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o pdb_split pdb_split.o ../lib/libdsrpdb.la c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o pdb_transform pdb_transform.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o pdb_split pdb_split.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o pdb_align_points pdb_align_points.o ../lib/libdsrpdb.la /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o pdb_stats pdb_stats.o ../lib/libdsrpdb.la /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o pdb_align pdb_align.o ../lib/libdsrpdb.la c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o pdb_align_points pdb_align_points.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o pdb_cat pdb_cat.o ../lib/libdsrpdb.la c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o pdb_stats pdb_stats.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o pdb_align pdb_align.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o pdb_cat pdb_cat.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o pdb_distance pdb_distance.o ../lib/libdsrpdb.la c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o pdb_distance pdb_distance.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/tools' Making all in test gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/test' if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT check_protein.o -MD -MP -MF ".deps/check_protein.Tpo" -c -o check_protein.o check_protein.cc; \ then mv -f ".deps/check_protein.Tpo" ".deps/check_protein.Po"; else rm -f ".deps/check_protein.Tpo"; exit 1; fi if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT check_pdb.o -MD -MP -MF ".deps/check_pdb.Tpo" -c -o check_pdb.o check_pdb.cc; \ then mv -f ".deps/check_pdb.Tpo" ".deps/check_pdb.Po"; else rm -f ".deps/check_pdb.Tpo"; exit 1; fi if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT check_transform.o -MD -MP -MF ".deps/check_transform.Tpo" -c -o check_transform.o check_transform.cc; \ then mv -f ".deps/check_transform.Tpo" ".deps/check_transform.Po"; else rm -f ".deps/check_transform.Tpo"; exit 1; fi if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT check_refine_alignment.o -MD -MP -MF ".deps/check_refine_alignment.Tpo" -c -o check_refine_alignment.o check_refine_alignment.cc; \ then mv -f ".deps/check_refine_alignment.Tpo" ".deps/check_refine_alignment.Po"; else rm -f ".deps/check_refine_alignment.Tpo"; exit 1; fi if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT check_bonds.o -MD -MP -MF ".deps/check_bonds.Tpo" -c -o check_bonds.o check_bonds.cc; \ then mv -f ".deps/check_bonds.Tpo" ".deps/check_bonds.Po"; else rm -f ".deps/check_bonds.Tpo"; exit 1; fi /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o check_pdb check_pdb.o ../lib/libdsrpdb.la /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o check_bonds check_bonds.o ../lib/libdsrpdb.la mkdir .libs c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o check_pdb check_pdb.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o check_bonds check_bonds.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o check_transform check_transform.o ../lib/libdsrpdb.la c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o check_transform check_transform.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o check_protein check_protein.o ../lib/libdsrpdb.la c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o check_protein check_protein.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options /bin/sh ../libtool --tag=CXX --mode=link c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -L/usr/local/lib -lboost_program_options -o check_refine_alignment check_refine_alignment.o ../lib/libdsrpdb.la c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -o check_refine_alignment check_refine_alignment.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/test' Making all in include gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include' Making all in dsrpdb gmake[4]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb' gmake[5]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb' gmake[5]: Nothing to be done for 'all-am'. gmake[5]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb' gmake[4]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb' Making all in dsrpdb_internal gmake[4]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[5]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[5]: Nothing to be done for 'all-am'. gmake[5]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[4]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb_internal' Making all in tnt gmake[4]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/tnt' gmake[4]: Nothing to be done for 'all'. gmake[4]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/tnt' gmake[4]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include' gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include' gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' gmake[2]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' gmake[1]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' SUCCEEDED 00:00:13 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for dsr-pdb-1.0.3_5 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' Making install in lib gmake[2]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/lib' gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/lib' test -z "/usr/local/lib" || /bin/sh ../config/mkinstalldirs "/construction/biology/dsr-pdb/stage/usr/local/lib" /bin/sh ../libtool --mode=install /usr/bin/install -c 'libdsrpdb.la' '/construction/biology/dsr-pdb/stage/usr/local/lib/libdsrpdb.la' /usr/bin/install -c .libs/libdsrpdb.lai /construction/biology/dsr-pdb/stage/usr/local/lib/libdsrpdb.la /usr/bin/install -c .libs/libdsrpdb.a /construction/biology/dsr-pdb/stage/usr/local/lib/libdsrpdb.a ranlib /construction/biology/dsr-pdb/stage/usr/local/lib/libdsrpdb.a chmod 644 /construction/biology/dsr-pdb/stage/usr/local/lib/libdsrpdb.a libtool: install: warning: remember to run `libtool --finish /usr/local/lib' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/lib' gmake[2]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/lib' Making install in tools gmake[2]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/tools' gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/tools' test -z "/usr/local/bin" || /bin/sh ../config/mkinstalldirs "/construction/biology/dsr-pdb/stage/usr/local/bin" /bin/sh ../libtool --mode=install install -s -m 555 'pdb_stats' '/construction/biology/dsr-pdb/stage/usr/local/bin/pdb_stats' install -m 555 -s pdb_stats /construction/biology/dsr-pdb/stage/usr/local/bin/pdb_stats /bin/sh ../libtool --mode=install install -s -m 555 'pdb_split' '/construction/biology/dsr-pdb/stage/usr/local/bin/pdb_split' install -m 555 -s pdb_split /construction/biology/dsr-pdb/stage/usr/local/bin/pdb_split /bin/sh ../libtool --mode=install install -s -m 555 'pdb_transform' '/construction/biology/dsr-pdb/stage/usr/local/bin/pdb_transform' install -m 555 -s pdb_transform /construction/biology/dsr-pdb/stage/usr/local/bin/pdb_transform /bin/sh ../libtool --mode=install install -s -m 555 'pdb_cat' '/construction/biology/dsr-pdb/stage/usr/local/bin/pdb_cat' install -m 555 -s pdb_cat /construction/biology/dsr-pdb/stage/usr/local/bin/pdb_cat /bin/sh ../libtool --mode=install install -s -m 555 'pdb_align' '/construction/biology/dsr-pdb/stage/usr/local/bin/pdb_align' install -m 555 -s pdb_align /construction/biology/dsr-pdb/stage/usr/local/bin/pdb_align /bin/sh ../libtool --mode=install install -s -m 555 'pdb_align_points' '/construction/biology/dsr-pdb/stage/usr/local/bin/pdb_align_points' install -m 555 -s pdb_align_points /construction/biology/dsr-pdb/stage/usr/local/bin/pdb_align_points /bin/sh ../libtool --mode=install install -s -m 555 'pdb_distance_matrix' '/construction/biology/dsr-pdb/stage/usr/local/bin/pdb_distance_matrix' install -m 555 -s pdb_distance_matrix /construction/biology/dsr-pdb/stage/usr/local/bin/pdb_distance_matrix /bin/sh ../libtool --mode=install install -s -m 555 'pdb_distance' '/construction/biology/dsr-pdb/stage/usr/local/bin/pdb_distance' install -m 555 -s pdb_distance /construction/biology/dsr-pdb/stage/usr/local/bin/pdb_distance gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/tools' gmake[2]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/tools' Making install in test gmake[2]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/test' gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/test' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/test' gmake[2]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/test' Making install in include gmake[2]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include' Making install in dsrpdb gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb' gmake[4]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb' gmake[5]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb' gmake[5]: Nothing to be done for 'install-exec-am'. test -z "/usr/local/include/dsrpdb" || /bin/sh ../../config/mkinstalldirs "/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb" mkdir -p -- /construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb install -m 0644 'Atom.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/Atom.h' install -m 0644 'Matrix.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/Matrix.h' install -m 0644 'Model.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/Model.h' install -m 0644 'PDB.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/PDB.h' install -m 0644 'PDB_index.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/PDB_index.h' install -m 0644 'Point.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/Point.h' install -m 0644 'Protein.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/Protein.h' install -m 0644 'Residue.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/Residue.h' install -m 0644 'Transform.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/Transform.h' install -m 0644 'align.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/align.h' install -m 0644 'config.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/config.h' install -m 0644 'distance.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/distance.h' install -m 0644 'geometry.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/geometry.h' install -m 0644 'geometry_internal.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/geometry_internal.h' install -m 0644 'iterator.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/iterator.h' install -m 0644 'label.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/label.h' install -m 0644 'labeled_index.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/labeled_index.h' install -m 0644 'small_map.h' '/construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb/small_map.h' gmake[5]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb' gmake[4]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb' gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb' Making install in dsrpdb_internal gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[4]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[5]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[5]: Nothing to be done for 'install-exec-am'. gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[4]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb_internal' Making install in tnt gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/tnt' gmake[4]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/tnt' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/tnt' gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include/tnt' gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include' gmake[4]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include' gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include' gmake[2]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3/include' gmake[2]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' gmake[3]: Entering directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' gmake[2]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' gmake[1]: Leaving directory '/construction/biology/dsr-pdb/dsr-pdb-1.0.3' install -m 0644 /construction/biology/dsr-pdb/dsr-pdb-1.0.3/config.h /construction/biology/dsr-pdb/stage/usr/local/include/dsrpdb install -s -m 0644 /construction/biology/dsr-pdb/dsr-pdb-1.0.3/lib/libdsrpdb.so /construction/biology/dsr-pdb/stage/usr/local/lib ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for dsr-pdb-1.0.3_5 file sizes/checksums [28]: 0% file sizes/checksums [28]: 100% packing files [28]: 0% packing files [28]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:35