=>> Building biology/garlic build started at Wed Apr 3 12:55:19 BST 2024 port directory: /usr/ports/biology/garlic package name: garlic-1.6_1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1594 Mar 8 2023 /usr/ports/biology/garlic/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 18 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/18/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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 garlic-1.6_1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples OPTIMIZED_CFLAGS=off: Use extra compiler optimizations ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/garlic/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/garlic/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/garlic/work/.cache HOME=/wrkdirs/usr/ports/biology/garlic/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/garlic/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/garlic/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/garlic/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/garlic/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/garlic/work/.cache HOME=/wrkdirs/usr/ports/biology/garlic/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/garlic/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/garlic/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="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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-- PORTDOCS="" PORTEXAMPLES="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/garlic" EXAMPLESDIR="share/examples/garlic" DATADIR="share/garlic" WWWDIR="www/garlic" ETCDIR="etc/garlic" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/garlic DOCSDIR=/usr/local/share/doc/garlic EXAMPLESDIR=/usr/local/share/examples/garlic WWWDIR=/usr/local/www/garlic ETCDIR=/usr/local/etc/garlic --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The garlic 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 ===> garlic-1.6_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> garlic-1.6_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of garlic-1.6_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The garlic 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 garlic-1.6_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The garlic 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 garlic-1.6_1 for building => SHA256 Checksum OK for garlic-1.6.tar.gz. => SHA256 Checksum OK for garlic-1.6-doc.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 garlic 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 garlic-1.6_1 for building ===> Extracting for garlic-1.6_1 => SHA256 Checksum OK for garlic-1.6.tar.gz. => SHA256 Checksum OK for garlic-1.6-doc.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 garlic-1.6_1 ===> Applying FreeBSD patches for garlic-1.6_1 from /usr/ports/biology/garlic/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> garlic-1.6_1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> garlic-1.6_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of garlic-1.6_1 ===> garlic-1.6_1 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found ===> Installing existing package /packages/All/libX11-1.8.7_1,1.pkg [pkg-builder.dan.net.uk] Installing libX11-1.8.7_1,1... [pkg-builder.dan.net.uk] `-- Installing libxcb-1.16.1... [pkg-builder.dan.net.uk] | `-- Installing libXau-1.0.9_1... [pkg-builder.dan.net.uk] | `-- Extracting libXau-1.0.9_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXdmcp-1.1.5... [pkg-builder.dan.net.uk] | | `-- Installing xorgproto-2023.2... [pkg-builder.dan.net.uk] | | `-- Extracting xorgproto-2023.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libXdmcp-1.1.5: ...... done [pkg-builder.dan.net.uk] `-- Extracting libxcb-1.16.1: .......... done [pkg-builder.dan.net.uk] Extracting libX11-1.8.7_1,1: .......... done ===> garlic-1.6_1 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> Returning to build of garlic-1.6_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for garlic-1.6_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for garlic-1.6_1 cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include garlic.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include print_usage.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include print_help.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include print_version.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include register.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include alloc_gui.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include alloc_config.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include alloc_mol_complex.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include free_memory.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include display_init.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include disp_color_cap.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include color_shifts.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include calc_params.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include errmsg.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include warnmsg.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include openfile_r.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include read_config.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include open_config_file.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_int.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include ex2ints.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_double.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include ex2doubles.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_phrase.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_index.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include ex_rot_steps.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include ex_trans_steps.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include ex_slab_steps.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include ex_fading_steps.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_args.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include parse_options.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include parse_color.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include load_font.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include prepare_cursor.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include print_config.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include create_windows.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include make_pixmap.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include make_pixmap2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include rgbs_from_xcolor.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include pixel_from_rgbs.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include size_hints.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include wmhints.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_events.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hide_control.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include load_complex.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include read_file.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include fileformat.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include is_pdb.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include read_pdb.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include init_header.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include pdb_atom.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_field.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include copypur.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include realloc_pdb.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include headerline.