=> Building biology/biococoa build started at Mon Mar 13 03:40:15 PDT 2017 port directory: /usr/ports/biology/biococoa building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.1380.gb4315f-DEVELOPMENT #0: Fri Mar 3 17:20:21 PST 2017 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: theraven@FreeBSD.org ident warning: no id keywords in /build/boomdata/data/.m/Release48-default/ref/../08//usr/ports/biology/biococoa/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400713 Jail OSVERSION: 400713 ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/Release48-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=biococoa-2.2.2_2 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/Release48-default/ref/.p/pool MASTERNAME=Release48-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PATH="/usr/local/GNUstep/System/Tools:/usr/local/GNUstep/Local/Tools:/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin" GNUSTEP_MAKEFILES="/usr/local/GNUstep/System/Library/Makefiles" GNUSTEP_SYSTEM_ROOT="/usr/local/GNUstep/System" OBJC="/usr/local/bin/clang38" OBJCFLAGS=" -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include" XDG_DATA_HOME=/wrkdirs/biology/biococoa XDG_CONFIG_HOME=/wrkdirs/biology/biococoa HOME=/wrkdirs/biology/biococoa TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- ADDITIONAL_CFLAGS=" -pipe -O2 -fno-strict-aliasing" ADDITIONAL_CPPFLAGS=" " ADDITIONAL_CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" ADDITIONAL_OBJCCFLAGS=" " ADDITIONAL_OBJCFLAGS=" -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include" ADDITIONAL_LDFLAGS=" -L/usr/local/lib" ADDITIONAL_FLAGS="" ADDITIONAL_INCLUDE_DIRS="" ADDITIONAL_LIB_DIRS="" PATH="/usr/local/GNUstep/System/Tools:/usr/local/GNUstep/Local/Tools:/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin" GNUSTEP_MAKEFILES="/usr/local/GNUstep/System/Library/Makefiles" GNUSTEP_SYSTEM_ROOT="/usr/local/GNUstep/System" GNUSTEP_INSTALLATION_DOMAIN=SYSTEM OBJC="/usr/local/bin/clang38" OBJCFLAGS=" -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include" XDG_DATA_HOME=/wrkdirs/biology/biococoa XDG_CONFIG_HOME=/wrkdirs/biology/biococoa HOME=/wrkdirs/biology/biococoa TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="/usr/local/bin/clang38" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="/usr/local/bin/clang-cpp38" CPPFLAGS="" LDFLAGS=" -L/usr/local/lib" LIBS="" CXX="/usr/local/bin/clang++38" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" 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=x86_64 VERSION=2.2.2 MAJORVERSION=2 LIBVERSION=0.0.1 MAJORLIBVERSION=0 OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " 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--- NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License LGPL21 accepted by the user =========================================================================== =================================================== ===> biococoa-2.2.2_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.4_1.txz Installing pkg-1.9.4_1... Extracting pkg-1.9.4_1: .......... done ===> biococoa-2.2.2_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of biococoa-2.2.2_2 =========================================================================== =================================================== =========================================================================== =================================================== ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by biococoa-2.2.2_2 for building =========================================================================== =================================================== ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by biococoa-2.2.2_2 for building => SHA256 Checksum OK for biococoa-2.2.2-src.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by biococoa-2.2.2_2 for building ===> Extracting for biococoa-2.2.2_2 => SHA256 Checksum OK for biococoa-2.2.2-src.