=>> Building biology/biococoa build started at Tue Jan 20 10:40:22 EST 2026 port directory: /usr/ports/biology/biococoa package name: biococoa-2.2.2_9 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p7 FreeBSD 14.3-RELEASE-p7 1403000 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 420 Aug 17 06:16 /usr/ports/biology/biococoa/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: 7ea9703cc4be Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 13 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p7 1403000 UNAME_r=14.3-RELEASE-p7 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_14_3_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_14_3_x64-HEAD-ALL/13/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_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--- ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake PATH="/wrkdirs/usr/ports/biology/biococoa/work/.bin:/usr/local/GNUstep/System/Tools:/usr/local/GNUstep/Local/Tools:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin" GNUSTEP_MAKEFILES="/usr/local/GNUstep/System/Library/Makefiles" OBJC="cc" OBJCFLAGS=" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/biococoa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biococoa/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/biococoa/work/.cache HOME=/wrkdirs/usr/ports/biology/biococoa/work TMPDIR="/tmp" PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/biococoa/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- ADDITIONAL_CFLAGS=" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing " ADDITIONAL_CPPFLAGS=" " ADDITIONAL_CXXFLAGS=" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing " ADDITIONAL_OBJCCFLAGS=" " ADDITIONAL_OBJCFLAGS=" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include" ADDITIONAL_LDFLAGS=" -L/usr/local/lib " ADDITIONAL_FLAGS="" ADDITIONAL_INCLUDE_DIRS="" ADDITIONAL_LIB_DIRS="" PATH="/wrkdirs/usr/ports/biology/biococoa/work/.bin:/usr/local/GNUstep/System/Tools:/usr/local/GNUstep/Local/Tools:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin" GNUSTEP_MAKEFILES="/usr/local/GNUstep/System/Library/Makefiles" GNUSTEP_INSTALLATION_DOMAIN=SYSTEM OBJC="cc" OBJCFLAGS=" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/biococoa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biococoa/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/biococoa/work/.cache HOME=/wrkdirs/usr/ports/biology/biococoa/work TMPDIR="/tmp" PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/biococoa/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=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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-- GNU_ARCH=amd64 VERSION=2.2.2 MAJORVERSION=2 LIBVERSION=0.0.1 MAJORLIBVERSION=0 OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/biococoa" EXAMPLESDIR="share/examples/biococoa" DATADIR="share/biococoa" WWWDIR="www/biococoa" ETCDIR="etc/biococoa" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/biococoa DOCSDIR=/usr/local/share/doc/biococoa EXAMPLESDIR=/usr/local/share/examples/biococoa WWWDIR=/usr/local/www/biococoa ETCDIR=/usr/local/etc/biococoa --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 biococoa 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 ===> biococoa-2.2.2_9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> biococoa-2.2.2_9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of biococoa-2.2.2_9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The biococoa 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 biococoa-2.2.2_9 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The biococoa 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 biococoa-2.2.2_9 for building => SHA256 Checksum OK for biococoa-2.2.2-src.tgz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The biococoa 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 biococoa-2.2.2_9 for building ===> Extracting for biococoa-2.2.2_9 => SHA256 Checksum OK for biococoa-2.2.2-src.tgz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for biococoa-2.2.2_9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> biococoa-2.2.2_9 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> biococoa-2.2.2_9 depends on package: gmake>=4.4.1 - found ===> Returning to build of biococoa-2.2.2_9 ===> biococoa-2.2.2_9 depends on package: gnustep-make>0 - not found ===> Installing existing package /packages/All/gnustep-make-2.9.3.pkg [pkg.DaveG.ca] Installing gnustep-make-2.9.3... [pkg.DaveG.ca] `-- Installing libobjc2-2.2.1... [pkg.DaveG.ca] `-- Extracting libobjc2-2.2.1: .......... done [pkg.DaveG.ca] Extracting gnustep-make-2.9.3: ......... done ===== Message from libobjc2-2.2.1: -- ===> NOTICE: The libobjc2 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 ===> biococoa-2.2.2_9 depends on package: gnustep-make>0 - found ===> Returning to build of biococoa-2.2.2_9 ===> biococoa-2.2.2_9 depends on package: gnustep-back>0 - not found ===> Installing existing package /packages/All/gnustep-back-0.32.0.pkg [pkg.DaveG.ca] Installing gnustep-back-0.32.0... [pkg.DaveG.ca] `-- Installing cairo-1.18.2,3... [pkg.DaveG.ca] | `-- Installing fontconfig-2.17.1,1... [pkg.DaveG.ca] | | `-- Installing expat-2.7.3... [pkg.DaveG.ca] | | `-- Extracting expat-2.7.3: .......... done [pkg.DaveG.ca] | | `-- Installing freetype2-2.14.1... [pkg.DaveG.ca] | | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | | `-- Installing png-1.6.53... 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[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 libXrender-0.9.12... [pkg.DaveG.ca] | `-- Extracting libXrender-0.9.12: ....... done [pkg.DaveG.ca] | `-- Installing lzo2-2.10_1... [pkg.DaveG.ca] | `-- Extracting lzo2-2.10_1: .......... done [pkg.DaveG.ca] | `-- Installing pixman-0.46.2... [pkg.DaveG.ca] | `-- Extracting pixman-0.46.2: ...... done [pkg.DaveG.ca] `-- Extracting cairo-1.18.2,3: .......... done [pkg.DaveG.ca] `-- Installing giflib-5.2.2... [pkg.DaveG.ca] `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] `-- Installing gnustep-base-1.31.1_1... [pkg.DaveG.ca] | `-- Installing avahi-app-0.8_6... [pkg.DaveG.ca] | | `-- Installing dbus-1.16.2_4,1... [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] | | `-- Installing libxml2-2.14.6... [pkg.DaveG.ca] | | `-- Extracting libxml2-2.14.6: .......... done ===> Creating groups Creating group 'messagebus' with gid '556' ===> Creating users Creating user 'messagebus' with uid '556' [pkg.DaveG.ca] | | `-- Extracting dbus-1.16.2_4,1: ......... done [pkg.DaveG.ca] | | `-- Installing dbus-glib-0.114... [pkg.DaveG.ca] | | `-- Extracting dbus-glib-0.114: .......... done [pkg.DaveG.ca] | | `-- Installing gdbm-1.26... [pkg.DaveG.ca] | | `-- Extracting gdbm-1.26: .......... done [pkg.DaveG.ca] | | `-- Installing gnome_subr-1.0... [pkg.DaveG.ca] | | `-- Extracting gnome_subr-1.0: . done [pkg.DaveG.ca] | | `-- Installing libdaemon-0.14_1... [pkg.DaveG.ca] | | `-- Extracting libdaemon-0.14_1: .......... done [pkg.DaveG.ca] | | `-- Installing libevent-2.1.12... [pkg.DaveG.ca] | | `-- Extracting libevent-2.1.12: .......... done ===> Creating groups Creating group 'avahi' with gid '558' ===> Creating users Creating user 'avahi' with uid '558' [pkg.DaveG.ca] | `-- Extracting avahi-app-0.8_6: .......... done [pkg.DaveG.ca] | `-- Installing curl-8.17.0... [pkg.DaveG.ca] | | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing libunistring-1.4.1... