=>> Building biology/protomol build started at Wed Nov 12 09:25:17 EST 2025 port directory: /usr/ports/biology/protomol package name: protomol-2.0.3_16 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1338 Aug 27 2024 /usr/ports/biology/protomol/Makefile Ports top last git commit: ec159283c191 Ports top unclean checkout: no Port dir last git commit: 98bf25875a99 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500064 Job Id: 10 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500064 UNAME_v=FreeBSD 15.0-ALPHA3 1500064 UNAME_r=15.0-ALPHA3 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=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/10/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_c_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/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--- ===> The following configuration options are available for protomol-2.0.3_16: EXAMPLES=on: Build and/or install examples GLUT=on: OpenGL Utility Toolkit support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --without-irix_mipspro_mpi --with-glut=yes --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/protomol/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/protomol/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/protomol/work/.cache HOME=/wrkdirs/usr/ports/biology/protomol/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/protomol/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/protomol/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh 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/protomol/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/protomol/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/protomol/work/.cache HOME=/wrkdirs/usr/ports/biology/protomol/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/protomol/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/protomol/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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-I/usr/local/include" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 " CXXSTD=c++98 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-- PORTEXAMPLES="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/protomol" EXAMPLESDIR="share/examples/protomol" DATADIR="share/protomol" WWWDIR="www/protomol" ETCDIR="etc/protomol" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/protomol DOCSDIR=/usr/local/share/doc/protomol EXAMPLESDIR=/usr/local/share/examples/protomol WWWDIR=/usr/local/www/protomol ETCDIR=/usr/local/etc/protomol --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---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 pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The protomol port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> protomol-2.0.3_16 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> protomol-2.0.3_16 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of protomol-2.0.3_16 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The protomol port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by protomol-2.0.3_16 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The protomol port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by protomol-2.0.3_16 for building => SHA256 Checksum OK for protomol-2.0.3-tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The protomol port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by protomol-2.0.3_16 for building ===> Extracting for protomol-2.0.3_16 => SHA256 Checksum OK for protomol-2.0.3-tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for protomol-2.0.3_16 ===> Applying FreeBSD patches for protomol-2.0.3_16 from /usr/ports/biology/protomol/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - not found ===> Installing existing package /packages/All/libXmu-1.1.4,1.pkg [pkg.DaveG.ca] Installing libXmu-1.1.4,1... [pkg.DaveG.ca] `-- Installing libX11-1.8.12,1... [pkg.DaveG.ca] | `-- Installing libxcb-1.17.0... [pkg.DaveG.ca] | | `-- Installing libXau-1.0.12... [pkg.DaveG.ca] | | `-- Extracting libXau-1.0.12: .......... done [pkg.DaveG.ca] | | `-- Installing libXdmcp-1.1.5... [pkg.DaveG.ca] | | `-- Installing xorgproto-2024.1... [pkg.DaveG.ca] | | `-- Extracting xorgproto-2024.1: .......... done [pkg.DaveG.ca] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg.DaveG.ca] | `-- Extracting libxcb-1.17.0: .......... done [pkg.DaveG.ca] `-- Extracting libX11-1.8.12,1: .......... done [pkg.DaveG.ca] `-- Installing libXext-1.3.6,1... [pkg.DaveG.ca] `-- Extracting libXext-1.3.6,1: .......... done [pkg.DaveG.ca] `-- Installing libXt-1.3.0,1... [pkg.DaveG.ca] | `-- Installing libICE-1.1.2,1... [pkg.DaveG.ca] | `-- Extracting libICE-1.1.2,1: .......... done [pkg.DaveG.ca] | `-- Installing libSM-1.2.6,1... [pkg.DaveG.ca] | `-- Extracting libSM-1.2.6,1: ........ done [pkg.DaveG.ca] `-- Extracting libXt-1.3.0,1: .......... done [pkg.DaveG.ca] Extracting libXmu-1.1.4,1: .......... done ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> Returning to build of protomol-2.0.3_16 ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/xi.pc - not found ===> Installing existing package /packages/All/libXi-1.8.2,1.pkg [pkg.DaveG.ca] Installing libXi-1.8.2,1... [pkg.DaveG.ca] `-- Installing libXfixes-6.0.1... [pkg.DaveG.ca] `-- Extracting libXfixes-6.0.1: ....... done [pkg.DaveG.ca] Extracting libXi-1.8.2,1: .......... done ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/xi.pc - found ===> Returning to build of protomol-2.0.3_16 ===> protomol-2.0.3_16 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> protomol-2.0.3_16 depends on file: /usr/local/bin/ccache - found ===> Returning to build of protomol-2.0.3_16 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> protomol-2.0.3_16 depends on shared library: libpng.so - not found ===> Installing existing package /packages/All/png-1.6.50.pkg [pkg.DaveG.ca] Installing png-1.6.50... [pkg.DaveG.ca] Extracting png-1.6.50: .......... done ===> protomol-2.0.3_16 depends on shared library: libpng.so - found (/usr/local/lib/libpng.so) ===> Returning to build of protomol-2.0.3_16 ===> protomol-2.0.3_16 depends on shared library: libtiff.so - not found ===> Installing existing package /packages/All/tiff-4.7.1.pkg [pkg.DaveG.ca] Installing tiff-4.7.1... [pkg.DaveG.ca] `-- Installing jbigkit-2.1_3... [pkg.DaveG.ca] `-- Extracting jbigkit-2.1_3: .......... done [pkg.DaveG.ca] `-- Installing jpeg-turbo-3.1.2... [pkg.DaveG.ca] `-- Extracting jpeg-turbo-3.1.2: .......... done [pkg.DaveG.ca] `-- Installing lerc-4.0.0... [pkg.DaveG.ca] `-- Extracting lerc-4.0.0: ..... done [pkg.DaveG.ca] `-- Installing libdeflate-1.24... [pkg.DaveG.ca] `-- Extracting libdeflate-1.24: .......... done [pkg.DaveG.ca] `-- Installing zstd-1.5.7... [pkg.DaveG.ca] | `-- Installing liblz4-1.10.0_2,1... [pkg.DaveG.ca] | `-- Extracting liblz4-1.10.0_2,1: .......... done [pkg.DaveG.ca] `-- Extracting zstd-1.5.7: .......... done [pkg.DaveG.ca] Extracting tiff-4.7.1: .......... done ===> protomol-2.0.3_16 depends on shared library: libtiff.so - found (/usr/local/lib/libtiff.so) ===> Returning to build of protomol-2.0.3_16 ===> protomol-2.0.3_16 depends on shared library: libjpeg.so - found (/usr/local/lib/libjpeg.so) ===> protomol-2.0.3_16 depends on shared library: libglut.so - not found ===> Installing existing package /packages/All/freeglut-3.2.1.pkg [pkg.DaveG.ca] Installing freeglut-3.2.1... [pkg.DaveG.ca] `-- Installing libGLU-9.0.3... [pkg.DaveG.ca] | `-- Installing libglvnd-1.7.0... [pkg.DaveG.ca] | `-- Extracting libglvnd-1.7.0: .......... done [pkg.DaveG.ca] `-- Extracting libGLU-9.0.3: ..... done [pkg.DaveG.ca] `-- Installing libXrandr-1.5.4... [pkg.DaveG.ca] | `-- Installing libXrender-0.9.12... [pkg.DaveG.ca] | `-- Extracting libXrender-0.9.12: ....... done [pkg.DaveG.ca] `-- Extracting libXrandr-1.5.4: .......... done [pkg.DaveG.ca] `-- Installing libXxf86vm-1.1.6... [pkg.DaveG.ca] `-- Extracting libXxf86vm-1.1.6: .......... done [pkg.DaveG.ca] Extracting freeglut-3.2.1: .......... done ===== Message from freeglut-3.2.1: -- Joystick support is untested and it is unknown if it works. Do not hesitate to contact x11@FreeBSD.org if this causes issues. ===> protomol-2.0.3_16 depends on shared library: libglut.so - found (/usr/local/lib/libglut.so) ===> Returning to build of protomol-2.0.3_16 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for protomol-2.0.3_16 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 make sets $(MAKE)... yes checking major version... 2 checking minor version... 0 checking patchlevel... 3 checking for C++ compiler default output... 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 make... GNU checking dependency style of c++... none checking preset g++ for SUN with optimization flags ... no checking preset CC fro IRIX with MPI and optimization flags ... no checking preset CC for IRIX with MPI and debugging flags ... no checking preset CC for IRIX with optimization flags ... no checking preset CC for IRIX with debugging flags ... no checking preset icc for generic with optimization flags ... no checking preset icc for generic with debugging flags ... no checking preset icc for generic with MPICH flags ... no checking preset icc for generic with MPICH and optimization flags ... no checking preset icc for generic with MPICH and debugging flags ... no checking preset g++ for generic with MPICH flags ... no checking preset g++ for generic with MPICH XEON flags ... no checking preset g++ for generic with MPICH debug flags ... no checking preset g++ for generic with optimization flags ... no checking preset g++ for generic with debugging flags ... no checking preset g++ for generic with debugging and gdb flags ... no checking preset xlC for PPC with optimization flags ... no checking preset xlC for PPC with debugging flags ... no checking preset xlC for AIX with optimization flags ... no checking preset xlC for AIX with debugging flags ... no checking preset xlC for AIX with MPI and optimization flags ... no checking preset xlC for AIX with MPI and debugging flags ... no checking preset aCC for HPUX with optimization flags ... no checking preset aCC for HPUX with debugging flags ... no checking preset aCC for HPUX with MPI and optimization flags ... no checking preset aCC for HPUX with MPI and debugging flags ... no CC : cc CFLAGS : -O2 -pipe -fstack-protector-strong -fno-strict-aliasing CXXFLAGS : -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 CXX : c++ CXXCPP : LIBS : CPP : cpp CPPFLAGS : -I/usr/local/include checking whether we are using the GNU C++ compiler... (cached) yes checking whether c++ accepts -g... (cached) yes checking dependency style of c++... (cached) none checking how to run the C++ preprocessor... c++ -E 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... none checking for a BSD-compatible install... /usr/bin/install -c checking for ranlib... ranlib checking using MPI... no checking for X... libraries /usr/local/lib, headers /usr/local/include checking for gethostbyname... (cached) yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for limits ... yes checking for sstream ... yes checking for partial template specialization... yes checking for socket in -lsocket... no checking for egrep... grep -E 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 sys/socket.h... (cached) yes checking for socketlen type... socklen_t checking for char... (cached) yes checking size of char... 1 checking for short... (cached) yes checking size of short... 2 checking for int... (cached) yes checking size of int... 4 checking for long... (cached) yes checking size of long... 8 checking for size_t... (cached) yes checking size of size_t... 8 checking for void*... yes checking size of void*... 