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include geomcenter.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include init_slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include init_fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include flip_vector.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include translate_complex.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extent.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include stereo_data.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include strong_bonds.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include pseudo_bonds.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include check_dist.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include add_bond.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include event_loop.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include alloc_nearest.c alloc_nearest.c:70:54: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] fprintf (stderr, "A total of %d bytes required.\n", mem_size); ~~ ^~~~~~~~ %zu 1 warning generated. cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include init_nearest.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include main_refresh.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include key_press.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include rotation_angle.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include rotate.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include translation_shift.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include translate.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include slab_shift.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include move_back_slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include move_front_slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include fading_shift.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include move_back_fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include move_front_fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include key_release.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include refresh_pixmap.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include no_slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include planar_slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include sphere_slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include half_sphere_slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include cylin_slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include half_cylin_slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include project_atoms.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include prepare_color.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include no_fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include planar_fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include sphere_fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include half_sphere_fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include cylin_fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include half_cylin_fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include reset_pos_flag.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include atoms_style1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include atoms_style2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include atoms_style3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include atoms_style4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include atoms_style5.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include atoms_style6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include atoms_style7.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bonds_style1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style1_quad1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style1_quad2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style1_quad3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style1_quad4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bonds_style2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style2_quad1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style2_quad2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style2_quad3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style2_quad4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bonds_style3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include interpolate_color.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style3_quad1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style3_quad2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style3_quad3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style3_quad4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bonds_style4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include add_two_colors.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style4_quad1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style4_quad2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style4_quad3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style4_quad4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bonds_style5.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include add_three_colors.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style5_quad1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style5_quad2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style5_quad3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_style5_quad4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_system.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include motion_notify.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include assign_hyphob.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include control_refresh.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include print_cursor_names.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include main_resize.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include init_runtime.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include add_char.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include input_refresh.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include eat_left_char.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include eat_right_char.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include execute_command1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include execute_command2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include truncate_comm.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include create_log_file.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include load.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include catch.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include discard.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include full_select.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include include.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chains.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include residue_ranges.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_token.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_serials.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include residue_names.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include atom_names.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include exclude.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include skip_keyword.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include apply_selection.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include show.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hide.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include color_schemes.