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for biococoa-2.2.2_2 =========================================================================== =================================================== ===> biococoa-2.2.2_2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... `-- Installing indexinfo-0.2.6... `-- Extracting indexinfo-0.2.6: .... done `-- Installing gettext-runtime-0.19.8.1_1... `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_1: .......... done ===> biococoa-2.2.2_2 depends on executable: gmake - found ===> Returning to build of biococoa-2.2.2_2 ===> biococoa-2.2.2_2 depends on package: gnustep-make>0 - not found ===> Installing existing package /packages/All/gnustep-make-2.6.7_2.txz Installing gnustep-make-2.6.7_2... `-- Installing libobjc2-1.8.1... `-- Extracting libobjc2-1.8.1: .......... done Extracting gnustep-make-2.6.7_2: ......... done ===> biococoa-2.2.2_2 depends on package: gnustep-make>0 - found ===> Returning to build of biococoa-2.2.2_2 ===> biococoa-2.2.2_2 depends on file: /usr/local/bin/clang38 - not found ===> Installing existing package /packages/All/clang38-3.8_1.txz Installing clang38-3.8_1... `-- Installing llvm38-3.8.1_5... | `-- Installing python27-2.7.13_1... | | `-- Installing expat-2.2.0_1... | | `-- Extracting expat-2.2.0_1: .......... done | | `-- Installing readline-6.3.8... | | `-- Installing ncurses-6.0_3... | | `-- Extracting ncurses-6.0_3: .......... done | | `-- Extracting readline-6.3.8: .......... done | | `-- Installing libffi-3.2.1... | | `-- Extracting libffi-3.2.1: .......... done | | `-- Installing libressl-2.4.5... | | `-- Extracting libressl-2.4.5: .......... done | `-- Extracting python27-2.7.13_1: .......... done | `-- Installing perl5-5.24.1... | `-- Extracting perl5-5.24.1: .......... done | `-- Installing libedit-3.1.20150325_2,1... | `-- Extracting libedit-3.1.20150325_2,1: .......... done `-- Extracting llvm38-3.8.1_5: .......... done Message from ncurses-6.0_3: ===> NOTICE: The ncurses 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from python27-2.7.13_1: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from perl5-5.24.1: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> biococoa-2.2.2_2 depends on file: /usr/local/bin/clang38 - found ===> Returning to build of biococoa-2.2.2_2 ===> biococoa-2.2.2_2 depends on package: gnustep-back>0 - not found ===> Installing existing package /packages/All/gnustep-back-0.24.1.txz Installing gnustep-back-0.24.1... `-- Installing giflib-5.1.4... `-- Extracting giflib-5.1.4: .......... done `-- Installing libXft-2.3.2_1... | `-- Installing xproto-7.0.31... | `-- Extracting xproto-7.0.31: .......... done | `-- Installing fontconfig-2.12.1,1... | | `-- Installing freetype2-2.6.3... | | `-- Extracting freetype2-2.6.3: .......... done | `-- Extracting fontconfig-2.12.1,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded | `-- Installing libXrender-0.9.10... | | `-- Installing renderproto-0.11.1... | | `-- Extracting renderproto-0.11.1: .... done | | `-- Installing libX11-1.6.4,1... | | `-- Installing kbproto-1.0.7... | | `-- Extracting kbproto-1.0.7: .......... done | | `-- Installing libXdmcp-1.1.2... | | `-- Extracting libXdmcp-1.1.2: ......... done | | `-- Installing libxcb-1.12... | | | `-- Installing libxml2-2.9.4... | | | `-- Extracting libxml2-2.9.4: .......... done | | | `-- Installing libpthread-stubs-0.3_6... | | | `-- Extracting libpthread-stubs-0.3_6: ..... done | | | `-- Installing libXau-1.0.8_3... | | | `-- Extracting libXau-1.0.8_3: .......... done | | `-- Extracting libxcb-1.12: .......... done | | `-- Extracting libX11-1.6.4,1: .......... done | `-- Extracting libXrender-0.9.10: .......... done `-- Extracting libXft-2.3.2_1: ......... done `-- Installing gnustep-base-1.24.8_6... | `-- Installing avahi-app-0.6.31_5... | | `-- Installing gnome_subr-1.0... | | `-- Extracting gnome_subr-1.0: . done | | `-- Installing gobject-introspection-1.46.0... | | `-- Installing glib-2.46.2_4... | | | `-- Installing libiconv-1.14_10... | | | `-- Extracting libiconv-1.14_10: .......... done | | | `-- Installing pcre-8.40... | | | `-- Extracting pcre-8.40: .......... done | | `-- Extracting glib-2.46.2_4: .......... done No schema files found: doing nothing. | | `-- Installing python2-2_3... | | `-- Extracting python2-2_3: ...... done | | `-- Extracting gobject-introspection-1.46.0: .......... done | | `-- Installing gdbm-1.12... | | `-- Extracting gdbm-1.12: .......... done | | `-- Installing libdaemon-0.14_1... | | `-- Extracting libdaemon-0.14_1: .......... done | | `-- Installing dbus-glib-0.104... | | `-- Installing dbus-1.10.14_2... | | | `-- Installing libICE-1.0.9_1,1... | | | `-- Extracting libICE-1.0.9_1,1: .......... done | | | `-- Installing libSM-1.2.2_3,1... | | | `-- Extracting libSM-1.2.2_3,1: .......... done ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. | | `-- Extracting dbus-1.10.14_2: ......... done | | `-- Extracting dbus-glib-0.104: .......... done ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. | `-- Extracting avahi-app-0.6.31_5: .......... done | `-- Installing libxslt-1.1.29_1... | | `-- Installing libgcrypt-1.7.6... | | `-- Installing libgpg-error-1.26... | | `-- Extracting libgpg-error-1.26: .......... done | | `-- Extracting libgcrypt-1.7.6: .......... done | `-- Extracting libxslt-1.1.29_1: .......... done | `-- Installing gmp-5.1.3_3... | `-- Extracting gmp-5.1.3_3: .......... done | `-- Installing icu-58.2,1... | `-- Extracting icu-58.2,1: .......... done | `-- Installing gnutls-3.5.8... | | `-- Installing nettle-3.3... | | `-- Extracting nettle-3.3: .......... done | | `-- Installing ca_root_nss-3.28.1... | | `-- Extracting ca_root_nss-3.28.1: ........ done | | `-- Installing libtasn1-4.10... | | `-- Extracting libtasn1-4.10: .......... done | | `-- Installing trousers-0.3.14_1... | | `-- Installing tpm-emulator-0.7.4_1... ===> Creating groups. Creating group '_tss' with gid '601'. ===> Creating users Creating user '_tss' with uid '601'. | | `-- Extracting tpm-emulator-0.7.4_1: ......... done ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | `-- Extracting trousers-0.3.14_1: .......... done | | `-- Installing p11-kit-0.23.3... | | `-- Extracting p11-kit-0.23.3: .......... done | | `-- Installing libunistring-0.9.7... | | `-- Extracting libunistring-0.9.7: .......... done | | `-- Installing libidn-1.33_1... | | `-- Extracting libidn-1.33_1: .......... done | `-- Extracting gnutls-3.5.8: .......... done `-- Extracting gnustep-base-1.24.8_6: .......... done `-- Installing cairo-1.14.6_1,2... | `-- Installing glproto-1.4.17... | `-- Extracting glproto-1.4.17: ...... done | `-- Installing libEGL-11.2.2... | | `-- Installing libdevq-0.0.4... | | `-- Extracting libdevq-0.0.4: .......... done | | `-- Installing libXdamage-1.1.4_3... | | `-- Installing libXfixes-5.0.3... | | | `-- Installing fixesproto-5.0... | | | `-- Extracting fixesproto-5.0: .... done | | `-- Extracting libXfixes-5.0.3: .......... done | | `-- Installing damageproto-1.2.1... | | `-- Extracting damageproto-1.2.1: .... done | | `-- Extracting libXdamage-1.1.4_3: ...... done | | `-- Installing libxshmfence-1.2... | | `-- Extracting libxshmfence-1.2: ......... done | | `-- Installing libXext-1.3.3_1,1... | | `-- Installing xextproto-7.3.0... | | `-- Extracting xextproto-7.3.0: .......... done | | `-- Extracting libXext-1.3.3_1,1: .......... done | | `-- Installing gbm-11.2.2... | | `-- Installing libglapi-11.2.2... | | | `-- Installing libXvMC-1.0.10... | | | `-- Installing libXv-1.0.11,1... | | | | `-- Installing videoproto-2.3.3... | | | | `-- Extracting videoproto-2.3.3: ......... done | | | `-- Extracting libXv-1.0.11,1: .......... done | | | `-- Extracting libXvMC-1.0.10: .......... done | | | `-- Installing libdrm-2.4.74_1,1... | | | `-- Installing libpciaccess-0.13.4... | | | | `-- Installing pciids-20170128... | | | | `-- Extracting pciids-20170128: ..... done | | | `-- Extracting libpciaccess-0.13.4: ...... done | | | `-- Extracting libdrm-2.4.74_1,1: .......... done | | | `-- Installing libelf-0.8.13_2... | | | `-- Extracting libelf-0.8.13_2: .......... done | | `-- Extracting libglapi-11.2.2: ... done | | `-- Extracting gbm-11.2.2: ..... done | | `-- Installing llvm37-3.7.1_4... | | `-- Extracting llvm37-3.7.1_4: .......... done | `-- Extracting libEGL-11.2.2: .......... done | `-- Installing libGL-11.2.2... | | `-- Installing dri2proto-2.8... | | `-- Extracting dri2proto-2.8: .... done | | `-- Installing libXxf86vm-1.1.4_1... | | `-- Installing xf86vidmodeproto-2.3.1... | | `-- Extracting xf86vidmodeproto-2.3.1: .... done | | `-- Extracting libXxf86vm-1.1.4_1: .......... done | `-- Extracting libGL-11.2.2: .......... done | `-- Installing xcb-util-renderutil-0.3.9_1... | | `-- Installing xcb-util-0.4.0_2,1... | | `-- Extracting xcb-util-0.4.0_2,1: .......... done | `-- Extracting xcb-util-renderutil-0.3.9_1: ...... done | `-- Installing png-1.6.27... | `-- Extracting png-1.6.27: .......... done | `-- Installing pixman-0.34.0... | `-- Extracting pixman-0.34.0: .......... done `-- Extracting cairo-1.14.6_1,2: .......... done `-- Installing gnustep-gui-0.24.1_6... | `-- Installing libsndfile-1.0.27... | | `-- Installing