8 checking for 32-bit int... int checking for inline... inline checking whether time.h and sys/time.h may both be included... yes checking for sys/time.h... (cached) yes checking c_asm.h usability... no checking c_asm.h presence... no checking for c_asm.h... no checking intrinsics.h usability... no checking intrinsics.h presence... no checking for intrinsics.h... no checking for hrtime_t... no checking for gethrtime... no checking for clock_gettime... (cached) yes checking for read_real_time... no checking for time_base_to_time... no checking for _rtc intrinsic... no checking for zfftm1di in -lcomplib.sgimath... no checking for zfftm1d in -lcomplib.sgimath... no checking for zfft2di in -lcomplib.sgimath... no checking for zfft2d in -lcomplib.sgimath... no checking for zfft3di in -lcomplib.sgimath... no checking for zfft3d in -lcomplib.sgimath... no checking fft.h usability... no checking fft.h presence... no checking for fft.h... no checking for dcft in -lessl... no checking essl.h usability... no checking essl.h presence... no checking for essl.h... no checking for fftw3d_mpi_create_plan in -lfftw_mpi... no checking for fftw3d_create_plan in -lfftw... no checking fftw_mpi.h usability... no checking fftw_mpi.h presence... no checking for fftw_mpi.h... no checking fftw.h usability... no checking fftw.h presence... no checking for fftw.h... no checking for fftw_plan_dft_3d in -lfftw3... no checking fftw3.h usability... no checking fftw3.h presence... no checking for fftw3.h... no checking for fftw3d_create_plan in -lfftw... no checking fftw.h usability... no checking fftw.h presence... no checking for fftw.h... no checking FFT SGI complib.sgimath... no checking FFT ESSL... no checking FFT FFTW3... no checking FFT FFTW2... no checking FFT FFTW2 MPI... no using FFT ZFFT checking for compress in -lz... yes checking png.h usability... yes checking png.h presence... yes checking for png.h... yes checking for png_create_write_struct in -lpng... yes using PNG... yes checking for pthread_cancel in -lpthread... yes checking for dlopen in -ldl... yes checking for XmuAllStandardColormaps in -lXmu... yes checking for XtAppInitialize in -lXt... yes checking for SmcOpenConnection in -lSM... yes checking for IceAcceptConnection in -lICE... yes checking for XextCreateExtension in -lXext... yes checking for XOpenDisplay in -lX11... yes checking for XOpenDevice in -lXi... yes checking for pthread_cancel in -lpthread... (cached) yes checking for dlopen in -ldl... (cached) yes checking for glClear in -lGL... yes checking for gluLookAt in -lGLU... yes checking for glutMainLoop in -lglut... yes checking GL/glut.h usability... yes checking GL/glut.h presence... yes checking for GL/glut.h... yes checking for jpeg_CreateDecompress in -ljpeg... yes checking for TIFFSetErrorHandler in -ltiff... yes checking found GLUT... yes using GLUT... yes ./configure: perl: not found configure: creating ./config.status config.status: creating Makefile config.status: creating framework/Makefile config.status: creating framework/base/Makefile config.status: creating framework/io/Makefile config.status: creating framework/parallel/Makefile config.status: creating framework/topology/Makefile config.status: creating framework/forces/Makefile config.status: creating framework/imd/Makefile config.status: creating framework/integrators/Makefile config.status: creating framework/frontend/Makefile config.status: creating framework/factories/Makefile config.status: creating applications/Makefile config.status: creating applications/protomol-app/Makefile config.status: creating applications/coulomb-app/Makefile config.status: creating applications/dcd2dcd-app/Makefile config.status: creating applications/iSGProtomol-app/Makefile config.status: creating applications/iSGProtomol-app/base/Makefile config.status: creating applications/iSGProtomol-app/io/Makefile config.status: creating applications/iSGProtomol-app/frontend/Makefile config.status: creating applications/iSGProtomol-app/forces/Makefile config.status: creating applications/iSGProtomol-app/factories/Makefile config.status: creating applications/iSGProtomol-app/integrators/Makefile config.status: creating applications/coords2coords-app/Makefile config.status: creating applications/xyzviz-app/Makefile config.status: creating protomol_config.h config.status: executing depfiles commands CC : cc CFLAGS : -O2 -pipe -fstack-protector-strong -fno-strict-aliasing CXXFLAGS : -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 CXX : c++ CXXCPP : c++ -E LIBS : CPP : cpp CPPFLAGS : -I/usr/local/include make clean; make =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for protomol-2.0.3_16 --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in framework --- all-recursive --- Making all in base --- BSpline.o --- --- BSplineType.o --- --- Configuration.o --- --- ConstraintValueType.o --- --- FFTComplex.o --- --- Lagrange.o --- --- Makeable.o --- --- Matrix3by3.o --- --- iSGPAR.o --- --- PAR.o --- --- PDB.o --- --- PPM.o --- --- PGM.o --- --- PSF.o --- --- Parameter.o --- --- ReducedHessAngle.o --- --- reducedHessBond.o --- --- Report.o --- --- ScalarStructure.o --- --- Timer.o --- --- TimerStatistic.o --- --- Value.o --- --- ValueType.o --- --- Vector3DBlock.o --- --- XYZ.o --- --- pmconstants.o --- --- fft.o --- --- mathutilities.o --- --- stringutilities.o --- --- systemutilities.o --- --- BSpline.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o BSpline.o `test -f 'BSpline.cpp' || echo './'`BSpline.cpp --- BSplineType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o BSplineType.o `test -f 'BSplineType.cpp' || echo './'`BSplineType.cpp --- Configuration.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Configuration.o `test -f 'Configuration.cpp' || echo './'`Configuration.cpp --- ConstraintValueType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ConstraintValueType.o `test -f 'ConstraintValueType.cpp' || echo './'`ConstraintValueType.cpp --- FFTComplex.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o FFTComplex.o `test -f 'FFTComplex.cpp' || echo './'`FFTComplex.cpp --- Lagrange.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Lagrange.o `test -f 'Lagrange.cpp' || echo './'`Lagrange.cpp --- Makeable.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Makeable.o `test -f 'Makeable.cpp' || echo './'`Makeable.cpp --- Matrix3by3.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Matrix3by3.o `test -f 'Matrix3by3.cpp' || echo './'`Matrix3by3.cpp --- iSGPAR.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGPAR.o `test -f 'iSGPAR.cpp' || echo './'`iSGPAR.cpp --- PAR.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PAR.o `test -f 'PAR.cpp' || echo './'`PAR.cpp --- PDB.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PDB.o `test -f 'PDB.cpp' || echo './'`PDB.cpp --- PPM.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PPM.o `test -f 'PPM.cpp' || echo './'`PPM.cpp --- PGM.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PGM.o `test -f 'PGM.cpp' || echo './'`PGM.cpp --- PSF.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PSF.o `test -f 'PSF.cpp' || echo './'`PSF.cpp --- Parameter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Parameter.o `test -f 'Parameter.cpp' || echo './'`Parameter.cpp --- ReducedHessAngle.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ReducedHessAngle.o `test -f 'ReducedHessAngle.cpp' || echo './'`ReducedHessAngle.cpp --- reducedHessBond.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o reducedHessBond.o `test -f 'reducedHessBond.cpp' || echo './'`reducedHessBond.cpp --- Report.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Report.o `test -f 'Report.cpp' || echo './'`Report.cpp --- ScalarStructure.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ScalarStructure.o `test -f 'ScalarStructure.cpp' || echo './'`ScalarStructure.cpp --- Timer.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp --- TimerStatistic.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o TimerStatistic.o `test -f 'TimerStatistic.cpp' || echo './'`TimerStatistic.cpp --- Value.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Value.o `test -f 'Value.cpp' || echo './'`Value.cpp --- ValueType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ValueType.o `test -f 'ValueType.cpp' || echo './'`ValueType.cpp --- Vector3DBlock.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Vector3DBlock.o `test -f 'Vector3DBlock.cpp' || echo './'`Vector3DBlock.cpp --- XYZ.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZ.o `test -f 'XYZ.cpp' || echo './'`XYZ.cpp --- pmconstants.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o pmconstants.o `test -f 'pmconstants.cpp' || echo './'`pmconstants.cpp --- fft.o --- cc -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -c `test -f 'fft.c' || echo './'`fft.c --- mathutilities.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o mathutilities.o `test -f 'mathutilities.cpp' || echo './'`mathutilities.cpp --- stringutilities.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o stringutilities.o `test -f 'stringutilities.cpp' || echo './'`stringutilities.cpp --- systemutilities.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o systemutilities.o `test -f 'systemutilities.cpp' || echo './'`systemutilities.cpp --- PGM.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ScalarStructure.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PPM.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- BSpline.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- BSplineType.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PSF.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Lagrange.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ConstraintValueType.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Report.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] Report.cpp:91:2: warning: add explicit braces to avoid dangling else [-Wdangling-else] 91 | else | ^ 1 warning generated. --- TimerStatistic.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- systemutilities.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- reducedHessBond.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Timer.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PDB.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- FFTComplex.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Matrix3by3.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ReducedHessAngle.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- XYZ.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ValueType.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- pmconstants.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- mathutilities.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGPAR.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PAR.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Configuration.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Vector3DBlock.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Parameter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- stringutilities.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Makeable.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Value.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libbase.a --- rm -f libbase.a ar cru libbase.a BSpline.o BSplineType.o Configuration.o ConstraintValueType.o FFTComplex.o Lagrange.o Makeable.o Matrix3by3.o iSGPAR.o PAR.o PDB.o PPM.o PGM.o PSF.o Parameter.o ReducedHessAngle.o reducedHessBond.o Report.o ScalarStructure.o Timer.o TimerStatistic.o Value.o ValueType.o Vector3DBlock.o XYZ.o pmconstants.o fft.o mathutilities.o stringutilities.o systemutilities.o ranlib libbase.a Making all in io --- ConfigurationReader.o --- --- DCDTrajectoryReader.o --- --- DCDTrajectoryWriter.o --- --- File.o --- --- PARReader.o --- --- PARWriter.o --- --- PDBReader.o --- --- PDBWriter.o --- --- PNGWriter.o --- --- PPMReader.o --- --- PPMWriter.o --- --- PGMReader.o --- --- PGMWriter.o --- --- PSFReader.o --- --- PSFWriter.o --- --- Reader.o --- --- Writer.o --- --- XFigWriter.o --- --- XYZBinReader.o --- --- XYZBinWriter.o --- --- XYZReader.o --- --- XYZTrajectoryReader.o --- --- XYZTrajectoryWriter.o --- --- XYZWriter.o --- --- ConfigurationReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ConfigurationReader.o `test -f 'ConfigurationReader.cpp' || echo './'`ConfigurationReader.cpp --- DCDTrajectoryReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DCDTrajectoryReader.o `test -f 'DCDTrajectoryReader.cpp' || echo './'`DCDTrajectoryReader.cpp --- DCDTrajectoryWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DCDTrajectoryWriter.o `test -f 'DCDTrajectoryWriter.cpp' || echo './'`DCDTrajectoryWriter.cpp --- File.