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include init_colors.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include color.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include special_select.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_hetero.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_element.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_atoms.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include quick_select.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include replace_command.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include atoms.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bonds.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include execute_script.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include comm_rotate.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include comm_translate.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include comm_slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include comm_fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include log.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include prepare_backbone.c prepare_backbone.c:103:54: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] fprintf (stderr, "A total of %d bytes required.\n", mem_size); ~~ ^~~~~~~~ %zu 1 warning generated. cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include background.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include text_background.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include text_foreground.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include change_slab.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include change_fading.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include full_colors.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include is_old.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include font.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include cpk.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include zebra.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chain.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include color_hyphob.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include mix_colors.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include comm_backbone.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hide_no_refresh.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include show_no_refresh.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include backbone.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hybonds.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include generate_hybonds.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hybond_style.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include show_backbone.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hide_backbone.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include pdb_id.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include generate_plane.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include stereo.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include mono.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include position.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include copy_doubles.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include title.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include free_runtime.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_titles.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include foreground.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include prepare_oc.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_complement.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include labels.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_labels.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include assign_radii.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include spacefill.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include spacefill_color.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_balls.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include center.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include save.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include write_line.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include big_spheres.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include tag.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_tags.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include tag_position.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include button_press.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include control_click.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include identify_button.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include init_buttons.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include write_hints.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_sequence.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include count_residues.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include sequence.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include parse_sequence.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include sequence_from.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include load_sequence.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_sequence.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include compare_sequences.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include dihedral_angles.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_ncaco.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include phi_from_cncac.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include psi_from_ncaco.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include vector_product.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include absolute_value.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include scalar_product.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include omega_from_cacnca.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_cis_trans.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include ramachandran.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_ramachandran.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include rama_frame.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include rama_mouse.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include read_fasta.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include save_sequence.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include wheel.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include wheel_top_view.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include wheel_bottom_view.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hydrophobicity.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include weight_colors.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include angle.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include radius.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_sphere.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include disulfide_bonds.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include venn.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_venn.c draw_venn.c:481:32: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] sprintf (stringA, "TOTAL: %d", residuesN); ~~ ^~~~~~~~~ %zu 1 warning generated. cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include spacefill2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include sp2_color.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include save_seq_w_numbers.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include ssb.