flac-1.3.2... | | `-- Installing libogg-1.3.2_2,4... | | `-- Extracting libogg-1.3.2_2,4: .......... done | | `-- Extracting flac-1.3.2: .......... done | | `-- Installing libvorbis-1.3.5_1,3... | | `-- Extracting libvorbis-1.3.5_1,3: .......... done | `-- Extracting libsndfile-1.0.27: .......... done | `-- Installing libXt-1.1.5,1... | `-- Extracting libXt-1.1.5,1: .......... done | `-- Installing libao-1.2.0_3... | `-- Extracting libao-1.2.0_3: .......... done | `-- Installing cups-2.2.2_1... | | `-- Installing libpaper-1.1.24.4... | | `-- Extracting libpaper-1.1.24.4: .......... done ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. | `-- Extracting cups-2.2.2_1: .......... done | `-- Installing tiff-4.0.7_1... | | `-- Installing jbigkit-2.1_1... | | `-- Extracting jbigkit-2.1_1: .......... done | | `-- Installing jpeg-turbo-1.5.1... | | `-- Extracting jpeg-turbo-1.5.1: .......... done | `-- Extracting tiff-4.0.7_1: .......... done `-- Extracting gnustep-gui-0.24.1_6: .......... done `-- Installing libXcursor-1.1.14_3... `-- Extracting libXcursor-1.1.14_3: .......... done `-- Installing libGLU-9.0.0_2... `-- Extracting libGLU-9.0.0_2: ...... done `-- Installing libXmu-1.1.2_3,1... `-- Extracting libXmu-1.1.2_3,1: .......... done Extracting gnustep-back-0.24.1: .......... done Message from ca_root_nss-3.28.1: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** Message from trousers-0.3.14_1: To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account ===> biococoa-2.2.2_2 depends on package: gnustep-back>0 - found ===> Returning to build of biococoa-2.2.2_2 =========================================================================== =================================================== ===> biococoa-2.2.2_2 depends on shared library: libobjc.so.4.6 - found (/usr/local/lib/libobjc.so.4.6) =========================================================================== =================================================== ===> Configuring for biococoa-2.2.2_2 =========================================================================== =================================================== ===> Building for biococoa-2.2.2_2 gmake[1]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2' This is gnustep-make 2.6.7. Type 'gmake print-gnustep-make-help' for help. Making build-headers in subprojects of framework BioCocoa... gmake[2]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCTools' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... 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[2]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation' Making build-headers for framework BioCocoa... /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[2]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation' cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj Making all in subprojects of subproject BCFoundation... gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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/ /usr/local/bin/clang38 BCPairwiseAlignment.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCAlignment.obj/BCPairwiseAlignment.m.o /usr/local/bin/clang38 BCScoreMatrix.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCAlignment.obj/BCScoreMatrix.m.o /usr/local/bin/clang38 BCSequenceAlignment.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCAlignment.obj/BCSequenceAlignment.m.o In file included from BCSequenceAlignment.m:31: In file included from ./BCSequenceAlignment.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCScoreMatrix.m:31: In file included from ./BCScoreMatrix.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. 2 warnings generated. In file included from BCPairwiseAlignment.m:31: In file included from ./BCSequenceAlignment.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. /usr/local/bin/clang38 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./obj/subproject.o obj/BCAlignment.obj/BCPairwiseAlignment.m.o obj/BCAlignment.obj/BCScoreMatrix.m.o obj/BCAlignment.obj/BCSequenceAlignment.m.o ; clang-3.8: warning: argument unused during compilation: '-pthread' gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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/ /usr/local/bin/clang38 BCMCP.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCAnalysis.obj/BCMCP.m.o /usr/local/bin/clang38 BCSuffixArray.