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.4.1: .......... done [pkg.DaveG.ca] | | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | | `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] | | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | | `-- Installing libssh2-1.11.1,3... 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[pkg.DaveG.ca] | | `-- Installing libgpg-error-1.58... [pkg.DaveG.ca] | | `-- Extracting libgpg-error-1.58: .......... done [pkg.DaveG.ca] | `-- Extracting libgcrypt-1.11.2: .......... done [pkg.DaveG.ca] | `-- Installing libxslt-1.1.43_1... [pkg.DaveG.ca] | `-- Extracting libxslt-1.1.43_1: .......... done [pkg.DaveG.ca] `-- Extracting gnustep-base-1.31.1_1: .......... done [pkg.DaveG.ca] `-- Installing gnustep-gui-0.32.0... [pkg.DaveG.ca] | `-- Installing cups-2.4.16... [pkg.DaveG.ca] | | `-- Installing libpaper-1.1.28_1... [pkg.DaveG.ca] | | `-- Extracting libpaper-1.1.28_1: .......... done ===> Creating groups Creating group 'cups' with gid '193' ===> Creating users Creating user 'cups' with uid '193' [pkg.DaveG.ca] | `-- Extracting cups-2.4.16: .......... done [pkg.DaveG.ca] | `-- Installing flite-2.1... [pkg.DaveG.ca] | `-- Extracting flite-2.1: .......... done [pkg.DaveG.ca] | `-- Installing jpeg-turbo-3.1.3... [pkg.DaveG.ca] | `-- Extracting jpeg-turbo-3.1.3: .......... done [pkg.DaveG.ca] | `-- Installing libXt-1.3.0,1... [pkg.DaveG.ca] | `-- Extracting libXt-1.3.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libao-1.2.0_7... [pkg.DaveG.ca] | `-- Extracting libao-1.2.0_7: .......... done [pkg.DaveG.ca] | `-- Installing libsndfile-1.2.2_2... [pkg.DaveG.ca] | | `-- Installing flac-1.5.0,1... [pkg.DaveG.ca] | | `-- Installing libogg-1.3.6,4... [pkg.DaveG.ca] | | `-- Extracting libogg-1.3.6,4: .......... done [pkg.DaveG.ca] | | `-- Extracting flac-1.5.0,1: .......... done [pkg.DaveG.ca] | | `-- Installing lame-3.100_5... [pkg.DaveG.ca] | | `-- Extracting lame-3.100_5: .......... done [pkg.DaveG.ca] | | `-- Installing libvorbis-1.3.7_2,3... [pkg.DaveG.ca] | | `-- Extracting libvorbis-1.3.7_2,3: .......... done [pkg.DaveG.ca] | | `-- Installing mpg123-1.33.4... [pkg.DaveG.ca] | | `-- Extracting mpg123-1.33.4: .......... done [pkg.DaveG.ca] | | `-- Installing opus-1.6.1... [pkg.DaveG.ca] | | `-- Extracting opus-1.6.1: .......... done [pkg.DaveG.ca] | `-- Extracting libsndfile-1.2.2_2: .......... done [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 lerc-4.0.0... [pkg.DaveG.ca] | | `-- Extracting lerc-4.0.0: ..... done [pkg.DaveG.ca] | | `-- Installing libdeflate-1.25... [pkg.DaveG.ca] | | `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] | `-- Extracting tiff-4.7.1: .......... done [pkg.DaveG.ca] `-- Extracting gnustep-gui-0.32.0: .......... done [pkg.DaveG.ca] `-- Installing libXcursor-1.2.3... [pkg.DaveG.ca] | `-- Installing libXfixes-6.0.1... [pkg.DaveG.ca] | `-- Extracting libXfixes-6.0.1: ....... done [pkg.DaveG.ca] `-- Extracting libXcursor-1.2.3: .......... done [pkg.DaveG.ca] `-- Installing libXft-2.3.8... [pkg.DaveG.ca] `-- Extracting libXft-2.3.8: .......... done [pkg.DaveG.ca] `-- Installing libXmu-1.1.4,1... [pkg.DaveG.ca] `-- Extracting libXmu-1.1.4,1: .......... done [pkg.DaveG.ca] `-- Installing libglvnd-1.7.0... [pkg.DaveG.ca] `-- Extracting libglvnd-1.7.0: .......... done [pkg.DaveG.ca] Extracting gnustep-back-0.32.0: ........ done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from freetype2-2.14.1: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from libinotify-20240724_3: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===== Message from flite-2.1: -- ===> NOTICE: The flite 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 ===> biococoa-2.2.2_9 depends on package: gnustep-back>0 - found ===> Returning to build of biococoa-2.2.2_9 ===> biococoa-2.2.2_9 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. ===> biococoa-2.2.2_9 depends on file: /usr/local/bin/ccache - found ===> Returning to build of biococoa-2.2.2_9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> biococoa-2.2.2_9 depends on shared library: libobjc.so.4.6 - found (/usr/local/lib/libobjc.so.4.6) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for biococoa-2.2.2_9 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for biococoa-2.2.2_9 This is gnustep-make 2.9.3. Type 'gmake print-gnustep-make-help' for help. Running in gnustep-make version 2 strict mode. Making build-headers in subprojects of framework BioCocoa... gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ../../BioCocoa.framework/Versions/2/Headers install -c BCPairwiseAlignment.h ../../BioCocoa.framework/Versions/2/Headers/BCPairwiseAlignment.h install -c BCScoreMatrix.h ../../BioCocoa.framework/Versions/2/Headers/BCScoreMatrix.h install -c BCSequenceAlignment.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceAlignment.h gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAlignment' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... install -c BCMCP.h ../../BioCocoa.framework/Versions/2/Headers/BCMCP.h install -c BCSuffixArray.h ../../BioCocoa.framework/Versions/2/Headers/BCSuffixArray.h gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAnalysis' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... install -c BCSeries.h ../../BioCocoa.framework/Versions/2/Headers/BCSeries.h install -c BCSample.h ../../BioCocoa.framework/Versions/2/Headers/BCSample.h install -c BCPlatform.h ../../BioCocoa.framework/Versions/2/Headers/BCPlatform.h install -c BCParseSOFT.h ../../BioCocoa.framework/Versions/2/Headers/BCParseSOFT.h gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneExpression' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... install -c BCCodonDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCCodonDNA.h install -c BCCodon.h ../../BioCocoa.framework/Versions/2/Headers/BCCodon.h install -c BCCodonRNA.h ../../BioCocoa.framework/Versions/2/Headers/BCCodonRNA.h install -c BCGeneticCode.h ../../BioCocoa.framework/Versions/2/Headers/BCGeneticCode.h gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneticCode' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... install -c BCAtom.h ../../BioCocoa.framework/Versions/2/Headers/BCAtom.h install -c BCProteinStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCProteinStructure.h install -c BCSecondaryStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCSecondaryStructure.h install -c BCChain.h ../../BioCocoa.framework/Versions/2/Headers/BCChain.h install -c BCResidue.h ../../BioCocoa.framework/Versions/2/Headers/BCResidue.h install -c BCSequenceStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceStructure.h gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCProteinStructure' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... install -c BCAnnotation.h ../../BioCocoa.framework/Versions/2/Headers/BCAnnotation.h install -c BCSequence.h ../../BioCocoa.framework/Versions/2/Headers/BCSequence.h install -c BCSequenceArray.