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o File.o `test -f 'File.cpp' || echo './'`File.cpp --- PARReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PARReader.o `test -f 'PARReader.cpp' || echo './'`PARReader.cpp --- PARWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PARWriter.o `test -f 'PARWriter.cpp' || echo './'`PARWriter.cpp --- PDBReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PDBReader.o `test -f 'PDBReader.cpp' || echo './'`PDBReader.cpp --- PDBWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PDBWriter.o `test -f 'PDBWriter.cpp' || echo './'`PDBWriter.cpp --- PNGWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PNGWriter.o `test -f 'PNGWriter.cpp' || echo './'`PNGWriter.cpp --- PPMReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PPMReader.o `test -f 'PPMReader.cpp' || echo './'`PPMReader.cpp --- PPMWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PPMWriter.o `test -f 'PPMWriter.cpp' || echo './'`PPMWriter.cpp --- PGMReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PGMReader.o `test -f 'PGMReader.cpp' || echo './'`PGMReader.cpp --- PGMWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PGMWriter.o `test -f 'PGMWriter.cpp' || echo './'`PGMWriter.cpp --- PSFReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PSFReader.o `test -f 'PSFReader.cpp' || echo './'`PSFReader.cpp --- PSFWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PSFWriter.o `test -f 'PSFWriter.cpp' || echo './'`PSFWriter.cpp --- Reader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Reader.o `test -f 'Reader.cpp' || echo './'`Reader.cpp --- Writer.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Writer.o `test -f 'Writer.cpp' || echo './'`Writer.cpp --- XFigWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XFigWriter.o `test -f 'XFigWriter.cpp' || echo './'`XFigWriter.cpp --- XYZBinReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZBinReader.o `test -f 'XYZBinReader.cpp' || echo './'`XYZBinReader.cpp --- XYZBinWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZBinWriter.o `test -f 'XYZBinWriter.cpp' || echo './'`XYZBinWriter.cpp --- XYZReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZReader.o `test -f 'XYZReader.cpp' || echo './'`XYZReader.cpp --- XYZTrajectoryWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZTrajectoryWriter.o `test -f 'XYZTrajectoryWriter.cpp' || echo './'`XYZTrajectoryWriter.cpp --- XYZWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZWriter.o `test -f 'XYZWriter.cpp' || echo './'`XYZWriter.cpp --- XYZTrajectoryReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZTrajectoryReader.o `test -f 'XYZTrajectoryReader.cpp' || echo './'`XYZTrajectoryReader.cpp --- Writer.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Reader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- XYZWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PPMWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PNGWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] PNGWriter.cpp:118:23: warning: conversion from string literal to 'png_charp' (aka 'char *') is deprecated [-Wc++11-compat-deprecated-writable-strings] 118 | text_ptr[0].key = "Description"; | ^ PNGWriter.cpp:119:24: warning: conversion from string literal to 'png_charp' (aka 'char *') is deprecated [-Wc++11-compat-deprecated-writable-strings] 119 | text_ptr[0].text = "ProtoMol PNG Writer"; | ^ PNGWriter.cpp:125:23: warning: conversion from string literal to 'png_charp' (aka 'char *') is deprecated [-Wc++11-compat-deprecated-writable-strings] 125 | text_ptr[1].key = "Software"; | ^ PNGWriter.cpp:126:24: warning: conversion from string literal to 'png_charp' (aka 'char *') is deprecated [-Wc++11-compat-deprecated-writable-strings] 126 | text_ptr[1].text = "ProtoMol"; | ^ 4 warnings generated. --- XYZBinWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PPMReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PGMReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- XYZReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PSFWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PGMWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- File.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- XFigWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- XYZTrajectoryReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- DCDTrajectoryWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- XYZTrajectoryWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- DCDTrajectoryReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PDBWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PDBReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PSFReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- XYZBinReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ConfigurationReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PARWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PARReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libio.a --- rm -f libio.a ar cru libio.a ConfigurationReader.o DCDTrajectoryReader.o DCDTrajectoryWriter.o File.o PARReader.o PARWriter.o PDBReader.o PDBWriter.o PNGWriter.o PPMReader.o PPMWriter.o PGMReader.o PGMWriter.o PSFReader.o PSFWriter.o Reader.o Writer.o XFigWriter.o XYZBinReader.o XYZBinWriter.o XYZReader.o XYZTrajectoryReader.o XYZTrajectoryWriter.o XYZWriter.o ranlib libio.a Making all in parallel --- Parallel.o --- --- ParallelType.o --- --- Parallel.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Parallel.o `test -f 'Parallel.cpp' || echo './'`Parallel.cpp --- ParallelType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ParallelType.o `test -f 'ParallelType.cpp' || echo './'`ParallelType.cpp c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Parallel.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libparallel.a --- rm -f libparallel.a ar cru libparallel.a Parallel.o ParallelType.o ranlib libparallel.a Making all in topology --- ArrayCellListStructure.o --- --- C1SwitchingFunctionBase.o --- --- C1SwitchingFunction.o --- --- C2SwitchingFunctionBase.o --- --- C2SwitchingFunction.o --- --- buildCellLists.o --- --- ComplementSwitchingFunctionBase.o --- --- CubicCellManager.o --- --- CutoffSwitchingFunctionBase.o --- --- CutoffSwitchingFunction.o --- --- ExclusionTable.o --- --- ExclusionType.o --- --- GenericTopology.o --- --- LennardJonesParameterTable.o --- --- PeriodicBoundaryConditions.o --- --- RangeSwitchingFunctionBase.o --- --- ShiftSwitchingFunctionBase.o --- --- ShiftSwitchingFunction.o --- --- topologyutilities.o --- --- UniversalSwitchingFunctionBase.o --- --- VacuumBoundaryConditions.o --- --- AngleInfo.o --- --- ArrayCellListStructure.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ArrayCellListStructure.o `test -f 'ArrayCellListStructure.cpp' || echo './'`ArrayCellListStructure.cpp --- C1SwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o C1SwitchingFunctionBase.o `test -f 'C1SwitchingFunctionBase.cpp' || echo './'`C1SwitchingFunctionBase.cpp --- C1SwitchingFunction.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o C1SwitchingFunction.o `test -f 'C1SwitchingFunction.cpp' || echo './'`C1SwitchingFunction.cpp --- C2SwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o C2SwitchingFunctionBase.o `test -f 'C2SwitchingFunctionBase.cpp' || echo './'`C2SwitchingFunctionBase.cpp --- C2SwitchingFunction.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o C2SwitchingFunction.o `test -f 'C2SwitchingFunction.cpp' || echo './'`C2SwitchingFunction.cpp --- buildCellLists.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o buildCellLists.o `test -f 'buildCellLists.cpp' || echo './'`buildCellLists.cpp --- ComplementSwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ComplementSwitchingFunctionBase.o `test -f 'ComplementSwitchingFunctionBase.cpp' || echo './'`ComplementSwitchingFunctionBase.cpp --- CubicCellManager.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CubicCellManager.o `test -f 'CubicCellManager.cpp' || echo './'`CubicCellManager.cpp --- CutoffSwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CutoffSwitchingFunctionBase.o `test -f 'CutoffSwitchingFunctionBase.cpp' || echo './'`CutoffSwitchingFunctionBase.cpp --- CutoffSwitchingFunction.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CutoffSwitchingFunction.o `test -f 'CutoffSwitchingFunction.cpp' || echo './'`CutoffSwitchingFunction.cpp --- ExclusionTable.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExclusionTable.o `test -f 'ExclusionTable.cpp' || echo './'`ExclusionTable.cpp --- ExclusionType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExclusionType.o `test -f 'ExclusionType.cpp' || echo './'`ExclusionType.cpp --- GenericTopology.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o GenericTopology.o `test -f 'GenericTopology.cpp' || echo './'`GenericTopology.cpp --- LennardJonesParameterTable.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o LennardJonesParameterTable.o `test -f 'LennardJonesParameterTable.cpp' || echo './'`LennardJonesParameterTable.cpp --- PeriodicBoundaryConditions.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PeriodicBoundaryConditions.o `test -f 'PeriodicBoundaryConditions.cpp' || echo './'`PeriodicBoundaryConditions.cpp --- RangeSwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o RangeSwitchingFunctionBase.o `test -f 'RangeSwitchingFunctionBase.cpp' || echo './'`RangeSwitchingFunctionBase.cpp --- ShiftSwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ShiftSwitchingFunctionBase.o `test -f 'ShiftSwitchingFunctionBase.cpp' || echo './'`ShiftSwitchingFunctionBase.cpp --- ShiftSwitchingFunction.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ShiftSwitchingFunction.o `test -f 'ShiftSwitchingFunction.cpp' || echo './'`ShiftSwitchingFunction.cpp --- topologyutilities.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o topologyutilities.o `test -f 'topologyutilities.cpp' || echo './'`topologyutilities.cpp --- VacuumBoundaryConditions.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o VacuumBoundaryConditions.o `test -f 'VacuumBoundaryConditions.cpp' || echo './'`VacuumBoundaryConditions.cpp --- AngleInfo.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o AngleInfo.o `test -f 'AngleInfo.cpp' || echo './'`AngleInfo.cpp --- UniversalSwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o UniversalSwitchingFunctionBase.o `test -f 'UniversalSwitchingFunctionBase.cpp' || echo './'`UniversalSwitchingFunctionBase.cpp --- C1SwitchingFunctionBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ShiftSwitchingFunctionBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ComplementSwitchingFunctionBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- RangeSwitchingFunctionBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- UniversalSwitchingFunctionBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- CutoffSwitchingFunctionBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- C2SwitchingFunctionBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- AngleInfo.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ArrayCellListStructure.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- LennardJonesParameterTable.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- VacuumBoundaryConditions.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ExclusionType.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ShiftSwitchingFunction.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- buildCellLists.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- CubicCellManager.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ExclusionTable.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- C2SwitchingFunction.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- C1SwitchingFunction.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- CutoffSwitchingFunction.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PeriodicBoundaryConditions.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- GenericTopology.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- topologyutilities.