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCAnalysis.obj/BCSuffixArray.m.o In file included from BCMCP.m:31: In file included from ../BCAnalysis/BCMCP.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCSuffixArray.m:40: In file included from ../BCAnalysis/BCSuffixArray.h:45: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ BCSuffixArray.m:644:26: warning: expression which evaluates to zero treated as a null pointer constant of type 'BCSuffixArray *' [-Wnon-literal-null-conversion] if (!aSequence) return NO; ^~ /usr/local/include/objc/runtime.h:195:13: note: expanded from macro 'NO' # define NO ((BOOL)0) ^~~~~~~~~ 2 warnings generated. 3 warnings generated. /usr/local/bin/clang38 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./obj/subproject.o obj/BCAnalysis.obj/BCMCP.m.o obj/BCAnalysis.obj/BCSuffixArray.m.o ; clang-3.8: warning: argument unused during compilation: '-pthread' gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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/ /usr/local/bin/clang38 BCSeries.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCGeneExpression.obj/BCSeries.m.o /usr/local/bin/clang38 BCSample.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCGeneExpression.obj/BCSample.m.o /usr/local/bin/clang38 BCPlatform.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCGeneExpression.obj/BCPlatform.m.o /usr/local/bin/clang38 BCParseSOFT.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCGeneExpression.obj/BCParseSOFT.m.o In file included from BCSample.m:31: In file included from ./BCSample.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCSeries.m:32: In file included from ./BCSeries.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCPlatform.m:31: In file included from ./BCPlatform.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCParseSOFT.m:31: In file included from ./BCParseSOFT.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. 2 warnings generated. BCParseSOFT.m:259:61: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat] 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] 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] 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] NSLog(@"ERROR: sample data columns %d != %d entries\n", [sampleSetColumns count], [f count]); ~~ ^~~~~~~~~ %lu 2 warnings generated. 6 warnings generated. /usr/local/bin/clang38 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./obj/subproject.o obj/BCGeneExpression.obj/BCSeries.m.o obj/BCGeneExpression.obj/BCSample.m.o obj/BCGeneExpression.obj/BCPlatform.m.o obj/BCGeneExpression.obj/BCParseSOFT.m.o ; clang-3.8: warning: argument unused during compilation: '-pthread' gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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/ /usr/local/bin/clang38 BCCodonDNA.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCGeneticCode.obj/BCCodonDNA.m.o /usr/local/bin/clang38 BCCodon.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCGeneticCode.obj/BCCodon.m.o /usr/local/bin/clang38 BCCodonRNA.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCGeneticCode.obj/BCCodonRNA.m.o /usr/local/bin/clang38 BCGeneticCode.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCGeneticCode.obj/BCGeneticCode.m.o In file included from BCGeneticCode.m:33: In file included from ../BCSequence/BCSequence.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCCodonDNA.m:31: In file included from ../BCGeneticCode/BCCodonDNA.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCCodonRNA.m:31: In file included from ../BCGeneticCode/BCCodonRNA.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCCodon.m:31: In file included from ../BCGeneticCode/BCCodon.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. /usr/local/bin/clang38 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./obj/subproject.o obj/BCGeneticCode.obj/BCCodonDNA.m.o obj/BCGeneticCode.obj/BCCodon.m.o obj/BCGeneticCode.obj/BCCodonRNA.m.o obj/BCGeneticCode.obj/BCGeneticCode.m.o ; clang-3.8: warning: argument unused during compilation: '-pthread' gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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/ /usr/local/bin/clang38 BCAtom.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCProteinStructure.obj/BCAtom.m.o /usr/local/bin/clang38 BCProteinStructure.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCProteinStructure.obj/BCProteinStructure.m.o /usr/local/bin/clang38 BCSecondaryStructure.