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_alternate.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_model.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include color_model.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include window.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include plot.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_plots.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include weighted_hydrophobicity.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include average_hydrophobicity.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include init_hyphob.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include plot_mouse.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include project_planes.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_planes.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include plane_extent.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include rotate_plane.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include translate_plane.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include comm_move.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include plane.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_above.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_below.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include big2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include scale.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include pattern.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include dock.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include align_normal.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include align_complexes.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include docking_window.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include docking_resize.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include docking_refresh.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include docking_project.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include list_exposed_polar.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include is_polar.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include representative_atoms.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include exclude_distant.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_bottom.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_top.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include copy_sequence.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include compare.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_comparison.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include neighborhood.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_balls2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include comparison_mouse.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include structure.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include parse_sec_structure.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include copy_sec_structure.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include load_sec_structure.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include save_sec_structure.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include alloc_sec_structure.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include sec_structure_from.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include create.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include open_template_file.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include read_template_file.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include ex_template_residues.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include count_template_res.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include create_structure.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include required_atoms.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include copy_template_atoms.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include fix_chain.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include reset_phi.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_hncac.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include phi_from_hncac.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include rotate_atom.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include parallel_part.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include reset_psi.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include build_chain.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_ncac.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include translate_range.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include rotate_range.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include apply_structure.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include generate_phi_psi.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_nca.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_c.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include replace.c replace.c:205:23: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] selected_residuesN, runtimeSP->residuesN); ^~~~~~~~~~~~~~~~~~~~ 1 warning generated. cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_n.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include refresh_backbone.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include edit.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_edit_symbol.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_squid.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_seahorse.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include are_atoms_bound.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include bond_partners.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include edit_phi.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include edit_psi.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_cac.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include small_ramachandran.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include edit_omega.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include small_omega.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_h.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_o.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include psi_from_ncacn.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include is_standard.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_four_atoms.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi1_from_ncacbcg.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi1_from_ncacbsg.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi1_from_ncacbcg1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi1_from_ncacbog.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi1_from_ncacbog1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcgcd.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcgod1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcgnd1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcg1cd.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcgcd1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi2_from_cacbcgsd.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi3_from_cbcgcdne.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi3_from_cbcgcdoe1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi3_from_cbcgcdce.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi3_from_cbcgsdce.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi4_from_cgcdnecz.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi4_from_cgcdcenz.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include chi5_from_cdnecznh1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include is_part_of_ring.