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libtopology.a --- rm -f libtopology.a ar cru libtopology.a ArrayCellListStructure.o C1SwitchingFunctionBase.o C1SwitchingFunction.o C2SwitchingFunctionBase.o C2SwitchingFunction.o buildCellLists.o ComplementSwitchingFunctionBase.o CubicCellManager.o CutoffSwitchingFunctionBase.o CutoffSwitchingFunction.o ExclusionTable.o ExclusionType.o GenericTopology.o LennardJonesParameterTable.o PeriodicBoundaryConditions.o RangeSwitchingFunctionBase.o ShiftSwitchingFunctionBase.o ShiftSwitchingFunction.o topologyutilities.o UniversalSwitchingFunctionBase.o VacuumBoundaryConditions.o AngleInfo.o ranlib libtopology.a Making all in forces --- AngleSystemForceBase.o --- --- BondSystemForceBase.o --- --- CompareForce.o --- --- CoulombEwaldRealForce.o --- --- CoulombEwaldRealTableForce.o --- --- CoulombForce.o --- --- CoulombMultiGridDirectForceBase.o --- --- CoulombMultiGridDirectTableForceBase.o --- --- DihedralSystemForceBase.o --- --- HarmDihedralSystemForceBase.o --- --- ElectricFieldSystemForceBase.o --- --- ExternalGravitationSystemForce.o --- --- ExternalMagneticFieldExtendedForce.o --- --- ExtendedCompareForce.o --- --- ExtendedForce.o --- --- ExtendedTimeForce.o --- --- Force.o --- --- ForceGroup.o --- --- FrictionExtendedForce.o --- --- GravitationForce.o --- --- Hermite.o --- --- ImproperSystemForceBase.o --- --- LennardJonesForce.o --- --- LennardJonesTableForce.o --- --- MagneticDipoleForce.o --- --- MagneticDipoleMirrorSystemForceBase.o --- --- MetaForce.o --- --- MollyForce.o --- --- NonbondedCutoffForceBase.o --- --- NonbondedFullEwaldSystemForceBase.o --- --- NonbondedFullSystemForceBase.o --- --- NonbondedMultiGridSystemForceBase.o --- --- NonbondedPMEwaldSystemForceBase.o --- --- NonbondedSimpleFullSystemForceBase.o --- --- PaulTrapExtendedForceBase.o --- --- ReducedHessCoulomb.o --- --- ReducedHessLennardJones.o --- --- SphericalSystemForce.o --- --- SystemCompareForce.o --- --- SystemForce.o --- --- SystemTimeForce.o --- --- TimeForce.o --- --- WrapperMetaForce.o --- --- AngleSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o AngleSystemForceBase.o `test -f 'AngleSystemForceBase.cpp' || echo './'`AngleSystemForceBase.cpp --- BondSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o BondSystemForceBase.o `test -f 'BondSystemForceBase.cpp' || echo './'`BondSystemForceBase.cpp --- CompareForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CompareForce.o `test -f 'CompareForce.cpp' || echo './'`CompareForce.cpp --- CoulombEwaldRealForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CoulombEwaldRealForce.o `test -f 'CoulombEwaldRealForce.cpp' || echo './'`CoulombEwaldRealForce.cpp --- CoulombEwaldRealTableForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CoulombEwaldRealTableForce.o `test -f 'CoulombEwaldRealTableForce.cpp' || echo './'`CoulombEwaldRealTableForce.cpp --- CoulombForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CoulombForce.o `test -f 'CoulombForce.cpp' || echo './'`CoulombForce.cpp --- CoulombMultiGridDirectForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CoulombMultiGridDirectForceBase.o `test -f 'CoulombMultiGridDirectForceBase.cpp' || echo './'`CoulombMultiGridDirectForceBase.cpp --- CoulombMultiGridDirectTableForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CoulombMultiGridDirectTableForceBase.o `test -f 'CoulombMultiGridDirectTableForceBase.cpp' || echo './'`CoulombMultiGridDirectTableForceBase.cpp --- DihedralSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DihedralSystemForceBase.o `test -f 'DihedralSystemForceBase.cpp' || echo './'`DihedralSystemForceBase.cpp --- HarmDihedralSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o HarmDihedralSystemForceBase.o `test -f 'HarmDihedralSystemForceBase.cpp' || echo './'`HarmDihedralSystemForceBase.cpp --- ElectricFieldSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ElectricFieldSystemForceBase.o `test -f 'ElectricFieldSystemForceBase.cpp' || echo './'`ElectricFieldSystemForceBase.cpp --- ExternalGravitationSystemForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExternalGravitationSystemForce.o `test -f 'ExternalGravitationSystemForce.cpp' || echo './'`ExternalGravitationSystemForce.cpp --- ExternalMagneticFieldExtendedForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExternalMagneticFieldExtendedForce.o `test -f 'ExternalMagneticFieldExtendedForce.cpp' || echo './'`ExternalMagneticFieldExtendedForce.cpp --- ExtendedCompareForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExtendedCompareForce.o `test -f 'ExtendedCompareForce.cpp' || echo './'`ExtendedCompareForce.cpp --- ExtendedForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExtendedForce.o `test -f 'ExtendedForce.cpp' || echo './'`ExtendedForce.cpp --- ExtendedTimeForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExtendedTimeForce.o `test -f 'ExtendedTimeForce.cpp' || echo './'`ExtendedTimeForce.cpp --- Force.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Force.o `test -f 'Force.cpp' || echo './'`Force.cpp --- ForceGroup.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ForceGroup.o `test -f 'ForceGroup.cpp' || echo './'`ForceGroup.cpp --- FrictionExtendedForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o FrictionExtendedForce.o `test -f 'FrictionExtendedForce.cpp' || echo './'`FrictionExtendedForce.cpp --- GravitationForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o GravitationForce.o `test -f 'GravitationForce.cpp' || echo './'`GravitationForce.cpp --- Hermite.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Hermite.o `test -f 'Hermite.cpp' || echo './'`Hermite.cpp --- ImproperSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ImproperSystemForceBase.o `test -f 'ImproperSystemForceBase.cpp' || echo './'`ImproperSystemForceBase.cpp --- LennardJonesForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o LennardJonesForce.o `test -f 'LennardJonesForce.cpp' || echo './'`LennardJonesForce.cpp --- LennardJonesTableForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o LennardJonesTableForce.o `test -f 'LennardJonesTableForce.cpp' || echo './'`LennardJonesTableForce.cpp --- MagneticDipoleForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MagneticDipoleForce.o `test -f 'MagneticDipoleForce.cpp' || echo './'`MagneticDipoleForce.cpp --- MagneticDipoleMirrorSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MagneticDipoleMirrorSystemForceBase.o `test -f 'MagneticDipoleMirrorSystemForceBase.cpp' || echo './'`MagneticDipoleMirrorSystemForceBase.cpp --- MetaForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MetaForce.o `test -f 'MetaForce.cpp' || echo './'`MetaForce.cpp --- MollyForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MollyForce.o `test -f 'MollyForce.cpp' || echo './'`MollyForce.cpp --- NonbondedCutoffForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedCutoffForceBase.o `test -f 'NonbondedCutoffForceBase.cpp' || echo './'`NonbondedCutoffForceBase.cpp --- NonbondedFullEwaldSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedFullEwaldSystemForceBase.o `test -f 'NonbondedFullEwaldSystemForceBase.cpp' || echo './'`NonbondedFullEwaldSystemForceBase.cpp --- NonbondedFullSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedFullSystemForceBase.o `test -f 'NonbondedFullSystemForceBase.cpp' || echo './'`NonbondedFullSystemForceBase.cpp --- NonbondedMultiGridSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedMultiGridSystemForceBase.o `test -f 'NonbondedMultiGridSystemForceBase.cpp' || echo './'`NonbondedMultiGridSystemForceBase.cpp --- NonbondedPMEwaldSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedPMEwaldSystemForceBase.o `test -f 'NonbondedPMEwaldSystemForceBase.cpp' || echo './'`NonbondedPMEwaldSystemForceBase.cpp --- NonbondedSimpleFullSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedSimpleFullSystemForceBase.o `test -f 'NonbondedSimpleFullSystemForceBase.cpp' || echo './'`NonbondedSimpleFullSystemForceBase.cpp --- PaulTrapExtendedForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PaulTrapExtendedForceBase.o `test -f 'PaulTrapExtendedForceBase.cpp' || echo './'`PaulTrapExtendedForceBase.cpp --- ReducedHessCoulomb.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ReducedHessCoulomb.o `test -f 'ReducedHessCoulomb.cpp' || echo './'`ReducedHessCoulomb.cpp --- ReducedHessLennardJones.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ReducedHessLennardJones.o `test -f 'ReducedHessLennardJones.cpp' || echo './'`ReducedHessLennardJones.cpp --- SphericalSystemForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o SphericalSystemForce.o `test -f 'SphericalSystemForce.cpp' || echo './'`SphericalSystemForce.cpp --- SystemCompareForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o SystemCompareForce.o `test -f 'SystemCompareForce.cpp' || echo './'`SystemCompareForce.cpp --- SystemForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o SystemForce.o `test -f 'SystemForce.cpp' || echo './'`SystemForce.cpp --- SystemTimeForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o SystemTimeForce.o `test -f 'SystemTimeForce.cpp' || echo './'`SystemTimeForce.cpp --- TimeForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o TimeForce.o `test -f 'TimeForce.cpp' || echo './'`TimeForce.cpp --- WrapperMetaForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o WrapperMetaForce.o `test -f 'WrapperMetaForce.cpp' || echo './'`WrapperMetaForce.cpp --- HarmDihedralSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ImproperSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- NonbondedFullEwaldSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- NonbondedCutoffForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- BondSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- NonbondedSimpleFullSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- DihedralSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- AngleSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- CoulombMultiGridDirectForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- NonbondedPMEwaldSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- NonbondedMultiGridSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- NonbondedFullSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- CoulombMultiGridDirectTableForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PaulTrapExtendedForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- MagneticDipoleMirrorSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ElectricFieldSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Hermite.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ReducedHessLennardJones.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- SystemForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ReducedHessCoulomb.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- MetaForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ExtendedForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ExtendedCompareForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- LennardJonesForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- MollyForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ExtendedTimeForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Force.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- SystemCompareForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- FrictionExtendedForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- SystemTimeForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- MagneticDipoleForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- CoulombForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- TimeForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ExternalMagneticFieldExtendedForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- GravitationForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- SphericalSystemForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- LennardJonesTableForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- CoulombEwaldRealTableForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- CoulombEwaldRealForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- WrapperMetaForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- CompareForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ExternalGravitationSystemForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ForceGroup.