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCProteinStructure.obj/BCSecondaryStructure.m.o /usr/local/bin/clang38 BCChain.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCProteinStructure.obj/BCChain.m.o /usr/local/bin/clang38 BCResidue.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCProteinStructure.obj/BCResidue.m.o In file included from BCSecondaryStructure.m:31: In file included from ../BCProteinStructure/BCSecondaryStructure.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCResidue.m:31: In file included from ../BCProteinStructure/BCResidue.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCProteinStructure.m:31: In file included from ../BCProteinStructure/BCProteinStructure.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. In file included from BCAtom.m:31: In file included from ../BCProteinStructure/BCAtom.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. /usr/local/bin/clang38 BCSequenceStructure.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCProteinStructure.obj/BCSequenceStructure.m.o In file included from BCChain.m:31: In file included from ../BCProteinStructure/BCChain.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. In file included from BCSequenceStructure.m:31: In file included from ../BCProteinStructure/BCSequenceStructure.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. 2 warnings generated. 2 warnings generated. /usr/local/bin/clang38 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./obj/subproject.o obj/BCProteinStructure.obj/BCAtom.m.o obj/BCProteinStructure.obj/BCProteinStructure.m.o obj/BCProteinStructure.obj/BCSecondaryStructure.m.o obj/BCProteinStructure.obj/BCChain.m.o obj/BCProteinStructure.obj/BCResidue.m.o obj/BCProteinStructure.obj/BCSequenceStructure.m.o ; clang-3.8: warning: argument unused during compilation: '-pthread' gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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/ /usr/local/bin/clang38 BCAnnotation.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSequence.obj/BCAnnotation.m.o /usr/local/bin/clang38 BCSequence.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSequence.obj/BCSequence.m.o /usr/local/bin/clang38 BCSequenceArray.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSequence.obj/BCSequenceArray.m.o /usr/local/bin/clang38 BCSequenceCodon.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSequence.obj/BCSequenceCodon.m.o In file included from BCSequenceArray.m:31: In file included from ../BCSequence/BCSequenceArray.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCAnnotation.m:31: In file included from ../BCSequence/BCAnnotation.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCSequence.m:31: In file included from ../BCSequence/BCSequence.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCSequenceCodon.m:31: In file included from ../BCSequence/BCSequenceCodon.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. /usr/local/bin/clang38 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./obj/subproject.o obj/BCSequence.obj/BCAnnotation.m.o obj/BCSequence.obj/BCSequence.m.o obj/BCSequence.obj/BCSequenceArray.m.o obj/BCSequence.obj/BCSequenceCodon.m.o ; clang-3.8: warning: argument unused during compilation: '-pthread' gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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/ /usr/local/bin/clang38 BCSequenceReader.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSequenceIO.obj/BCSequenceReader.m.o /usr/local/bin/clang38 BCSequenceWriter.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSequenceIO.obj/BCSequenceWriter.m.o /usr/local/bin/clang38 BCCachedSequenceFile.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSequenceIO.obj/BCCachedSequenceFile.m.o /usr/local/bin/clang38 BCCachedFastaFile.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSequenceIO.obj/BCCachedFastaFile.m.o In file included from BCCachedSequenceFile.m:31: In file included from ../BCSequenceIO/BCCachedSequenceFile.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCSequenceReader.m:31: In file included from ../BCSequenceIO/BCSequenceReader.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCSequenceWriter.m:31: In file included from ../BCSequenceIO/BCSequenceWriter.