=>> Building biology/dsr-pdb build started at Sun May 4 18:21:38 EDT 2025 port directory: /usr/ports/biology/dsr-pdb package name: dsr-pdb-1.0.3_15 building for: FreeBSD 13amd64-weekly-desktop-job-04 13.4-RELEASE-p4 FreeBSD 13.4-RELEASE-p4 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1217 Mar 1 07:51 /usr/ports/biology/dsr-pdb/Makefile Ports top last git commit: 57a50b106b87 Ports top unclean checkout: yes Port dir last git commit: fa53920e7219 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1304000 Job Id: 04 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1304000 UNAME_v=FreeBSD 13.4-RELEASE-p4 UNAME_r=13.4-RELEASE-p4 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/mnt/data/.m/13amd64-weekly-desktop/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/mnt/data/.m/13amd64-weekly-desktop/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13amd64-weekly-desktop SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/mnt/data/.m/13amd64-weekly-desktop/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work/.cache HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/dsr-pdb/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/dsr-pdb/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work/.cache HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/dsr-pdb/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/dsr-pdb/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include " 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" --End MAKE_ENV-- --PLIST_SUB-- OSREL=13.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/dsr-pdb" EXAMPLESDIR="share/examples/dsr-pdb" DATADIR="share/dsr-pdb" WWWDIR="www/dsr-pdb" ETCDIR="etc/dsr-pdb" --End PLIST_SUB-- --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 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # Work around some weirdness when fetching golang modules GO_TAGS+=netcgo .if ${.CURDIR:M*/www/chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/www/ungoogled-chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/lang/rust*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/lang/gcc*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/www/iridium*} MAKE_JOBS_NUMBER=16 .endif .if ${.CURDIR:M*/devel/electron*} MAKE_JOBS_NUMBER=20 .endif .if ${.CURDIR:M*/databases/mongodb*} MAKE_JOBS_NUMBER=12 .endif .if ${.CURDIR:M*/devel/llvm*} MAKE_JOBS_NUMBER=16 .endif # Speed things up a bit MAKE_JOBS_NUMBER?=8 #### #### #MAKE_JOBS_NUMBER?=4 # Alows us to build ports non-interactivly DISABLE_LICENSES=yes LICENSES_ACCEPTED+= DCC # Enable SNDIO on anything that supports it #OPTIONS_SET+=PULSEAUDIO OPTIONS_SET+=SNDIO # Yes we have MS Windows x11-fonts_webfonts_SET+=EXTRAFONTS CLEARTYPE # Desktop Specific Options sysutils_gksu_UNSET+=NAUTILUS x11-wm_compiz-fusion_UNSET+=EMERALD accessibility_redshift_SET+=GUI VIDMODE # These ports default to other audio servers, audio_espeak_UNSET+=PORTAUDIO www_qt5-webengine_UNSET+=ALSA www_qt6-webengine_UNSET+=ALSA audio_rhvoice_UNSET+=AO comms_morse_UNSET+=OSS audio_harp_UNSET+=OSS # Somehow these options are being set and result in ports being rebuilt needlessly becuase they are actually turned off audio_alsa-plugins_SET+=FFMPEG JACK PULSEAUDIO SAMPLERATE SPEEX #### Misc Poudriere #### .include "/etc/make.conf.ports_env" ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> dsr-pdb-1.0.3_15 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.0.6.pkg [13amd64-weekly-desktop-job-04] Installing pkg-2.0.6... [13amd64-weekly-desktop-job-04] Extracting pkg-2.0.6: .......... done ===> dsr-pdb-1.0.3_15 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of dsr-pdb-1.0.3_15 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by dsr-pdb-1.0.3_15 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by dsr-pdb-1.0.3_15 for building => SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Fetching all distfiles required by dsr-pdb-1.0.3_15 for building ===> Extracting for dsr-pdb-1.0.3_15 => SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for dsr-pdb-1.0.3_15 ===> Applying FreeBSD patches for dsr-pdb-1.0.3_15 from /usr/ports/biology/dsr-pdb/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> dsr-pdb-1.0.3_15 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [13amd64-weekly-desktop-job-04] Installing gmake-4.4.1... [13amd64-weekly-desktop-job-04] `-- Installing gettext-runtime-0.23.1... [13amd64-weekly-desktop-job-04] | `-- Installing indexinfo-0.3.1_1... [13amd64-weekly-desktop-job-04] | `-- Extracting indexinfo-0.3.1_1: . done [13amd64-weekly-desktop-job-04] `-- Extracting gettext-runtime-0.23.1: .......... done [13amd64-weekly-desktop-job-04] Extracting gmake-4.4.1: .......... done ===> dsr-pdb-1.0.3_15 depends on package: gmake>=4.4.1 - found ===> Returning to build of dsr-pdb-1.0.3_15 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> dsr-pdb-1.0.3_15 depends on shared library: libboost_program_options.so - not found ===> Installing existing package /packages/All/boost-libs-1.87.0_1.pkg [13amd64-weekly-desktop-job-04] Installing boost-libs-1.87.0_1... [13amd64-weekly-desktop-job-04] `-- Installing icu-76.1,1... [13amd64-weekly-desktop-job-04] `-- Extracting icu-76.1,1: .......... done [13amd64-weekly-desktop-job-04] Extracting boost-libs-1.87.0_1: .......... done ===== Message from boost-libs-1.87.