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libforces.a --- rm -f libforces.a ar cru libforces.a AngleSystemForceBase.o BondSystemForceBase.o CompareForce.o CoulombEwaldRealForce.o CoulombEwaldRealTableForce.o CoulombForce.o CoulombMultiGridDirectForceBase.o CoulombMultiGridDirectTableForceBase.o DihedralSystemForceBase.o HarmDihedralSystemForceBase.o ElectricFieldSystemForceBase.o ExternalGravitationSystemForce.o ExternalMagneticFieldExtendedForce.o ExtendedCompareForce.o ExtendedForce.o ExtendedTimeForce.o Force.o ForceGroup.o FrictionExtendedForce.o GravitationForce.o Hermite.o ImproperSystemForceBase.o LennardJonesForce.o LennardJonesTableForce.o MagneticDipoleForce.o MagneticDipoleMirrorSystemForceBase.o MetaForce.o MollyForce.o NonbondedCutoffForceBase.o NonbondedFullEwaldSystemForceBase.o NonbondedFullSystemForceBase.o NonbondedMultiGridSystemForceBase.o NonbondedPMEwaldSystemForceBase.o NonbondedSimpleFullSystemForceBase.o PaulTrapExtendedForceBase.o ReducedHessCoulomb.o ReducedHessLennardJones.o SphericalSystemForce.o SystemCompareForce.o SystemForce.o SystemTimeForce.o TimeForce.o WrapperMetaForce.o ranlib libforces.a Making all in imd --- IMDElf.o --- --- imd.o --- --- vmdsock.o --- --- HapticSystemForce.o --- --- IMDElf.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o IMDElf.o `test -f 'IMDElf.cpp' || echo './'`IMDElf.cpp --- imd.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o imd.o `test -f 'imd.cpp' || echo './'`imd.cpp --- vmdsock.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o vmdsock.o `test -f 'vmdsock.cpp' || echo './'`vmdsock.cpp --- HapticSystemForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o HapticSystemForce.o `test -f 'HapticSystemForce.cpp' || echo './'`HapticSystemForce.cpp --- vmdsock.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] In file included from vmdsock.cpp:52: ./vmdsock.h:2:9: warning: 'VMDSOCK_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] 2 | #ifndef VMDSOCK_H | ^~~~~~~~~ ./vmdsock.h:3:9: note: 'IVMDSOCK_H' is defined here; did you mean 'VMDSOCK_H'? 3 | #define IVMDSOCK_H | ^~~~~~~~~~ | VMDSOCK_H 1 warning generated. --- imd.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] In file included from imd.cpp:2: ./vmdsock.h:2:9: warning: 'VMDSOCK_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] 2 | #ifndef VMDSOCK_H | ^~~~~~~~~ ./vmdsock.h:3:9: note: 'IVMDSOCK_H' is defined here; did you mean 'VMDSOCK_H'? 3 | #define IVMDSOCK_H | ^~~~~~~~~~ | VMDSOCK_H 1 warning generated. --- IMDElf.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] In file included from IMDElf.cpp:4: ./vmdsock.h:2:9: warning: 'VMDSOCK_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] 2 | #ifndef VMDSOCK_H | ^~~~~~~~~ ./vmdsock.h:3:9: note: 'IVMDSOCK_H' is defined here; did you mean 'VMDSOCK_H'? 3 | #define IVMDSOCK_H | ^~~~~~~~~~ | VMDSOCK_H 1 warning generated. --- HapticSystemForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libimd.a --- rm -f libimd.a ar cru libimd.a IMDElf.o imd.o vmdsock.o HapticSystemForce.o ranlib libimd.a Making all in integrators --- ModifierMetaShake.o --- --- ModifierMetaRattle.o --- --- ModifierMetaRattleShake.o --- --- NPTVerletIntegrator.o --- --- NVTVerletIntegrator.o --- --- BSplineMOLLYIntegrator.o --- --- EquilibriumMOLLYIntegrator.o --- --- DihedralHMCIntegrator.o --- --- DLMCIntegrator.o --- --- ShadowHMCIntegrator.o --- --- HMCIntegrator.o --- --- MCIntegrator.o --- --- ImpulseIntegrator.o --- --- Integrator.o --- --- IntegratorDefinition.o --- --- LeapfrogIntegrator.o --- --- DMDLeapfrogIntegrator.o --- --- BBKIntegrator.o --- --- ModifierShake.o --- --- ModifierRattle.o --- --- ModifierNPTShake.o --- --- ModifierNPTRattle.o --- --- ModifierNVTShake.o --- --- ModifierNVTRattle.o --- --- PLeapfrogIntegrator.o --- --- MOLLYIntegrator.o --- --- UmbrellaIntegrator.o --- --- MTSIntegrator.o --- --- NoseNVTLeapfrogIntegrator.o --- --- PaulTrapIntegrator.o --- --- LangevinImpulseIntegrator.o --- --- StandardIntegrator.o --- --- STSIntegrator.o --- --- ModifierMetaShake.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierMetaShake.o `test -f 'ModifierMetaShake.cpp' || echo './'`ModifierMetaShake.cpp --- ModifierMetaRattle.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierMetaRattle.o `test -f 'ModifierMetaRattle.cpp' || echo './'`ModifierMetaRattle.cpp --- ModifierMetaRattleShake.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierMetaRattleShake.o `test -f 'ModifierMetaRattleShake.cpp' || echo './'`ModifierMetaRattleShake.cpp --- NPTVerletIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NPTVerletIntegrator.o `test -f 'NPTVerletIntegrator.cpp' || echo './'`NPTVerletIntegrator.cpp --- NVTVerletIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NVTVerletIntegrator.o `test -f 'NVTVerletIntegrator.cpp' || echo './'`NVTVerletIntegrator.cpp --- BSplineMOLLYIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o BSplineMOLLYIntegrator.o `test -f 'BSplineMOLLYIntegrator.cpp' || echo './'`BSplineMOLLYIntegrator.cpp --- EquilibriumMOLLYIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o EquilibriumMOLLYIntegrator.o `test -f 'EquilibriumMOLLYIntegrator.cpp' || echo './'`EquilibriumMOLLYIntegrator.cpp --- DihedralHMCIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DihedralHMCIntegrator.o `test -f 'DihedralHMCIntegrator.cpp' || echo './'`DihedralHMCIntegrator.cpp --- DLMCIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DLMCIntegrator.o `test -f 'DLMCIntegrator.cpp' || echo './'`DLMCIntegrator.cpp --- ShadowHMCIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ShadowHMCIntegrator.o `test -f 'ShadowHMCIntegrator.cpp' || echo './'`ShadowHMCIntegrator.cpp --- HMCIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o HMCIntegrator.o `test -f 'HMCIntegrator.cpp' || echo './'`HMCIntegrator.cpp --- MCIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MCIntegrator.o `test -f 'MCIntegrator.cpp' || echo './'`MCIntegrator.cpp --- ImpulseIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ImpulseIntegrator.o `test -f 'ImpulseIntegrator.cpp' || echo './'`ImpulseIntegrator.cpp --- Integrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Integrator.o `test -f 'Integrator.cpp' || echo './'`Integrator.cpp --- IntegratorDefinition.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o IntegratorDefinition.o `test -f 'IntegratorDefinition.cpp' || echo './'`IntegratorDefinition.cpp --- LeapfrogIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o LeapfrogIntegrator.o `test -f 'LeapfrogIntegrator.cpp' || echo './'`LeapfrogIntegrator.cpp --- DMDLeapfrogIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DMDLeapfrogIntegrator.o `test -f 'DMDLeapfrogIntegrator.cpp' || echo './'`DMDLeapfrogIntegrator.cpp --- BBKIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o BBKIntegrator.o `test -f 'BBKIntegrator.cpp' || echo './'`BBKIntegrator.cpp --- ModifierShake.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierShake.o `test -f 'ModifierShake.cpp' || echo './'`ModifierShake.cpp --- ModifierRattle.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierRattle.o `test -f 'ModifierRattle.cpp' || echo './'`ModifierRattle.cpp --- ModifierNPTShake.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierNPTShake.o `test -f 'ModifierNPTShake.cpp' || echo './'`ModifierNPTShake.cpp --- ModifierNPTRattle.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierNPTRattle.o `test -f 'ModifierNPTRattle.cpp' || echo './'`ModifierNPTRattle.cpp --- ModifierNVTShake.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierNVTShake.o `test -f 'ModifierNVTShake.cpp' || echo './'`ModifierNVTShake.cpp --- ModifierNVTRattle.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierNVTRattle.o `test -f 'ModifierNVTRattle.cpp' || echo './'`ModifierNVTRattle.cpp --- PLeapfrogIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PLeapfrogIntegrator.o `test -f 'PLeapfrogIntegrator.cpp' || echo './'`PLeapfrogIntegrator.cpp --- MOLLYIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MOLLYIntegrator.o `test -f 'MOLLYIntegrator.cpp' || echo './'`MOLLYIntegrator.cpp --- UmbrellaIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o UmbrellaIntegrator.o `test -f 'UmbrellaIntegrator.cpp' || echo './'`UmbrellaIntegrator.cpp --- MTSIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MTSIntegrator.o `test -f 'MTSIntegrator.cpp' || echo './'`MTSIntegrator.cpp --- NoseNVTLeapfrogIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NoseNVTLeapfrogIntegrator.o `test -f 'NoseNVTLeapfrogIntegrator.cpp' || echo './'`NoseNVTLeapfrogIntegrator.cpp --- PaulTrapIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PaulTrapIntegrator.o `test -f 'PaulTrapIntegrator.cpp' || echo './'`PaulTrapIntegrator.cpp --- StandardIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o StandardIntegrator.o `test -f 'StandardIntegrator.cpp' || echo './'`StandardIntegrator.cpp --- LangevinImpulseIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o LangevinImpulseIntegrator.o `test -f 'LangevinImpulseIntegrator.cpp' || echo './'`LangevinImpulseIntegrator.cpp --- STSIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o STSIntegrator.o `test -f 'STSIntegrator.cpp' || echo './'`STSIntegrator.cpp --- ModifierNPTShake.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ModifierRattle.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ImpulseIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- HMCIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- IntegratorDefinition.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ModifierMetaRattle.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- MOLLYIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ModifierNPTRattle.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ModifierNVTRattle.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ModifierMetaShake.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ModifierShake.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- LangevinImpulseIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- NPTVerletIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- BBKIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- LeapfrogIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ModifierMetaRattleShake.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ModifierNVTShake.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- MCIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Integrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- DLMCIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- NoseNVTLeapfrogIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- MTSIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- StandardIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- DMDLeapfrogIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PLeapfrogIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- UmbrellaIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- EquilibriumMOLLYIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- STSIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- NVTVerletIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- DihedralHMCIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ShadowHMCIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- BSplineMOLLYIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- PaulTrapIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libintegrators.a --- rm -f libintegrators.a ar cru libintegrators.a ModifierMetaShake.o ModifierMetaRattle.o ModifierMetaRattleShake.o NPTVerletIntegrator.o NVTVerletIntegrator.o BSplineMOLLYIntegrator.o EquilibriumMOLLYIntegrator.o DihedralHMCIntegrator.o DLMCIntegrator.o ShadowHMCIntegrator.o HMCIntegrator.o MCIntegrator.o ImpulseIntegrator.o Integrator.o IntegratorDefinition.o LeapfrogIntegrator.o DMDLeapfrogIntegrator.o BBKIntegrator.o ModifierShake.o ModifierRattle.o ModifierNPTShake.o ModifierNPTRattle.o ModifierNVTShake.o ModifierNVTRattle.o PLeapfrogIntegrator.o MOLLYIntegrator.o UmbrellaIntegrator.o MTSIntegrator.o NoseNVTLeapfrogIntegrator.o PaulTrapIntegrator.o LangevinImpulseIntegrator.o StandardIntegrator.o STSIntegrator.o NPTVerletIntegrator.o NVTVerletIntegrator.o ranlib libintegrators.a Making all in frontend --- HelpTextFactory.o --- --- ForceFactoryDetails.o --- --- InputPosVel.o --- --- InputPosVelType.o --- --- IntegratorFactoryDetails.o --- --- Output.o --- --- OutputCache.o --- --- OutputCollection.o --- --- OutputDCDTrajectory.o --- --- OutputDiffusion.o --- --- OutputDihedrals.o --- --- OutputEnergies.o --- --- OutputFactoryDetails.o --- --- OutputFile.o --- --- OutputFinalXYZBinPos.o --- --- OutputFinalXYZBinVel.o --- --- OutputFinalXYZPos.o --- --- OutputFinalPDBPos.o --- --- OutputFinalXYZVel.o --- --- OutputMomentum.o --- --- OutputPaulTrap.o --- --- OutputPDBFramePos.o --- --- OutputScreen.o --- --- OutputTemperatures.o --- --- OutputXYZTrajectoryForce.o --- --- OutputXYZTrajectoryPos.o --- --- OutputXYZTrajectoryVel.o --- --- TopologyFactoryDetails.o --- --- buildTopology.o --- --- inputValueDefinitions.o --- --- parseCommandLine.o --- --- HelpTextFactory.