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include edit_bond.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include edit_chi2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_cacb.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include edit_chi1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_cbxg.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include resize_complex.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include membrane.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include inform_user.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include alpha_membrane.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_ca.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_vector.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include alpha_membrane_center.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include init_membrane.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include alpha_normal.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include project_membranes.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_membranes.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include rotate_membrane.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include translate_membrane.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_triplet.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include set.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include set_phi.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include set_psi.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include set_omega.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include set_chi1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include set_chi2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include set_chi3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_cgxd.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include set_chi4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_cdxe.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include set_chi5.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_necz.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include pick_bond.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include nice_bonds.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include covalent.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include covalent2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include half_nice_bond.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include probe.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include small_atoms.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include small_atoms2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include draw_sticks.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include half_stick.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include command_refresh.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include acceptor_dipole.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include donor_dipole.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include sticks.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include balls.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include blur.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include blur_main_window.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include group.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include beta_membrane.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include extract_cg.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_tm.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include parse_pattern.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_pattern.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hyphob_function1.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hyphob_function2.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hyphob_function3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hyphob_function4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hyphob_function5.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hyphob_function6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include hyphob_function7.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include color_size.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include command_dump.c command_dump.c:195:47: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] if (output_fileF) fprintf (outfileP, "%8d", residueI); ~~~ ^~~~~~~~ %8zu command_dump.c:196:32: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] else fprintf (stdout, "%8d", residueI); ~~~ ^~~~~~~~ %8zu 2 warnings generated. cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include is_aromatic.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_2c3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_2cz3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_2nz3.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_3c4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_3cz4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_3nz4.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_3c5.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_3cz5.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_3nz5.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_3p5.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4c5.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4cz5.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4nz5.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_3c6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_3cz6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_3nz6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4c6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4cz6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4nz6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4p6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_5c6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_5cz6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_5nz6.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4c7.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4cz7.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4nz7.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_5c7.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_5cz7.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_5nz7.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_5p7.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_6p7.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4c9.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4cz9.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_4nz9.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_5c9.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_5cz9.