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> dsr-pdb-1.0.3_15 depends on shared library: libboost_program_options.so - found (/usr/local/lib/libboost_program_options.so) ===> Returning to build of dsr-pdb-1.0.3_15 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for dsr-pdb-1.0.3_15 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/aclocal.m4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/configure configure: loading site script /usr/ports/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 /usr/local/bin/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 /usr/local/bin/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 /usr/local/bin/gmake sets $(MAKE)... (cached) yes checking build system type... amd64-portbld-freebsd13.4 checking host system type... amd64-portbld-freebsd13.4 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 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) 524288 checking command to parse /usr/bin/nm 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... yes 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... freebsd13.4 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... freebsd13.4 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... no checking boost/program_options.hpp presence... yes configure: WARNING: boost/program_options.hpp: present but cannot be compiled configure: WARNING: boost/program_options.hpp: check for missing prerequisite headers? configure: WARNING: boost/program_options.hpp: see the Autoconf documentation configure: WARNING: boost/program_options.hpp: section "Present But Cannot Be Compiled" configure: WARNING: boost/program_options.hpp: proceeding with the preprocessor's result configure: WARNING: boost/program_options.hpp: in the future, the compiler will take precedence configure: WARNING: ## -------------------------------------------- ## configure: WARNING: ## Report this to drussel@graphics.stanford.edu ## configure: WARNING: ## -------------------------------------------- ## 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. =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for dsr-pdb-1.0.3_15 /usr/local/bin/gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' Making all in lib gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib' if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 mkdir .libs c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 if /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -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 ranlib .libs/libdsrpdb.a creating libdsrpdb.la (cd .libs && rm -f libdsrpdb.la && ln -s ../libdsrpdb.la libdsrpdb.la) gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib' Making all in tools gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/tools' if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o pdb_transform pdb_transform.o ../lib/libdsrpdb.la /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o pdb_distance_matrix pdb_distance_matrix.o ../lib/libdsrpdb.la mkdir .libs c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -o pdb_transform pdb_transform.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -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++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o pdb_split pdb_split.o ../lib/libdsrpdb.la c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -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++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o pdb_cat pdb_cat.o ../lib/libdsrpdb.la /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o pdb_align_points pdb_align_points.o ../lib/libdsrpdb.la c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -o pdb_cat pdb_cat.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -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++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o pdb_stats pdb_stats.o ../lib/libdsrpdb.la c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -o pdb_stats pdb_stats.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o pdb_align pdb_align.o ../lib/libdsrpdb.la c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -o pdb_align pdb_align.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o pdb_distance pdb_distance.o ../lib/libdsrpdb.la c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -o pdb_distance pdb_distance.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/tools' Making all in test gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/test' if c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o check_pdb check_pdb.o ../lib/libdsrpdb.la mkdir .libs c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -o check_pdb check_pdb.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o check_bonds check_bonds.o ../lib/libdsrpdb.la c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -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++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o check_transform check_transform.o ../lib/libdsrpdb.la c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -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++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o check_protein check_protein.o ../lib/libdsrpdb.la c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -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++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o check_refine_alignment check_refine_alignment.o ../lib/libdsrpdb.la c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -o check_refine_alignment check_refine_alignment.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/test' Making all in include gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include' Making all in dsrpdb gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb' Making all in dsrpdb_internal gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb_internal' Making all in tnt gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/tnt' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/tnt' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include' gmake[3]: Nothing to be done for 'all-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for dsr-pdb-1.0.3_15 ===> Generating temporary packing list Making install in lib gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib' test -z "/usr/local/lib" || /bin/sh ../config/mkinstalldirs "/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/lib" /bin/sh ../libtool --mode=install /usr/bin/install -c 'libdsrpdb.la' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/lib/libdsrpdb.la' /usr/bin/install -c .libs/libdsrpdb.lai /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/lib/libdsrpdb.la /usr/bin/install -c .libs/libdsrpdb.a /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/lib/libdsrpdb.a ranlib /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/lib/libdsrpdb.a chmod 