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o HelpTextFactory.o `test -f 'HelpTextFactory.cpp' || echo './'`HelpTextFactory.cpp --- ForceFactoryDetails.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ForceFactoryDetails.o `test -f 'ForceFactoryDetails.cpp' || echo './'`ForceFactoryDetails.cpp --- InputPosVel.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o InputPosVel.o `test -f 'InputPosVel.cpp' || echo './'`InputPosVel.cpp --- InputPosVelType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o InputPosVelType.o `test -f 'InputPosVelType.cpp' || echo './'`InputPosVelType.cpp --- IntegratorFactoryDetails.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o IntegratorFactoryDetails.o `test -f 'IntegratorFactoryDetails.cpp' || echo './'`IntegratorFactoryDetails.cpp --- Output.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Output.o `test -f 'Output.cpp' || echo './'`Output.cpp --- OutputCache.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputCache.o `test -f 'OutputCache.cpp' || echo './'`OutputCache.cpp --- OutputCollection.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputCollection.o `test -f 'OutputCollection.cpp' || echo './'`OutputCollection.cpp --- OutputDCDTrajectory.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputDCDTrajectory.o `test -f 'OutputDCDTrajectory.cpp' || echo './'`OutputDCDTrajectory.cpp --- OutputDiffusion.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputDiffusion.o `test -f 'OutputDiffusion.cpp' || echo './'`OutputDiffusion.cpp --- OutputDihedrals.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputDihedrals.o `test -f 'OutputDihedrals.cpp' || echo './'`OutputDihedrals.cpp --- OutputEnergies.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputEnergies.o `test -f 'OutputEnergies.cpp' || echo './'`OutputEnergies.cpp --- OutputFactoryDetails.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFactoryDetails.o `test -f 'OutputFactoryDetails.cpp' || echo './'`OutputFactoryDetails.cpp --- OutputFile.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFile.o `test -f 'OutputFile.cpp' || echo './'`OutputFile.cpp --- OutputFinalXYZBinPos.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalXYZBinPos.o `test -f 'OutputFinalXYZBinPos.cpp' || echo './'`OutputFinalXYZBinPos.cpp --- OutputFinalXYZBinVel.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalXYZBinVel.o `test -f 'OutputFinalXYZBinVel.cpp' || echo './'`OutputFinalXYZBinVel.cpp --- OutputFinalXYZPos.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalXYZPos.o `test -f 'OutputFinalXYZPos.cpp' || echo './'`OutputFinalXYZPos.cpp --- OutputFinalPDBPos.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalPDBPos.o `test -f 'OutputFinalPDBPos.cpp' || echo './'`OutputFinalPDBPos.cpp --- OutputFinalXYZVel.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalXYZVel.o `test -f 'OutputFinalXYZVel.cpp' || echo './'`OutputFinalXYZVel.cpp --- OutputMomentum.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputMomentum.o `test -f 'OutputMomentum.cpp' || echo './'`OutputMomentum.cpp --- OutputPaulTrap.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputPaulTrap.o `test -f 'OutputPaulTrap.cpp' || echo './'`OutputPaulTrap.cpp --- OutputPDBFramePos.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputPDBFramePos.o `test -f 'OutputPDBFramePos.cpp' || echo './'`OutputPDBFramePos.cpp --- OutputScreen.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputScreen.o `test -f 'OutputScreen.cpp' || echo './'`OutputScreen.cpp --- OutputTemperatures.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputTemperatures.o `test -f 'OutputTemperatures.cpp' || echo './'`OutputTemperatures.cpp --- OutputXYZTrajectoryForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputXYZTrajectoryForce.o `test -f 'OutputXYZTrajectoryForce.cpp' || echo './'`OutputXYZTrajectoryForce.cpp --- OutputXYZTrajectoryPos.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputXYZTrajectoryPos.o `test -f 'OutputXYZTrajectoryPos.cpp' || echo './'`OutputXYZTrajectoryPos.cpp --- TopologyFactoryDetails.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o TopologyFactoryDetails.o `test -f 'TopologyFactoryDetails.cpp' || echo './'`TopologyFactoryDetails.cpp --- OutputXYZTrajectoryVel.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputXYZTrajectoryVel.o `test -f 'OutputXYZTrajectoryVel.cpp' || echo './'`OutputXYZTrajectoryVel.cpp --- buildTopology.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o buildTopology.o `test -f 'buildTopology.cpp' || echo './'`buildTopology.cpp --- parseCommandLine.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o parseCommandLine.o `test -f 'parseCommandLine.cpp' || echo './'`parseCommandLine.cpp --- inputValueDefinitions.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o inputValueDefinitions.o `test -f 'inputValueDefinitions.cpp' || echo './'`inputValueDefinitions.cpp --- InputPosVelType.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputFile.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- HelpTextFactory.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- inputValueDefinitions.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- InputPosVel.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- TopologyFactoryDetails.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputFinalXYZBinVel.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputFinalXYZBinPos.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputCollection.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- Output.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputScreen.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputDCDTrajectory.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputEnergies.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- parseCommandLine.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- IntegratorFactoryDetails.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputFinalPDBPos.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputPDBFramePos.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputFactoryDetails.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputDiffusion.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputXYZTrajectoryVel.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputTemperatures.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputFinalXYZVel.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputCache.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputFinalXYZPos.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputXYZTrajectoryPos.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputXYZTrajectoryForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ForceFactoryDetails.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputMomentum.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputPaulTrap.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputDihedrals.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- buildTopology.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libfrontend.a --- rm -f libfrontend.a ar cru libfrontend.a HelpTextFactory.o ForceFactoryDetails.o InputPosVel.o InputPosVelType.o IntegratorFactoryDetails.o Output.o OutputCache.o OutputCollection.o OutputDCDTrajectory.o OutputDiffusion.o OutputDihedrals.o OutputEnergies.o OutputFactoryDetails.o OutputFile.o OutputFinalXYZBinPos.o OutputFinalXYZBinVel.o OutputFinalXYZPos.o OutputFinalPDBPos.o OutputFinalXYZVel.o OutputMomentum.o OutputPaulTrap.o OutputPDBFramePos.o OutputScreen.o OutputTemperatures.o OutputXYZTrajectoryForce.o OutputXYZTrajectoryPos.o OutputXYZTrajectoryVel.o TopologyFactoryDetails.o buildTopology.o inputValueDefinitions.o parseCommandLine.o ranlib libfrontend.a Making all in factories --- registerForceExemplars.o --- --- registerForceExemplarsBonded.o --- --- registerForceExemplarsCutoff.o --- --- registerForceExemplarsFastElectrostatic.o --- --- registerForceExemplarsFull.o --- --- registerForceExemplarsOther.o --- --- registerForceExemplarsSimpleFull.o --- --- registerIntegratorExemplars.o --- --- registerOutputExemplars.o --- --- registerTopologyExemplars.o --- --- registerForceExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplars.o `test -f 'registerForceExemplars.cpp' || echo './'`registerForceExemplars.cpp --- registerForceExemplarsBonded.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsBonded.o `test -f 'registerForceExemplarsBonded.cpp' || echo './'`registerForceExemplarsBonded.cpp --- registerForceExemplarsCutoff.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsCutoff.o `test -f 'registerForceExemplarsCutoff.cpp' || echo './'`registerForceExemplarsCutoff.cpp --- registerForceExemplarsFull.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsFull.o `test -f 'registerForceExemplarsFull.cpp' || echo './'`registerForceExemplarsFull.cpp --- registerForceExemplarsFastElectrostatic.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsFastElectrostatic.o `test -f 'registerForceExemplarsFastElectrostatic.cpp' || echo './'`registerForceExemplarsFastElectrostatic.cpp --- registerOutputExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerOutputExemplars.o `test -f 'registerOutputExemplars.cpp' || echo './'`registerOutputExemplars.cpp --- registerIntegratorExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerIntegratorExemplars.o `test -f 'registerIntegratorExemplars.cpp' || echo './'`registerIntegratorExemplars.cpp --- registerForceExemplarsOther.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsOther.o `test -f 'registerForceExemplarsOther.cpp' || echo './'`registerForceExemplarsOther.cpp --- registerForceExemplarsSimpleFull.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsSimpleFull.o `test -f 'registerForceExemplarsSimpleFull.cpp' || echo './'`registerForceExemplarsSimpleFull.cpp --- registerTopologyExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerTopologyExemplars.o `test -f 'registerTopologyExemplars.cpp' || echo './'`registerTopologyExemplars.cpp --- registerForceExemplars.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerOutputExemplars.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerIntegratorExemplars.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerForceExemplarsBonded.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerForceExemplarsFull.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerTopologyExemplars.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerForceExemplarsOther.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerForceExemplarsSimpleFull.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerForceExemplarsCutoff.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerForceExemplarsFastElectrostatic.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libfactories.a --- rm -f libfactories.a ar cru libfactories.a registerForceExemplars.o registerForceExemplarsBonded.o registerForceExemplarsCutoff.o registerForceExemplarsFastElectrostatic.o registerForceExemplarsFull.o registerForceExemplarsOther.o registerForceExemplarsSimpleFull.o registerIntegratorExemplars.o registerOutputExemplars.o registerTopologyExemplars.o ranlib libfactories.a Making all in applications --- all-recursive --- Making all in protomol-app --- protomol.