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include select_5nz9.c cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include color_weighted.c cc -o garlic -L/usr/local/lib garlic.o print_usage.o print_help.o print_version.o register.o alloc_gui.o alloc_config.o alloc_mol_complex.o free_memory.o display_init.o disp_color_cap.o color_shifts.o calc_params.o errmsg.o warnmsg.o openfile_r.o read_config.o open_config_file.o extract_int.o ex2ints.o extract_double.o ex2doubles.o extract_phrase.o extract_index.o ex_rot_steps.o ex_trans_steps.o ex_slab_steps.o ex_fading_steps.o extract_args.o parse_options.o parse_color.o load_font.o prepare_cursor.o print_config.o create_windows.o make_pixmap.o make_pixmap2.o rgbs_from_xcolor.o pixel_from_rgbs.o size_hints.o wmhints.o select_events.o hide_control.o load_complex.o read_file.o fileformat.o is_pdb.o read_pdb.o init_header.o pdb_atom.o extract_field.o copypur.o realloc_pdb.o headerline.o geomcenter.o init_slab.o init_fading.o flip_vector.o translate_complex.o extent.o stereo_data.o strong_bonds.o pseudo_bonds.o check_dist.o add_bond.o event_loop.o alloc_nearest.o init_nearest.o main_refresh.o key_press.o rotation_angle.o rotate.o translation_shift.o translate.o slab_shift.o move_back_slab.o move_front_slab.o fading_shift.o move_back_fading.o move_front_fading.o key_release.o refresh_pixmap.o slab.o no_slab.o planar_slab.o sphere_slab.o half_sphere_slab.o cylin_slab.o half_cylin_slab.o project_atoms.o fading.o prepare_color.o no_fading.o planar_fading.o sphere_fading.o half_sphere_fading.o cylin_fading.o half_cylin_fading.o reset_pos_flag.o atoms_style1.o atoms_style2.o atoms_style3.o atoms_style4.o atoms_style5.o atoms_style6.o atoms_style7.o bonds_style1.o bond_style1_quad1.o bond_style1_quad2.o bond_style1_quad3.o bond_style1_quad4.o bonds_style2.o bond_style2_quad1.o bond_style2_quad2.o bond_style2_quad3.o bond_style2_quad4.o bonds_style3.o interpolate_color.o bond_style3_quad1.o bond_style3_quad2.o bond_style3_quad3.o bond_style3_quad4.o bonds_style4.o add_two_colors.o bond_style4_quad1.o bond_style4_quad2.o bond_style4_quad3.o bond_style4_quad4.o bonds_style5.o add_three_colors.o bond_style5_quad1.o bond_style5_quad2.o bond_style5_quad3.o bond_style5_quad4.o draw_system.o motion_notify.o assign_hyphob.o control_refresh.o print_cursor_names.o main_resize.o init_runtime.o add_char.o input_refresh.o eat_left_char.o eat_right_char.o execute_command1.o execute_command2.o truncate_comm.o create_log_file.o load.o catch.o discard.o select.o full_select.o include.o chains.o residue_ranges.o extract_token.o extract_serials.o residue_names.o atom_names.o exclude.o skip_keyword.o apply_selection.o show.o hide.o color_schemes.o init_colors.o color.o special_select.o select_hetero.o select_element.o select_atoms.o quick_select.o replace_command.o atoms.o bonds.o execute_script.o comm_rotate.o comm_translate.o comm_slab.o comm_fading.o log.o prepare_backbone.o background.o text_background.o text_foreground.o change_slab.o change_fading.o full_colors.o is_old.o font.o cpk.o zebra.o chain.o color_hyphob.o mix_colors.o comm_backbone.o hide_no_refresh.o show_no_refresh.o backbone.o hybonds.o generate_hybonds.o hybond_style.o show_backbone.o hide_backbone.o pdb_id.o generate_plane.o stereo.o mono.o position.o copy_doubles.o title.o free_runtime.o draw_titles.o foreground.o prepare_oc.o select_complement.o labels.o draw_labels.o assign_radii.o spacefill.o spacefill_color.o draw_balls.o center.o save.o write_line.o big_spheres.o tag.o draw_tags.o tag_position.o button_press.o control_click.o identify_button.o init_buttons.o write_hints.o extract_sequence.o count_residues.o sequence.o parse_sequence.o sequence_from.o load_sequence.o select_sequence.o compare_sequences.o dihedral_angles.o extract_ncaco.o phi_from_cncac.o psi_from_ncaco.o vector_product.o absolute_value.o scalar_product.o omega_from_cacnca.o select_cis_trans.o ramachandran.o draw_ramachandran.o rama_frame.o rama_mouse.o read_fasta.o save_sequence.o wheel.o wheel_top_view.o wheel_bottom_view.o hydrophobicity.o weight_colors.o angle.o radius.o select_sphere.o disulfide_bonds.o venn.o draw_venn.o spacefill2.o sp2_color.o save_seq_w_numbers.o ssb.o select_alternate.o select_model.o color_model.o window.o plot.o draw_plots.o weighted_hydrophobicity.o average_hydrophobicity.o init_hyphob.o plot_mouse.o project_planes.o draw_planes.o plane_extent.o rotate_plane.o translate_plane.o comm_move.o plane.o select_above.o select_below.o big2.o scale.o pattern.o dock.o align_normal.o align_complexes.o docking_window.o docking_resize.o docking_refresh.o docking_project.o list_exposed_polar.o is_polar.o representative_atoms.o exclude_distant.o draw_bottom.o draw_top.o copy_sequence.o compare.o draw_comparison.o neighborhood.o draw_balls2.o comparison_mouse.o structure.o parse_sec_structure.o copy_sec_structure.o load_sec_structure.o save_sec_structure.o alloc_sec_structure.o sec_structure_from.o create.o open_template_file.o read_template_file.o ex_template_residues.o count_template_res.o create_structure.o required_atoms.o copy_template_atoms.o fix_chain.o reset_phi.o extract_hncac.o phi_from_hncac.o rotate_atom.o parallel_part.o reset_psi.o build_chain.o extract_ncac.o translate_range.o rotate_range.o apply_structure.o generate_phi_psi.o extract_nca.o extract_c.o replace.o extract_n.o refresh_backbone.o edit.o draw_edit_symbol.o draw_squid.o draw_seahorse.o are_atoms_bound.o bond_partners.o edit_phi.o edit_psi.o extract_cac.o small_ramachandran.o edit_omega.o small_omega.o extract_h.o extract_o.o psi_from_ncacn.o is_standard.o extract_four_atoms.o chi1_from_ncacbcg.o chi1_from_ncacbsg.o chi1_from_ncacbcg1.o chi1_from_ncacbog.o chi1_from_ncacbog1.o chi2_from_cacbcgcd.o chi2_from_cacbcgod1.o chi2_from_cacbcgnd1.o chi2_from_cacbcg1cd.o chi2_from_cacbcgcd1.o chi2_from_cacbcgsd.o chi3_from_cbcgcdne.o chi3_from_cbcgcdoe1.o chi3_from_cbcgcdce.o chi3_from_cbcgsdce.o chi4_from_cgcdnecz.o chi4_from_cgcdcenz.o chi5_from_cdnecznh1.o is_part_of_ring.o edit_bond.o edit_chi2.o extract_cacb.o edit_chi1.o extract_cbxg.o resize_complex.o membrane.o inform_user.o alpha_membrane.o extract_ca.o extract_vector.o alpha_membrane_center.o init_membrane.o alpha_normal.o project_membranes.o draw_membranes.o rotate_membrane.o translate_membrane.o select_triplet.o set.o set_phi.o set_psi.o set_omega.o set_chi1.o set_chi2.o set_chi3.o extract_cgxd.o set_chi4.o extract_cdxe.o set_chi5.o extract_necz.o pick_bond.o nice_bonds.o covalent.o covalent2.o half_nice_bond.o probe.o small_atoms.o small_atoms2.o draw_sticks.o half_stick.o command_refresh.o acceptor_dipole.o donor_dipole.o sticks.o balls.o blur.o blur_main_window.o group.o beta_membrane.o extract_cg.o select_tm.o parse_pattern.o select_pattern.o hyphob_function1.o hyphob_function2.o hyphob_function3.o hyphob_function4.o hyphob_function5.o hyphob_function6.o hyphob_function7.o color_size.o command_dump.o is_aromatic.o select_2c3.o select_2cz3.o select_2nz3.o select_3c4.o select_3cz4.o select_3nz4.o select_3c5.o select_3cz5.o select_3nz5.o select_3p5.o select_4c5.o select_4cz5.o select_4nz5.o select_3c6.o select_3cz6.o select_3nz6.o select_4c6.o select_4cz6.o select_4nz6.o select_4p6.o select_5c6.o select_5cz6.o select_5nz6.o select_4c7.o select_4cz7.o select_4nz7.o select_5c7.o select_5cz7.o select_5nz7.o select_5p7.o select_6p7.o select_4c9.o select_4cz9.o select_4nz9.o select_5c9.o select_5cz9.o select_5nz9.o color_weighted.o -lX11 -lm =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> garlic-1.6_1 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for garlic-1.6_1 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/garlic/work/garlic-1.6/garlic /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/bin install -m 0644 /wrkdirs/usr/ports/biology/garlic/work/garlic-1.6/.garlicrc /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/share/garlic install -m 0644 /wrkdirs/usr/ports/biology/garlic/work/garlic-1.6/residues.pdb /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/share/garlic install -m 0644 /wrkdirs/usr/ports/biology/garlic/work/garlic-1.6/*.pdb /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/share/examples/garlic install -m 0644 /wrkdirs/usr/ports/biology/garlic/work/garlic-1.6/*.script /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/share/examples/garlic (cd /wrkdirs/usr/ports/biology/garlic/work/doc ; /usr/bin/tar -xzf /portdistfiles/garlic-1.6-doc.tar.gz ) /usr/bin/tar -C /wrkdirs/usr/ports/biology/garlic/work/doc/garlic-1.6 -cf - . | /usr/bin/tar -C /wrkdirs/usr/ports/biology/garlic/work/stage/usr/local/share/doc/garlic -xf - ====> 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=2024-04-03T11:55:19+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for garlic-1.6_1 ===> Building garlic-1.6_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for garlic-1.6_1 build of biology/garlic | garlic-1.6_1 ended at Wed Apr 3 13:00:52 BST 2024 build time: 00:05:39