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceArray.h install -c BCSequenceCodon.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceCodon.h gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequence' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... install -c BCSequenceReader.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceReader.h install -c BCSequenceWriter.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceWriter.h install -c BCCachedSequenceFile.h ../../BioCocoa.framework/Versions/2/Headers/BCCachedSequenceFile.h install -c BCCachedFastaFile.h ../../BioCocoa.framework/Versions/2/Headers/BCCachedFastaFile.h gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequenceIO' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... install -c BCAminoAcid.h ../../BioCocoa.framework/Versions/2/Headers/BCAminoAcid.h install -c BCNucleotide.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotide.h install -c BCSymbol.h ../../BioCocoa.framework/Versions/2/Headers/BCSymbol.h install -c BCNucleotideDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideDNA.h install -c BCNucleotideRNA.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideRNA.h install -c BCSymbolSet.h ../../BioCocoa.framework/Versions/2/Headers/BCSymbolSet.h gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSymbol' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCTools' Making build-headers for subproject BCTools... install -c BCSequenceTool.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceTool.h install -c BCToolDigest.h ../../BioCocoa.framework/Versions/2/Headers/BCToolDigest.h install -c BCToolHydropathyCalculator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolHydropathyCalculator.h install -c BCToolMassCalculator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolMassCalculator.h install -c BCToolComplement.h ../../BioCocoa.framework/Versions/2/Headers/BCToolComplement.h install -c BCToolSequenceFinder.h ../../BioCocoa.framework/Versions/2/Headers/BCToolSequenceFinder.h install -c BCToolSymbolCounter.h ../../BioCocoa.framework/Versions/2/Headers/BCToolSymbolCounter.h install -c BCToolTranslator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslator.h install -c BCToolTranslatorDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslatorDNA.h gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCTools' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... install -c BCDataMatrix.h ../../BioCocoa.framework/Versions/2/Headers/BCDataMatrix.h install -c BCUtilData.h ../../BioCocoa.framework/Versions/2/Headers/BCUtilData.h install -c BCUtilStrings.h ../../BioCocoa.framework/Versions/2/Headers/BCUtilStrings.h gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... cat: ./BCAlignment/obj/subproject.txt: No such file or directory cat: ./BCAnalysis/obj/subproject.txt: No such file or directory cat: ./BCGeneExpression/obj/subproject.txt: No such file or directory cat: ./BCGeneticCode/obj/subproject.txt: No such file or directory cat: ./BCProteinStructure/obj/subproject.txt: No such file or directory cat: ./BCSequence/obj/subproject.txt: No such file or directory cat: ./BCSequenceIO/obj/subproject.txt: No such file or directory cat: ./BCSymbol/obj/subproject.txt: No such file or directory cat: ./BCTools/obj/subproject.txt: No such file or directory cat: ./BCUtils/obj/subproject.txt: No such file or directory cat: ./BCAlignment/obj/subproject.txt: No such file or directory cat: ./BCAnalysis/obj/subproject.txt: No such file or directory cat: ./BCGeneExpression/obj/subproject.txt: No such file or directory cat: ./BCGeneticCode/obj/subproject.txt: No such file or directory cat: ./BCProteinStructure/obj/subproject.txt: No such file or directory cat: ./BCSequence/obj/subproject.txt: No such file or directory cat: ./BCSequenceIO/obj/subproject.txt: No such file or directory cat: ./BCSymbol/obj/subproject.txt: No such file or directory cat: ./BCTools/obj/subproject.txt: No such file or directory cat: ./BCUtils/obj/subproject.txt: No such file or directory cat: ./BCAlignment/obj/subproject.txt: No such file or directory cat: ./BCAnalysis/obj/subproject.txt: No such file or directory cat: ./BCGeneExpression/obj/subproject.txt: No such file or directory cat: ./BCGeneticCode/obj/subproject.txt: No such file or directory cat: ./BCProteinStructure/obj/subproject.txt: No such file or directory cat: ./BCSequence/obj/subproject.txt: No such file or directory cat: ./BCSequenceIO/obj/subproject.txt: No such file or directory cat: ./BCSymbol/obj/subproject.txt: No such file or directory cat: ./BCTools/obj/subproject.txt: No such file or directory cat: ./BCUtils/obj/subproject.txt: No such file or directory cat: ./BCAlignment/obj/subproject.txt: No such file or directory cat: ./BCAnalysis/obj/subproject.txt: No such file or directory cat: ./BCGeneExpression/obj/subproject.txt: No such file or directory cat: ./BCGeneticCode/obj/subproject.txt: No such file or directory cat: ./BCProteinStructure/obj/subproject.txt: No such file or directory cat: ./BCSequence/obj/subproject.txt: No such file or directory cat: ./BCSequenceIO/obj/subproject.txt: No such file or directory cat: ./BCSymbol/obj/subproject.txt: No such file or directory cat: ./BCTools/obj/subproject.txt: No such file or directory cat: ./BCUtils/obj/subproject.txt: No such file or directory install -c BCFoundation.h ../BioCocoa.framework/Versions/2/Headers/BCFoundation.h install -c BCFoundationDefines.h ../BioCocoa.framework/Versions/2/Headers/BCFoundationDefines.h install -c BCStringDefinitions.h ../BioCocoa.framework/Versions/2/Headers/BCStringDefinitions.h install -c BCPreferences.h ../BioCocoa.framework/Versions/2/Headers/BCPreferences.h gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation' Making build-headers for framework BioCocoa... cat: ./BCFoundation/obj/subproject.txt: No such file or directory cat: ./BCFoundation/obj/subproject.txt: No such file or directory cat: ./BCFoundation/obj/subproject.txt: No such file or directory cat: ./BCFoundation/obj/subproject.txt: No such file or directory /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./derived_src; \ touch derived_src/.stamp /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs BioCocoa.framework/Versions/2/Resources cd ./BioCocoa.framework/Versions; \ rm -f Current; \ ln -s 2 Current cd ./BioCocoa.framework; \ if [ ! -h "Resources" ]; then \ rm -f Resources; \ ln -s Versions/Current/Resources Resources; \ fi; \ if [ ! -h "Headers" ]; then \ rm -f Headers; \ ln -s Versions/Current/Headers Headers; \ fi cd ./derived_src; \ if [ ! -h "BioCocoa" ]; then \ rm -f ./BioCocoa; \ ln -s ../BioCocoa.framework/Headers \ ./BioCocoa; \ fi cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all in subprojects of framework BioCocoa... gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all in subprojects of subproject BCFoundation... gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAlignment' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all for subproject BCAlignment... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCAlignment.obj/ cc BCPairwiseAlignment.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCAlignment.obj/BCPairwiseAlignment.m.o cc BCScoreMatrix.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCAlignment.obj/BCScoreMatrix.m.o cc BCSequenceAlignment.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCAlignment.obj/BCSequenceAlignment.m.o gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAlignment' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAnalysis' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all for subproject BCAnalysis... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCAnalysis.obj/ cc BCMCP.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCAnalysis.obj/BCMCP.m.o cc BCSuffixArray.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCAnalysis.obj/BCSuffixArray.m.o BCSuffixArray.m:644:26: warning: expression which evaluates to zero treated as a null pointer constant of type 'BCSuffixArray *' [-Wnon-literal-null-conversion] 644 | if (!aSequence) return NO; | ^~ /usr/local/include/objc/runtime.h:207:14: note: expanded from macro 'NO' 207 | # define NO __objc_no | ^~~~~~~~~ 1 warning generated. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAnalysis' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneExpression' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all for subproject BCGeneExpression... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCGeneExpression.obj/ cc BCSeries.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCGeneExpression.obj/BCSeries.m.o cc BCSample.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCGeneExpression.obj/BCSample.m.o cc BCPlatform.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCGeneExpression.obj/BCPlatform.m.o cc BCParseSOFT.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCGeneExpression.obj/BCParseSOFT.m.o BCParseSOFT.m:259:61: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat] 259 | NSLog(@"ERROR: probe set columns %d != %d entries\n", [probeSetColumns count], [f count]); | ~~ ^~~~~~~~~~~~~~~~~~~~~~~ | %lu BCParseSOFT.m:259:86: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat] 259 | NSLog(@"ERROR: probe set columns %d != %d entries\n", [probeSetColumns count], [f count]); | ~~ ^~~~~~~~~ | %lu BCParseSOFT.m:332:63: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat] 332 | NSLog(@"ERROR: sample data columns %d != %d entries\n", [sampleSetColumns count], [f count]); | ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ | %lu BCParseSOFT.m:332:89: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat] 332 | NSLog(@"ERROR: sample data columns %d != %d entries\n", [sampleSetColumns count], [f count]); | ~~ ^~~~~~~~~ | %lu 4 warnings generated. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneExpression' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneticCode' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all for subproject BCGeneticCode... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCGeneticCode.obj/ cc BCCodonDNA.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCGeneticCode.obj/BCCodonDNA.m.o cc BCCodon.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCGeneticCode.obj/BCCodon.m.o cc BCCodonRNA.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCGeneticCode.obj/BCCodonRNA.m.o cc BCGeneticCode.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCGeneticCode.obj/BCGeneticCode.m.o BCGeneticCode.m:221:23: warning: variable 'RNACodon' set but not used [-Wunused-but-set-variable] 221 | BCCodon *aCodon, *RNACodon; | ^ 1 warning generated. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneticCode' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCProteinStructure' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all for subproject BCProteinStructure... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCProteinStructure.obj/ cc BCAtom.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCProteinStructure.obj/BCAtom.m.o cc BCProteinStructure.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCProteinStructure.obj/BCProteinStructure.m.o cc BCSecondaryStructure.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCProteinStructure.obj/BCSecondaryStructure.m.o cc BCChain.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCProteinStructure.obj/BCChain.m.o cc BCResidue.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCProteinStructure.obj/BCResidue.m.o cc BCSequenceStructure.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCProteinStructure.obj/BCSequenceStructure.m.o gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCProteinStructure' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequence' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all for subproject BCSequence... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCSequence.obj/ cc BCAnnotation.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSequence.obj/BCAnnotation.m.o cc BCSequence.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSequence.obj/BCSequence.m.o cc BCSequenceArray.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSequence.obj/BCSequenceArray.m.o cc BCSequenceCodon.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSequence.obj/BCSequenceCodon.m.o BCSequence.m:596:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 596 | NSData *data = [[self sequenceData] subdataWithRange: aRange]; // Man, I love Cocoa !! | ^ BCSequence.m:593:5: note: previous statement is here 593 | if ( aRange.location + aRange.length > [self length] ) | ^ BCSequence.m:622:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 622 | return [BCSequence sequenceWithSymbolArray: [symbolArray subarrayWithRange: aRange]]; | ^ BCSequence.m:619:5: note: previous statement is here 619 | if ( aRange.location + aRange.length > [symbolArray count] ) | ^ 2 warnings generated. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequence' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequenceIO' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all for subproject BCSequenceIO... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCSequenceIO.obj/ cc BCSequenceReader.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSequenceIO.obj/BCSequenceReader.m.o cc BCSequenceWriter.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSequenceIO.obj/BCSequenceWriter.m.o cc BCCachedSequenceFile.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSequenceIO.obj/BCCachedSequenceFile.m.o cc BCCachedFastaFile.