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o protomol.o `test -f 'protomol.cpp' || echo './'`protomol.cpp c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] protomol.cpp:68:6: warning: illegal character encoding in string literal [-Winvalid-source-encoding] 68 | << PACKAGE_CITE <265, 2004." | ^~~~ 1 warning generated. --- protomol --- c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o protomol protomol.o -L../../framework/base -L../../framework/io -L../../framework/parallel -L../../framework/topology -L../../framework/forces -L../../framework/imd -L../../framework/integrators -L../../framework/frontend -L../../framework/factories -lfactories -lfrontend -lintegrators -limd -lforces -ltopology -lparallel -lio -lbase -lpng Making all in coulomb-app --- ./Makefile.in --- --- coulomb.o --- --- registerForceExemplars.o --- --- registerIntegratorExemplars.o --- --- registerOutputExemplars.o --- --- registerTopologyExemplars.o --- --- ./Makefile.in --- cd ../.. && /bin/sh /wrkdirs/usr/ports/biology/protomol/work/protomol/missing --run automake-1.6 --foreign applications/coulomb-app/Makefile --- registerForceExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplars.o `test -f 'registerForceExemplars.cpp' || echo './'`registerForceExemplars.cpp --- coulomb.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o coulomb.o `test -f 'coulomb.cpp' || echo './'`coulomb.cpp --- registerIntegratorExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerIntegratorExemplars.o `test -f 'registerIntegratorExemplars.cpp' || echo './'`registerIntegratorExemplars.cpp --- registerOutputExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerOutputExemplars.o `test -f 'registerOutputExemplars.cpp' || echo './'`registerOutputExemplars.cpp --- registerTopologyExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerTopologyExemplars.o `test -f 'registerTopologyExemplars.cpp' || echo './'`registerTopologyExemplars.cpp --- ./Makefile.in --- /wrkdirs/usr/ports/biology/protomol/work/protomol/missing: automake-1.6: not found WARNING: `automake-1.6' is missing on your system. You should only need it if you modified `Makefile.am', `acinclude.m4' or `configure.in'. You might want to install the `Automake' and `Perl' packages. Grab them from any GNU archive site. --- Makefile --- cd ../.. && /bin/sh ./config.status applications/coulomb-app/Makefile config.status: creating applications/coulomb-app/Makefile --- registerOutputExemplars.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerIntegratorExemplars.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerTopologyExemplars.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- registerForceExemplars.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- coulomb.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] coulomb.cpp:66:6: warning: illegal character encoding in string literal [-Winvalid-source-encoding] 66 | << PACKAGE_CITE <265, 2004." | ^~~~ 1 warning generated. --- coulomb --- c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o coulomb coulomb.o registerForceExemplars.o registerIntegratorExemplars.o registerOutputExemplars.o registerTopologyExemplars.o -L../../framework/base -L../../framework/io -L../../framework/parallel -L../../framework/topology -L../../framework/forces -L../../framework/integrators -L../../framework/frontend -lfrontend -lintegrators -lforces -ltopology -lparallel -lio -lbase Making all in dcd2dcd-app --- dcd2dcd.o --- --- Makefile --- --- dcd2dcd.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o dcd2dcd.o `test -f 'dcd2dcd.cpp' || echo './'`dcd2dcd.cpp --- Makefile --- cd ../.. && /bin/sh ./config.status applications/dcd2dcd-app/Makefile config.status: creating applications/dcd2dcd-app/Makefile --- dcd2dcd.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- dcd2dcd --- c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o dcd2dcd dcd2dcd.o -L../../framework/base -L../../framework/io -lio -lbase Making all in coords2coords-app --- coords2coords.o --- --- Makefile --- --- coords2coords.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o coords2coords.o `test -f 'coords2coords.cpp' || echo './'`coords2coords.cpp --- Makefile --- cd ../.. && /bin/sh ./config.status applications/coords2coords-app/Makefile config.status: creating applications/coords2coords-app/Makefile --- coords2coords.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- coords2coords --- c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o coords2coords coords2coords.o -L../../framework/base -L../../framework/io -lio -lbase Making all in xyzviz-app --- openglutilities.o --- --- xyzviz.o --- --- Makefile --- --- openglutilities.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -DHAVE_GLUT -I/usr/local/include -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o openglutilities.o `test -f 'openglutilities.cpp' || echo './'`openglutilities.cpp --- xyzviz.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -DHAVE_GLUT -I/usr/local/include -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o xyzviz.o `test -f 'xyzviz.cpp' || echo './'`xyzviz.cpp --- Makefile --- cd ../.. && /bin/sh ./config.status applications/xyzviz-app/Makefile config.status: creating applications/xyzviz-app/Makefile --- openglutilities.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- xyzviz.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- xyzviz --- c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o xyzviz openglutilities.o xyzviz.o -L../../framework/base -L../../framework/io -lz -L/usr/local/lib -lglut -lGLU -lGL -lXmu -lXt -lSM -lICE -lXext -lX11 -lXi -lXext -lX11 -lpthread -ldl -ljpeg -ltiff -lio -lbase Making all in iSGProtomol-app --- all-recursive --- Making all in base --- XSC.o --- --- TRANS.o --- --- Makefile --- --- XSC.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/topology -I../../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XSC.o `test -f 'XSC.cpp' || echo './'`XSC.cpp --- TRANS.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/topology -I../../../framework/base -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o TRANS.o `test -f 'TRANS.cpp' || echo './'`TRANS.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/base/Makefile config.status: creating applications/iSGProtomol-app/base/Makefile --- XSC.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- TRANS.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libISGbase.a --- rm -f libISGbase.a ar cru libISGbase.a XSC.o TRANS.o ranlib libISGbase.a Making all in io --- iSGPARReader.o --- --- TRANSReader.o --- --- XSCReader.o --- --- XSCWriter.o --- --- Makefile --- --- iSGPARReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGPARReader.o `test -f 'iSGPARReader.cpp' || echo './'`iSGPARReader.cpp --- TRANSReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o TRANSReader.o `test -f 'TRANSReader.cpp' || echo './'`TRANSReader.cpp --- XSCWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XSCWriter.o `test -f 'XSCWriter.cpp' || echo './'`XSCWriter.cpp --- XSCReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XSCReader.o `test -f 'XSCReader.cpp' || echo './'`XSCReader.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/io/Makefile config.status: creating applications/iSGProtomol-app/io/Makefile --- XSCWriter.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- XSCReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- TRANSReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGPARReader.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libISGio.a --- rm -f libISGio.a ar cru libISGio.a iSGPARReader.o TRANSReader.o XSCReader.o XSCWriter.o ranlib libISGio.a Making all in forces --- iSGAngleSystemForceBase.o --- --- iSGBondSystemForceBase.o --- --- iSGDihedralSystemForceBase.o --- --- iSGImproperSystemForceBase.o --- --- iSGLennardJonesForce.o --- --- iSGCoulombForce.o --- --- iSGNonbondedFullEwaldSystemForceBase.o --- --- iSGNonbondedPMEwaldSystemForceBase.o --- --- iSGIdealGasCoulombForce.o --- --- iSGIdealGasLennardJonesForce.o --- --- iSGLennardJonesTableForce.o --- --- iSGCoulombEwaldRealForce.o --- --- iSGCoulombEwaldRealTableForce.o --- --- Makefile --- --- iSGAngleSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGAngleSystemForceBase.o `test -f 'iSGAngleSystemForceBase.cpp' || echo './'`iSGAngleSystemForceBase.cpp --- iSGBondSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGBondSystemForceBase.o `test -f 'iSGBondSystemForceBase.cpp' || echo './'`iSGBondSystemForceBase.cpp --- iSGDihedralSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGDihedralSystemForceBase.o `test -f 'iSGDihedralSystemForceBase.cpp' || echo './'`iSGDihedralSystemForceBase.cpp --- iSGImproperSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGImproperSystemForceBase.o `test -f 'iSGImproperSystemForceBase.cpp' || echo './'`iSGImproperSystemForceBase.cpp --- iSGLennardJonesForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGLennardJonesForce.o `test -f 'iSGLennardJonesForce.cpp' || echo './'`iSGLennardJonesForce.cpp --- iSGCoulombForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGCoulombForce.o `test -f 'iSGCoulombForce.cpp' || echo './'`iSGCoulombForce.cpp --- iSGNonbondedFullEwaldSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGNonbondedFullEwaldSystemForceBase.o `test -f 'iSGNonbondedFullEwaldSystemForceBase.cpp' || echo './'`iSGNonbondedFullEwaldSystemForceBase.cpp --- iSGIdealGasLennardJonesForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGIdealGasLennardJonesForce.o `test -f 'iSGIdealGasLennardJonesForce.cpp' || echo './'`iSGIdealGasLennardJonesForce.cpp --- iSGLennardJonesTableForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGLennardJonesTableForce.o `test -f 'iSGLennardJonesTableForce.cpp' || echo './'`iSGLennardJonesTableForce.cpp --- iSGNonbondedPMEwaldSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGNonbondedPMEwaldSystemForceBase.o `test -f 'iSGNonbondedPMEwaldSystemForceBase.cpp' || echo './'`iSGNonbondedPMEwaldSystemForceBase.cpp --- iSGIdealGasCoulombForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGIdealGasCoulombForce.o `test -f 'iSGIdealGasCoulombForce.cpp' || echo './'`iSGIdealGasCoulombForce.cpp --- iSGCoulombEwaldRealTableForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGCoulombEwaldRealTableForce.o `test -f 'iSGCoulombEwaldRealTableForce.cpp' || echo './'`iSGCoulombEwaldRealTableForce.cpp --- iSGCoulombEwaldRealForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGCoulombEwaldRealForce.o `test -f 'iSGCoulombEwaldRealForce.cpp' || echo './'`iSGCoulombEwaldRealForce.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/forces/Makefile config.status: creating applications/iSGProtomol-app/forces/Makefile --- iSGNonbondedPMEwaldSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGNonbondedFullEwaldSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGAngleSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGImproperSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGBondSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGDihedralSystemForceBase.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGIdealGasCoulombForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGIdealGasLennardJonesForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGCoulombEwaldRealTableForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGLennardJonesTableForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGLennardJonesForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGCoulombForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGCoulombEwaldRealForce.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libISGforces.a --- rm -f libISGforces.a ar cru libISGforces.a iSGAngleSystemForceBase.o iSGBondSystemForceBase.o iSGDihedralSystemForceBase.o iSGImproperSystemForceBase.o iSGLennardJonesForce.o iSGCoulombForce.o iSGNonbondedFullEwaldSystemForceBase.o iSGNonbondedPMEwaldSystemForceBase.o iSGIdealGasCoulombForce.o iSGIdealGasLennardJonesForce.o iSGLennardJonesTableForce.o iSGCoulombEwaldRealForce.o iSGCoulombEwaldRealTableForce.o ranlib libISGforces.a Making all in frontend --- OutputFinalXSC.o --- --- OutputISGProperties.o --- --- OutputFinalPSF.o --- --- buildISGTopology.o --- --- Makefile --- --- OutputFinalXSC.