644 /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/lib/libdsrpdb.a libtool: install: warning: remember to run `libtool --finish /usr/local/lib' gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib' Making install in tools gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/tools' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/tools' test -z "/usr/local/bin" || /bin/sh ../config/mkinstalldirs "/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin" /bin/sh ../libtool --mode=install install -s -m 555 'pdb_stats' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_stats' install -m 555 -s pdb_stats /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_stats /bin/sh ../libtool --mode=install install -s -m 555 'pdb_split' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_split' install -m 555 -s pdb_split /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_split /bin/sh ../libtool --mode=install install -s -m 555 'pdb_transform' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_transform' install -m 555 -s pdb_transform /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_transform /bin/sh ../libtool --mode=install install -s -m 555 'pdb_cat' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_cat' install -m 555 -s pdb_cat /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_cat /bin/sh ../libtool --mode=install install -s -m 555 'pdb_align' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_align' install -m 555 -s pdb_align /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_align /bin/sh ../libtool --mode=install install -s -m 555 'pdb_align_points' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_align_points' install -m 555 -s pdb_align_points /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_align_points /bin/sh ../libtool --mode=install install -s -m 555 'pdb_distance_matrix' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_distance_matrix' install -m 555 -s pdb_distance_matrix /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_distance_matrix /bin/sh ../libtool --mode=install install -s -m 555 'pdb_distance' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_distance' install -m 555 -s pdb_distance /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/bin/pdb_distance gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/tools' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/tools' Making install in test gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/test' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/test' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/test' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/test' Making install in include gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include' Making install in dsrpdb gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb' gmake[4]: Nothing to be done for 'install-exec-am'. test -z "/usr/local/include/dsrpdb" || /bin/sh ../../config/mkinstalldirs "/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb" mkdir -p -- /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb install -m 0644 'Atom.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/Atom.h' install -m 0644 'Matrix.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/Matrix.h' install -m 0644 'Model.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/Model.h' install -m 0644 'PDB.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/PDB.h' install -m 0644 'PDB_index.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/PDB_index.h' install -m 0644 'Point.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/Point.h' install -m 0644 'Protein.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/Protein.h' install -m 0644 'Residue.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/Residue.h' install -m 0644 'Transform.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/Transform.h' install -m 0644 'align.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/align.h' install -m 0644 'config.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/config.h' install -m 0644 'distance.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/distance.h' install -m 0644 'geometry.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/geometry.h' install -m 0644 'geometry_internal.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/geometry_internal.h' install -m 0644 'iterator.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/iterator.h' install -m 0644 'label.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/label.h' install -m 0644 'labeled_index.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/labeled_index.h' install -m 0644 'small_map.h' '/wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb/small_map.h' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb' Making install in dsrpdb_internal gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb_internal' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/dsrpdb_internal' Making install in tnt gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/tnt' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/tnt' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/tnt' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include/tnt' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/include' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' install -m 0644 /wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/config.h /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/include/dsrpdb install -s -m 0644 /wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib/libdsrpdb.so /wrkdirs/usr/ports/biology/dsr-pdb/work/stage/usr/local/lib ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-05-04T22:21:38+0000' 'PKG_NOTE_ports_top_git_hash=57a50b106b87' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=fa53920e7219' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for dsr-pdb-1.0.3_15 ===> Building dsr-pdb-1.0.3_15 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for dsr-pdb-1.0.3_15 build of biology/dsr-pdb | dsr-pdb-1.0.3_15 ended at Sun May 4 18:22:26 EDT 2025 build time: 00:00:48