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSequenceIO.obj/BCCachedFastaFile.m.o BCCachedFastaFile.m:126:71: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] 126 | NSLog(@"Attempting to read past end of forward stand: (%lu)\n", aPos); | ~~~ ^~~~ | %llu BCCachedFastaFile.m:133:72: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] 133 | NSLog(@"Attempting to read past end of reverse strand: (%lu)\n", aPos); | ~~~ ^~~~ | %llu 2 warnings generated. BCSequenceReader.m:167:63: warning: instance method '-initWithRTF:documentAttributes:' not found (return type defaults to 'id') [-Wobjc-method-access] 167 | NSAttributedString *rtfstring = [[NSAttributedString alloc] initWithRTF: [entryString dataUsingEncoding: NSUTF8StringEncoding] documentAttributes: nil]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/GNUstep/System/Library/Headers/Foundation/NSAttributedString.h:64:12: note: receiver is instance of class declared here 64 | @interface NSAttributedString : NSObject | ^ BCSequenceReader.m:651:18: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] 651 | NSMutableArray *annotationsArray; | ^ BCSequenceReader.m:830:12: warning: using 'stringWithString:' with a literal is redundant [-Wobjc-redundant-literal-use] 830 | name = [NSString stringWithString: @"alignment"]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSequenceReader.m:1113:31: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] 1113 | NSMutableArray *linesArray, *annotationsArray, *namesArray, *sequenceArray; | ^ 4 warnings generated. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequenceIO' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSymbol' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all for subproject BCSymbol... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCSymbol.obj/ cc BCAminoAcid.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSymbol.obj/BCAminoAcid.m.o cc BCNucleotide.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSymbol.obj/BCNucleotide.m.o cc BCSymbol.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSymbol.obj/BCSymbol.m.o cc BCNucleotideDNA.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSymbol.obj/BCNucleotideDNA.m.o cc BCNucleotideRNA.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSymbol.obj/BCNucleotideRNA.m.o cc BCSymbolSet.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCSymbol.obj/BCSymbolSet.m.o BCNucleotideRNA.m:454:43: warning: 'BCNucleotideRNA' may not respond to 'initWithDictionary:' 454 | aBase = [[[BCNucleotideRNA alloc] initWithDictionary: aBase] autorelease]; | ~~~~~~~~~~~~~~~~~~~~~~~ ^ 1 warning generated. BCNucleotideDNA.m:445:43: warning: 'BCNucleotideDNA' may not respond to 'initWithDictionary:' 445 | aBase = [[[BCNucleotideDNA alloc] initWithDictionary: aBase] autorelease]; | ~~~~~~~~~~~~~~~~~~~~~~~ ^ 1 warning generated. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSymbol' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCTools' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all for subproject BCTools... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCTools.obj/ cc BCSequenceTool.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCTools.obj/BCSequenceTool.m.o cc BCToolDigest.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCTools.obj/BCToolDigest.m.o cc BCToolHydropathyCalculator.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCTools.obj/BCToolHydropathyCalculator.m.o cc BCToolMassCalculator.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCTools.obj/BCToolMassCalculator.m.o cc BCToolComplement.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCTools.obj/BCToolComplement.m.o cc BCToolSequenceFinder.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCTools.obj/BCToolSequenceFinder.m.o cc BCToolSymbolCounter.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCTools.obj/BCToolSymbolCounter.m.o cc BCToolTranslator.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCTools.obj/BCToolTranslator.m.o cc BCToolTranslatorDNA.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCTools.obj/BCToolTranslatorDNA.m.o BCToolTranslator.m:99:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 99 | BCSequence *tempSequence; | ^ BCToolTranslator.m:95:5: note: previous statement is here 95 | if ( theCode == nil || [theCode count] == 0 ) | ^ 1 warning generated. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCTools' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCUtils' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all for subproject BCUtils... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCUtils.obj/ cc BCDataMatrix.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCUtils.obj/BCDataMatrix.m.o cc BCUtilData.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCUtils.obj/BCUtilData.m.o cc BCUtilStrings.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I.. -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCUtils.obj/BCUtilStrings.m.o BCDataMatrix.m:261:93: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat] 261 | NSLog(@"Invalid matrix format for data matrix, expected %d items, got %d", expectCols, [a count]); | ~~ ^~~~~~~~~ | %lu BCDataMatrix.m:341:77: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat] 341 | NSLog(@"Invalid list format for data matrix, expected 3 items, got %d", [a count]); | ~~ ^~~~~~~~~ | %lu 2 warnings generated. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCFoundation.obj/ cc BCStringDefinitions.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I. -I./BCAnalysis -I./BCGeneticCode -I./BCProteinStructure -I./BCSequence -I./BCSequenceIO -I./BCSymbol -I./BCTools -I./BCTools/BCDigest -I./BCTools/BCSequenceProperty -I./BCTools/BCSequenceTools -I./BCTools/BCTranslation -I./BCUtils -I./../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCFoundation.obj/BCStringDefinitions.m.o cc BCPreferences.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -fconstant-string-class=NSConstantString -I. -I./BCAnalysis -I./BCGeneticCode -I./BCProteinStructure -I./BCSequence -I./BCSequenceIO -I./BCSymbol -I./BCTools -I./BCTools/BCDigest -I./BCTools/BCSequenceProperty -I./BCTools/BCSequenceTools -I./BCTools/BCTranslation -I./BCUtils -I./../derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include \ -o obj/BCFoundation.obj/BCPreferences.m.o BCPreferences.m:69:7: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 69 | return nil; | ^ BCPreferences.m:67:5: note: previous statement is here 67 | if (![mgr createDirectoryAtPath: s attributes: d]) | ^ 1 warning generated. gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation' Making all for framework BioCocoa... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BioCocoa.obj/ classes=""; \ for object_file in ./BCFoundation/./obj/BCFoundation.obj/BCStringDefinitions.m.o ./BCFoundation/./obj/BCFoundation.obj/BCPreferences.m.o ./BCFoundation/./BCAlignment/./obj/BCAlignment.obj/BCPairwiseAlignment.m.o ./BCFoundation/./BCAlignment/./obj/BCAlignment.obj/BCScoreMatrix.m.o ./BCFoundation/./BCAlignment/./obj/BCAlignment.obj/BCSequenceAlignment.m.o ./BCFoundation/./BCAnalysis/./obj/BCAnalysis.obj/BCMCP.m.o ./BCFoundation/./BCAnalysis/./obj/BCAnalysis.obj/BCSuffixArray.m.o ./BCFoundation/./BCGeneExpression/./obj/BCGeneExpression.obj/BCSeries.m.o ./BCFoundation/./BCGeneExpression/./obj/BCGeneExpression.obj/BCSample.m.o ./BCFoundation/./BCGeneExpression/./obj/BCGeneExpression.obj/BCPlatform.m.o ./BCFoundation/./BCGeneExpression/./obj/BCGeneExpression.obj/BCParseSOFT.m.o ./BCFoundation/./BCGeneticCode/./obj/BCGeneticCode.obj/BCCodonDNA.m.o ./BCFoundation/./BCGeneticCode/./obj/BCGeneticCode.obj/BCCodon.m.o ./BCFoundation/./BCGeneticCode/./obj/BCGeneticCode.obj/BCCodonRNA.m.o ./BCFoundation/./BCGeneticCode/./obj/BCGeneticCode.obj/BCGeneticCode.m.o ./BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCAtom.m.o ./BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCProteinStructure.m.o ./BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCSecondaryStructure.m.o ./BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCChain.m.o ./BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCResidue.m.o ./BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCSequenceStructure.m.o ./BCFoundation/./BCSequence/./obj/BCSequence.obj/BCAnnotation.m.o ./BCFoundation/./BCSequence/./obj/BCSequence.obj/BCSequence.m.o ./BCFoundation/./BCSequence/./obj/BCSequence.obj/BCSequenceArray.m.o ./BCFoundation/./BCSequence/./obj/BCSequence.obj/BCSequenceCodon.m.o ./BCFoundation/./BCSequenceIO/./obj/BCSequenceIO.obj/BCSequenceReader.m.o ./BCFoundation/./BCSequenceIO/./obj/BCSequenceIO.obj/BCSequenceWriter.m.o ./BCFoundation/./BCSequenceIO/./obj/BCSequenceIO.obj/BCCachedSequenceFile.m.o ./BCFoundation/./BCSequenceIO/./obj/BCSequenceIO.obj/BCCachedFastaFile.m.o ./BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCAminoAcid.m.o ./BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCNucleotide.m.o ./BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCSymbol.m.o ./BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCNucleotideDNA.m.o ./BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCNucleotideRNA.m.o ./BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCSymbolSet.m.o ./BCFoundation/./BCTools/./obj/BCTools.obj/BCSequenceTool.m.o ./BCFoundation/./BCTools/./obj/BCTools.obj/BCToolDigest.m.o ./BCFoundation/./BCTools/./obj/BCTools.obj/BCToolHydropathyCalculator.m.o ./BCFoundation/./BCTools/./obj/BCTools.obj/BCToolMassCalculator.m.o ./BCFoundation/./BCTools/./obj/BCTools.obj/BCToolComplement.m.o ./BCFoundation/./BCTools/./obj/BCTools.obj/BCToolSequenceFinder.m.o ./BCFoundation/./BCTools/./obj/BCTools.obj/BCToolSymbolCounter.m.o ./BCFoundation/./BCTools/./obj/BCTools.obj/BCToolTranslator.m.o ./BCFoundation/./BCTools/./obj/BCTools.obj/BCToolTranslatorDNA.m.o ./BCFoundation/./BCUtils/./obj/BCUtils.obj/BCDataMatrix.m.o ./BCFoundation/./BCUtils/./obj/BCUtils.obj/BCUtilData.m.o ./BCFoundation/./BCUtils/./obj/BCUtils.obj/BCUtilStrings.m.o __dummy__; do \ if [ "$object_file" != "__dummy__" ]; then \ sym=`nm -Pg $object_file | sed -n -e '/^__objc_class_name_[A-Za-z0-9_.]* [^U]/ {s/^__objc_class_name_\([A-Za-z0-9_.]*\) [^U].*/\1/p;}' -e '/^\._OBJC_CLASS_[A-Za-z0-9_.]* [^U]/ {s/^\._OBJC_CLASS_\([A-Za-z0-9_.]*\) [^U].*/\1/p;}'`; \ classes="$classes $sym"; \ fi; \ done; \ classlist=""; \ classarray=""; \ for f in $classes __dummy__ ; do \ if [ "$f" != "__dummy__" ]; then \ if [ "$classlist" = "" ]; then \ classlist="@\"$f\""; \ classarray="(\"$f\""; \ else \ classlist="$classlist, @\"$f\""; \ classarray="$classarray, \"$f\""; \ fi; \ fi; \ done; \ if [ "$classlist" = "" ]; then \ classlist="NULL"; \ classarray="()"; \ else \ classlist="$classlist, NULL"; \ classarray="$classarray)"; \ fi; \ echo "$classarray" > ./derived_src/BioCocoa-class-list; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "@interface NSFramework_BioCocoa : NSObject" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses;" >> derived_src/NSFramework_BioCocoa.m; \ echo "@end" >> derived_src/NSFramework_BioCocoa.m; \ echo "@implementation NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion { return @\"2\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "static NSString *allClasses[] = {$classlist};" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses { return allClasses; }" >> derived_src/NSFramework_BioCocoa.m;\ echo "@end" >> derived_src/NSFramework_BioCocoa.m cc derived_src/NSFramework_BioCocoa.m -c -MMD -MP -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNUSTEP_RUNTIME=1 -D_NONFRAGILE_ABI=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fobjc-runtime=gnustep-2.2 -fblocks -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-import -I/usr/local/include -fconstant-string-class=NSConstantString -I./derived_src -I. -I/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -I/usr/local/include -o obj/BioCocoa.obj/NSFramework_BioCocoa.o \ cc -shared -Wl,-soname,libBioCocoa.so.2 -L/usr/local/lib -fuse-ld= -pthread -rdynamic -o ./BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 obj/BioCocoa.obj/NSFramework_BioCocoa.o BCFoundation/./obj/BCFoundation.obj/BCStringDefinitions.m.o BCFoundation/./obj/BCFoundation.obj/BCPreferences.m.o BCFoundation/./BCAlignment/./obj/BCAlignment.obj/BCPairwiseAlignment.m.o BCFoundation/./BCAlignment/./obj/BCAlignment.obj/BCScoreMatrix.m.o BCFoundation/./BCAlignment/./obj/BCAlignment.obj/BCSequenceAlignment.m.o BCFoundation/./BCAnalysis/./obj/BCAnalysis.obj/BCMCP.m.o BCFoundation/./BCAnalysis/./obj/BCAnalysis.obj/BCSuffixArray.m.o BCFoundation/./BCGeneExpression/./obj/BCGeneExpression.obj/BCSeries.m.o BCFoundation/./BCGeneExpression/./obj/BCGeneExpression.obj/BCSample.m.o BCFoundation/./BCGeneExpression/./obj/BCGeneExpression.obj/BCPlatform.m.o BCFoundation/./BCGeneExpression/./obj/BCGeneExpression.obj/BCParseSOFT.m.o BCFoundation/./BCGeneticCode/./obj/BCGeneticCode.obj/BCCodonDNA.m.o BCFoundation/./BCGeneticCode/./obj/BCGeneticCode.obj/BCCodon.m.o BCFoundation/./BCGeneticCode/./obj/BCGeneticCode.obj/BCCodonRNA.m.o BCFoundation/./BCGeneticCode/./obj/BCGeneticCode.obj/BCGeneticCode.m.o BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCAtom.m.o BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCProteinStructure.m.o BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCSecondaryStructure.m.o BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCChain.m.o BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCResidue.m.o BCFoundation/./BCProteinStructure/./obj/BCProteinStructure.obj/BCSequenceStructure.m.o BCFoundation/./BCSequence/./obj/BCSequence.obj/BCAnnotation.m.o BCFoundation/./BCSequence/./obj/BCSequence.obj/BCSequence.m.o BCFoundation/./BCSequence/./obj/BCSequence.obj/BCSequenceArray.m.o BCFoundation/./BCSequence/./obj/BCSequence.obj/BCSequenceCodon.m.o BCFoundation/./BCSequenceIO/./obj/BCSequenceIO.obj/BCSequenceReader.m.o BCFoundation/./BCSequenceIO/./obj/BCSequenceIO.obj/BCSequenceWriter.m.o BCFoundation/./BCSequenceIO/./obj/BCSequenceIO.obj/BCCachedSequenceFile.m.o BCFoundation/./BCSequenceIO/./obj/BCSequenceIO.obj/BCCachedFastaFile.m.o BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCAminoAcid.m.o BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCNucleotide.m.o BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCSymbol.m.o BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCNucleotideDNA.m.o BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCNucleotideRNA.m.o BCFoundation/./BCSymbol/./obj/BCSymbol.obj/BCSymbolSet.m.o BCFoundation/./BCTools/./obj/BCTools.obj/BCSequenceTool.m.o BCFoundation/./BCTools/./obj/BCTools.obj/BCToolDigest.m.o BCFoundation/./BCTools/./obj/BCTools.obj/BCToolHydropathyCalculator.m.o BCFoundation/./BCTools/./obj/BCTools.obj/BCToolMassCalculator.m.o BCFoundation/./BCTools/./obj/BCTools.obj/BCToolComplement.m.o BCFoundation/./BCTools/./obj/BCTools.obj/BCToolSequenceFinder.m.o BCFoundation/./BCTools/./obj/BCTools.obj/BCToolSymbolCounter.m.o BCFoundation/./BCTools/./obj/BCTools.obj/BCToolTranslator.m.o BCFoundation/./BCTools/./obj/BCTools.obj/BCToolTranslatorDNA.m.o BCFoundation/./BCUtils/./obj/BCUtils.obj/BCDataMatrix.m.o BCFoundation/./BCUtils/./obj/BCUtils.obj/BCUtilData.m.o BCFoundation/./BCUtils/./obj/BCUtils.obj/BCUtilStrings.m.o -L/wrkdirs/usr/ports/biology/biococoa/work/GNUstep/Library/Libraries -L/usr/local/GNUstep/Local/Library/Libraries -L/usr/local/GNUstep/System/Library/Libraries -L/usr/local/lib && (cd ./BioCocoa.framework/Versions/2/.; rm -f libBioCocoa.so; if [ "libBioCocoa.so.2" != "libBioCocoa.so.2.2.2" ]; then rm -f libBioCocoa.so.2; ln -s libBioCocoa.so.2.2.2 libBioCocoa.so.2; fi; ln -s libBioCocoa.so.2 libBioCocoa.so) || rm -f ./BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 ; \ (cd ./BioCocoa.framework/Versions/2/.; \ rm -f BioCocoa; \ ln -s libBioCocoa.so BioCocoa) \ for f in BCFoundation/BCSymbol/SymbolTemplates/nucleotides.plist BCFoundation/BCSymbol/SymbolTemplates/aminoacids.plist; do \ if [ -f .//$f -o -d .//$f ]; then \ cp -fr .//$f ./BioCocoa.framework/Versions/2/Resources/; \ else \ echo "Warning: .//$f not found - ignoring"; \ fi; \ done for subproject in BCFoundation; do \ if [ -d $subproject/Resources/Subproject ]; then \ for f in $subproject/Resources/Subproject/*; do \ if [ $f != $subproject'/Resources/Subproject/*' ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ fi; \ done; \ fi; \ done (echo "{"; echo ' NOTE = "Automatically generated, do not edit!";'; \ echo " NSExecutable = \"BioCocoa\";"; \ echo " NSMainNibFile = \"\";"; \ echo " NSPrincipalClass = \"BioCocoa\";"; \ echo " Classes = "; \ cat ./derived_src/BioCocoa-class-list; \ echo " ;"; \ echo "}") >BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist if [ -r "" ]; then \ plmerge BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist ; \ fi cd ./BioCocoa.framework/.; \ rm -f BioCocoa libBioCocoa.so; \ ln -s `/usr/local/GNUstep/System/Library/Makefiles/relative_path.sh . \ Versions/Current/./BioCocoa short` \ BioCocoa; \ ln -s `/usr/local/GNUstep/System/Library/Makefiles/relative_path.sh . \ Versions/Current/./libBioCocoa.so short` \ libBioCocoa.so =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> biococoa-2.2.2_9 depends on package: gnustep-back>0 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for biococoa-2.2.2_9 ===> Generating temporary packing list This is gnustep-make 2.9.3. Type 'gmake print-gnustep-make-help' for help. Running in gnustep-make version 2 strict mode. Making build-headers in subprojects of framework BioCocoa... gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... gmake[3]: Nothing to be done for 'internal-subproject-build-headers'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAlignment' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... gmake[3]: Nothing to be done for 'internal-subproject-build-headers'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAnalysis' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... gmake[3]: Nothing to be done for 'internal-subproject-build-headers'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneExpression' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... gmake[3]: Nothing to be done for 'internal-subproject-build-headers'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneticCode' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... gmake[3]: Nothing to be done for 'internal-subproject-build-headers'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCProteinStructure' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... gmake[3]: Nothing to be done for 'internal-subproject-build-headers'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequence' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... gmake[3]: Nothing to be done for 'internal-subproject-build-headers'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequenceIO' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... gmake[3]: Nothing to be done for 'internal-subproject-build-headers'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSymbol' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCTools' Making build-headers for subproject BCTools... gmake[3]: Nothing to be done for 'internal-subproject-build-headers'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCTools' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... gmake[3]: Nothing to be done for 'internal-subproject-build-headers'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... gmake[2]: Nothing to be done for 'internal-subproject-build-headers'. gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation' Making build-headers for framework BioCocoa... cd ./BioCocoa.framework; \ if [ ! -h "Resources" ]; then \ rm -f Resources; \ ln -s Versions/Current/Resources Resources; \ fi; \ if [ ! -h "Headers" ]; then \ rm -f Headers; \ ln -s Versions/Current/Headers Headers; \ fi cd ./derived_src; \ if [ ! -h "BioCocoa" ]; then \ rm -f ./BioCocoa; \ ln -s ../BioCocoa.framework/Headers \ ./BioCocoa; \ fi Making all in subprojects of framework BioCocoa... gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation' Making all in subprojects of subproject BCFoundation... gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAlignment' Making all for subproject BCAlignment... gmake[4]: Nothing to be done for 'internal-subproject-compile'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAlignment' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAnalysis' Making all for subproject BCAnalysis... gmake[4]: Nothing to be done for 'internal-subproject-compile'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAnalysis' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making all for subproject BCGeneExpression... gmake[4]: Nothing to be done for 'internal-subproject-compile'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneExpression' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making all for subproject BCGeneticCode... gmake[4]: Nothing to be done for 'internal-subproject-compile'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneticCode' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making all for subproject BCProteinStructure... gmake[4]: Nothing to be done for 'internal-subproject-compile'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCProteinStructure' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequence' Making all for subproject BCSequence... gmake[4]: Nothing to be done for 'internal-subproject-compile'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequence' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making all for subproject BCSequenceIO... gmake[4]: Nothing to be done for 'internal-subproject-compile'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequenceIO' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSymbol' Making all for subproject BCSymbol... gmake[4]: Nothing to be done for 'internal-subproject-compile'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSymbol' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCTools' Making all for subproject BCTools... gmake[4]: Nothing to be done for 'internal-subproject-compile'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCTools' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCUtils... gmake[4]: Nothing to be done for 'internal-subproject-compile'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... gmake[3]: Nothing to be done for 'internal-subproject-compile'. gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation' Making all for framework BioCocoa... gmake[2]: Nothing to be done for 'internal-framework-compile'. for f in BCFoundation/BCSymbol/SymbolTemplates/nucleotides.plist BCFoundation/BCSymbol/SymbolTemplates/aminoacids.plist; do \ if [ -f .//$f -o -d .//$f ]; then \ cp -fr .//$f ./BioCocoa.framework/Versions/2/Resources/; \ else \ echo "Warning: .//$f not found - ignoring"; \ fi; \ done for subproject in BCFoundation; do \ if [ -d $subproject/Resources/Subproject ]; then \ for f in $subproject/Resources/Subproject/*; do \ if [ $f != $subproject'/Resources/Subproject/*' ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ fi; \ done; \ fi; \ done cd ./BioCocoa.framework/.; \ rm -f BioCocoa libBioCocoa.so; \ ln -s `/usr/local/GNUstep/System/Library/Makefiles/relative_path.sh . \ Versions/Current/./BioCocoa short` \ BioCocoa; \ ln -s `/usr/local/GNUstep/System/Library/Makefiles/relative_path.sh . \ Versions/Current/./libBioCocoa.so short` \ libBioCocoa.so Making install in subprojects of framework BioCocoa... gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation' Making install in subprojects of subproject BCFoundation... gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAlignment' Making install for subproject BCAlignment... gmake[3]: Nothing to be done for 'internal-subproject-install'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAlignment' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAnalysis' Making install for subproject BCAnalysis... gmake[3]: Nothing to be done for 'internal-subproject-install'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCAnalysis' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making install for subproject BCGeneExpression... gmake[3]: Nothing to be done for 'internal-subproject-install'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneExpression' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making install for subproject BCGeneticCode... gmake[3]: Nothing to be done for 'internal-subproject-install'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCGeneticCode' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making install for subproject BCProteinStructure... gmake[3]: Nothing to be done for 'internal-subproject-install'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCProteinStructure' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequence' Making install for subproject BCSequence... gmake[3]: Nothing to be done for 'internal-subproject-install'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequence' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making install for subproject BCSequenceIO... gmake[3]: Nothing to be done for 'internal-subproject-install'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSequenceIO' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSymbol' Making install for subproject BCSymbol... gmake[3]: Nothing to be done for 'internal-subproject-install'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCSymbol' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCTools' Making install for subproject BCTools... gmake[3]: Nothing to be done for 'internal-subproject-install'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCTools' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCUtils... gmake[3]: Nothing to be done for 'internal-subproject-install'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCFoundation... gmake[2]: Nothing to be done for 'internal-subproject-install'. gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2/BCFoundation' Making install for framework BioCocoa... /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Frameworks /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Libraries/. /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Headers (cd .; \ tar cfX - /usr/local/GNUstep/System/Library/Makefiles/tar-exclude-list \ BioCocoa.framework) \ | (cd /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Frameworks; tar xf -) cd /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Headers; \ rm -f BioCocoa; \ ln -s `/usr/local/GNUstep/System/Library/Makefiles/relative_path.sh /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Headers /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Frameworks/BioCocoa.framework/Headers short` BioCocoa; \ cd /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Libraries/.; \ rm -f libBioCocoa.so; \ rm -f libBioCocoa.so.2; \ rm -f libBioCocoa.so.2.2.2; \ ln -s `/usr/local/GNUstep/System/Library/Makefiles/relative_path.sh /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Libraries/. /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so short` libBioCocoa.so; \ if test -r "/wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/./libBioCocoa.so.2"; then \ ln -s `/usr/local/GNUstep/System/Library/Makefiles/relative_path.sh /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Libraries/. /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/./libBioCocoa.so.2 short` libBioCocoa.so.2; \ fi; \ ln -s `/usr/local/GNUstep/System/Library/Makefiles/relative_path.sh /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Libraries/. /wrkdirs/usr/ports/biology/biococoa/work/stage//usr/local/GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 short` libBioCocoa.so.2.2.2 ====> 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=2026-01-20T15:40:22+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=7ea9703cc4be' '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 biococoa-2.2.2_9 ===> Building biococoa-2.2.2_9 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for biococoa-2.2.2_9 build of biology/biococoa | biococoa-2.2.2_9 ended at Tue Jan 20 10:40:35 EST 2026 build time: 00:00:14