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalXSC.o `test -f 'OutputFinalXSC.cpp' || echo './'`OutputFinalXSC.cpp --- OutputISGProperties.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputISGProperties.o `test -f 'OutputISGProperties.cpp' || echo './'`OutputISGProperties.cpp --- OutputFinalPSF.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalPSF.o `test -f 'OutputFinalPSF.cpp' || echo './'`OutputFinalPSF.cpp --- buildISGTopology.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o buildISGTopology.o `test -f 'buildISGTopology.cpp' || echo './'`buildISGTopology.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/frontend/Makefile config.status: creating applications/iSGProtomol-app/frontend/Makefile --- OutputFinalXSC.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputISGProperties.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- OutputFinalPSF.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- buildISGTopology.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libISGfrontend.a --- rm -f libISGfrontend.a ar cru libISGfrontend.a OutputFinalXSC.o OutputISGProperties.o OutputFinalPSF.o buildISGTopology.o ranlib libISGfrontend.a Making all in factories --- iSGregisterOutputExemplars.o --- --- iSGregisterIntegratorExemplars.o --- --- iSGregisterForceExemplars.o --- --- iSGregisterForceExemplarsBonded.o --- --- iSGregisterForceExemplarsCutoff.o --- --- iSGregisterForceExemplarsFull.o --- --- iSGregisterForceExemplarsSimpleFull.o --- --- iSGregisterForceExemplarsFastElectrostatic.o --- --- iSGregisterForceExemplarsIdealGas.o --- --- Makefile --- --- iSGregisterOutputExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterOutputExemplars.o `test -f 'iSGregisterOutputExemplars.cpp' || echo './'`iSGregisterOutputExemplars.cpp --- iSGregisterIntegratorExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterIntegratorExemplars.o `test -f 'iSGregisterIntegratorExemplars.cpp' || echo './'`iSGregisterIntegratorExemplars.cpp --- iSGregisterForceExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplars.o `test -f 'iSGregisterForceExemplars.cpp' || echo './'`iSGregisterForceExemplars.cpp --- iSGregisterForceExemplarsBonded.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsBonded.o `test -f 'iSGregisterForceExemplarsBonded.cpp' || echo './'`iSGregisterForceExemplarsBonded.cpp --- iSGregisterForceExemplarsCutoff.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsCutoff.o `test -f 'iSGregisterForceExemplarsCutoff.cpp' || echo './'`iSGregisterForceExemplarsCutoff.cpp --- iSGregisterForceExemplarsFull.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsFull.o `test -f 'iSGregisterForceExemplarsFull.cpp' || echo './'`iSGregisterForceExemplarsFull.cpp --- iSGregisterForceExemplarsFastElectrostatic.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsFastElectrostatic.o `test -f 'iSGregisterForceExemplarsFastElectrostatic.cpp' || echo './'`iSGregisterForceExemplarsFastElectrostatic.cpp --- iSGregisterForceExemplarsSimpleFull.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsSimpleFull.o `test -f 'iSGregisterForceExemplarsSimpleFull.cpp' || echo './'`iSGregisterForceExemplarsSimpleFull.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/factories/Makefile --- iSGregisterForceExemplarsIdealGas.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsIdealGas.o `test -f 'iSGregisterForceExemplarsIdealGas.cpp' || echo './'`iSGregisterForceExemplarsIdealGas.cpp --- Makefile --- config.status: creating applications/iSGProtomol-app/factories/Makefile --- iSGregisterForceExemplars.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGregisterOutputExemplars.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGregisterIntegratorExemplars.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGregisterForceExemplarsBonded.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGregisterForceExemplarsFull.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGregisterForceExemplarsIdealGas.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGregisterForceExemplarsSimpleFull.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGregisterForceExemplarsCutoff.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- iSGregisterForceExemplarsFastElectrostatic.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libISGfactories.a --- rm -f libISGfactories.a ar cru libISGfactories.a iSGregisterOutputExemplars.o iSGregisterIntegratorExemplars.o iSGregisterForceExemplars.o iSGregisterForceExemplarsBonded.o iSGregisterForceExemplarsCutoff.o iSGregisterForceExemplarsFull.o iSGregisterForceExemplarsSimpleFull.o iSGregisterForceExemplarsFastElectrostatic.o iSGregisterForceExemplarsIdealGas.o ranlib libISGfactories.a Making all in integrators --- iSGIntegrator.o --- --- ModifierISG.o --- --- Makefile --- --- iSGIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../framework/base -I../../../framework/frontend -I../../../applications/iSGProtomol-app/base -I../../../framework/topology -I../../../framework/frontend -I../../../framework/integrators -I../../../framework/forces -I../../../framework/parallel -I../../../applications/iSGProtomol-app/io -I../../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGIntegrator.o `test -f 'iSGIntegrator.cpp' || echo './'`iSGIntegrator.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/integrators/Makefile --- ModifierISG.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../framework/base -I../../../framework/frontend -I../../../applications/iSGProtomol-app/base -I../../../framework/topology -I../../../framework/frontend -I../../../framework/integrators -I../../../framework/forces -I../../../framework/parallel -I../../../applications/iSGProtomol-app/io -I../../../framework/io -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierISG.o `test -f 'ModifierISG.cpp' || echo './'`ModifierISG.cpp --- Makefile --- config.status: creating applications/iSGProtomol-app/integrators/Makefile --- iSGIntegrator.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- ModifierISG.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] --- libISGintegrators.a --- rm -f libISGintegrators.a ar cru libISGintegrators.a iSGIntegrator.o ModifierISG.o ranlib libISGintegrators.a --- iSGProtomol.o --- --- Makefile --- --- iSGProtomol.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I../../applications/iSGProtomol-app/base -I../../applications/iSGProtomol-app/io -I../../applications/iSGProtomol-app/forces -I../../applications/iSGProtomol-app/frontend -I../../applications/iSGProtomol-app/factories -I../../applications/iSGProtomol-app/integrators -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGProtomol.o `test -f 'iSGProtomol.cpp' || echo './'`iSGProtomol.cpp --- Makefile --- cd ../.. && /bin/sh ./config.status applications/iSGProtomol-app/Makefile config.status: creating applications/iSGProtomol-app/Makefile --- iSGProtomol.o --- c++: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] iSGProtomol.cpp:90:6: warning: illegal character encoding in string literal [-Winvalid-source-encoding] 90 | << PACKAGE_CITE <265, 2004." | ^~~~ 1 warning generated. --- iSGProtomol --- c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o iSGProtomol iSGProtomol.o -L../../framework/base -L../../framework/io -L../../framework/parallel -L../../framework/topology -L../../framework/forces -L../../framework/imd -L../../framework/integrators -L../../framework/frontend -L../../applications/iSGProtomol-app/base -L../../applications/iSGProtomol-app/io -L../../applications/iSGProtomol-app/forces -L../../applications/iSGProtomol-app/frontend -L../../applications/iSGProtomol-app/factories -L../../applications/iSGProtomol-app/integrators -lISGintegrators -lISGfactories -lISGfrontend -lISGforces -lISGio -lISGbase ../../framework/factories/registerTopologyExemplars.o -lfrontend -lintegrators -limd -lforces -ltopology -lparallel -lio -lbase -lpng --- Makefile --- cd .. && /bin/sh ./config.status applications/Makefile config.status: creating applications/Makefile --- Makefile --- cd . && /bin/sh ./config.status Makefile config.status: creating Makefile =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> protomol-2.0.3_16 depends on file: /usr/local/libdata/pkgconfig/xi.pc - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for protomol-2.0.3_16 ===> Generating temporary packing list Making install in framework Making install in base cd ../.. && /bin/sh ./config.status framework/base/Makefile config.status: creating framework/base/Makefile Making install in io cd ../.. && /bin/sh ./config.status framework/io/Makefile config.status: creating framework/io/Makefile Making install in parallel cd ../.. && /bin/sh ./config.status framework/parallel/Makefile config.status: creating framework/parallel/Makefile Making install in topology cd ../.. && /bin/sh ./config.status framework/topology/Makefile config.status: creating framework/topology/Makefile Making install in forces cd ../.. && /bin/sh ./config.status framework/forces/Makefile config.status: creating framework/forces/Makefile Making install in imd cd ../.. && /bin/sh ./config.status framework/imd/Makefile config.status: creating framework/imd/Makefile Making install in integrators cd ../.. && /bin/sh ./config.status framework/integrators/Makefile config.status: creating framework/integrators/Makefile Making install in frontend cd ../.. && /bin/sh ./config.status framework/frontend/Makefile config.status: creating framework/frontend/Makefile Making install in factories cd ../.. && /bin/sh ./config.status framework/factories/Makefile config.status: creating framework/factories/Makefile cd .. && /bin/sh ./config.status framework/Makefile config.status: creating framework/Makefile Making install in applications Making install in protomol-app cd ../.. && /bin/sh ./config.status applications/protomol-app/Makefile config.status: creating applications/protomol-app/Makefile /bin/sh ../../mkinstalldirs /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin install -s -m 555 protomol /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin/protomol Making install in coulomb-app /bin/sh ../../mkinstalldirs /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin install -s -m 555 coulomb /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin/coulomb Making install in dcd2dcd-app /bin/sh ../../mkinstalldirs /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin install -s -m 555 dcd2dcd /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin/dcd2dcd Making install in coords2coords-app /bin/sh ../../mkinstalldirs /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin install -s -m 555 coords2coords /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin/coords2coords Making install in xyzviz-app /bin/sh ../../mkinstalldirs /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin install -s -m 555 xyzviz /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin/xyzviz Making install in iSGProtomol-app Making install in base Making install in io Making install in forces Making install in frontend Making install in factories Making install in integrators /bin/sh ../../mkinstalldirs /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin install -s -m 555 iSGProtomol /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/bin/iSGProtomol cd /wrkdirs/usr/ports/biology/protomol/work/protomol/examples ; /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/protomol/work/stage/usr/local/share/examples/protomol "! -name .cvsignore" ====> 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=2025-11-12T14:25:17+0000' 'PKG_NOTE_ports_top_git_hash=ec159283c191' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=98bf25875a99' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for protomol-2.0.3_16 ===> Building protomol-2.0.3_16 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for protomol-2.0.3_16 build of biology/protomol | protomol-2.0.3_16 ended at Wed Nov 12 09:30:02 EST 2025 build time: 00:04:47