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCCachedFastaFile.m:31: In file included from ../BCSequenceIO/BCCachedFastaFile.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ BCSequenceReader.m:167:63: warning: instance method '-initWithRTF:documentAttributes:' not found (return type defaults to 'id') [-Wobjc-method-access] 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 @interface NSAttributedString : NSObject ^ BCSequenceReader.m:798:48: warning: incompatible pointer types sending 'id' to parameter of type 'NSString **' [-Wincompatible-pointer-types] [lineScanner scanUpToString:@" " intoString: nil]; ^~~ /usr/local/include/objc/runtime.h:207:14: note: expanded from macro 'nil' # define nil ((id)_OBJC_NULL_PTR) ^~~~~~~~~~~~~~~~~~~~ /usr/local/GNUstep/System/Library/Headers/Foundation/NSScanner.h:102:68: note: passing argument to parameter 'value' here - (BOOL) scanUpToString: (NSString*)string intoString: (NSString**)value; ^ BCSequenceReader.m:830:12: warning: using 'stringWithString:' with a literal is redundant [-Wobjc-redundant-literal-use] name = [NSString stringWithString: @"alignment"]; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCCachedFastaFile.m:126:71: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] NSLog(@"Attempting to read past end of forward stand: (%lu)\n", aPos); ~~~ ^~~~ %llu BCCachedFastaFile.m:132:16: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if (newPos < 0) { ~~~~~~ ^ ~ BCCachedFastaFile.m:133:72: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] NSLog(@"Attempting to read past end of reverse strand: (%lu)\n", aPos); ~~~ ^~~~ %llu 5 warnings generated. 5 warnings generated. 2 warnings generated. 2 warnings generated. /usr/local/bin/clang38 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./obj/subproject.o obj/BCSequenceIO.obj/BCSequenceReader.m.o obj/BCSequenceIO.obj/BCSequenceWriter.m.o obj/BCSequenceIO.obj/BCCachedSequenceFile.m.o obj/BCSequenceIO.obj/BCCachedFastaFile.m.o ; clang-3.8: warning: argument unused during compilation: '-pthread' gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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/ /usr/local/bin/clang38 BCAminoAcid.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSymbol.obj/BCAminoAcid.m.o /usr/local/bin/clang38 BCNucleotide.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSymbol.obj/BCNucleotide.m.o /usr/local/bin/clang38 BCSymbol.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSymbol.obj/BCSymbol.m.o /usr/local/bin/clang38 BCNucleotideDNA.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSymbol.obj/BCNucleotideDNA.m.o /usr/local/bin/clang38 BCNucleotideRNA.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSymbol.obj/BCNucleotideRNA.m.o In file included from BCNucleotideDNA.m:31: In file included from ../BCSymbol/BCNucleotideDNA.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCNucleotide.m:31: In file included from ../BCSymbol/BCNucleotide.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCAminoAcid.m:31: In file included from ../BCSymbol/BCAminoAcid.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ BCNucleotideDNA.m:445:43: warning: 'BCNucleotideDNA' may not respond to 'initWithDictionary:' aBase = [[[BCNucleotideDNA alloc] initWithDictionary: aBase] autorelease]; ~~~~~~~~~~~~~~~~~~~~~~~ ^ In file included from BCNucleotideRNA.m:31: In file included from ../BCSymbol/BCNucleotideRNA.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. /usr/local/bin/clang38 BCSymbolSet.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCSymbol.obj/BCSymbolSet.m.o BCNucleotideRNA.m:454:43: warning: 'BCNucleotideRNA' may not respond to 'initWithDictionary:' aBase = [[[BCNucleotideRNA alloc] initWithDictionary: aBase] autorelease]; ~~~~~~~~~~~~~~~~~~~~~~~ ^ In file included from BCSymbol.m:31: In file included from ../BCSymbol/BCSymbol.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 3 warnings generated. In file included from BCSymbolSet.m:31: In file included from ../BCSymbol/BCSymbolSet.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. 2 warnings generated. 3 warnings generated. 2 warnings generated. /usr/local/bin/clang38 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./obj/subproject.o obj/BCSymbol.obj/BCAminoAcid.m.o obj/BCSymbol.obj/BCNucleotide.m.o obj/BCSymbol.obj/BCSymbol.m.o obj/BCSymbol.obj/BCNucleotideDNA.m.o obj/BCSymbol.obj/BCNucleotideRNA.m.o obj/BCSymbol.obj/BCSymbolSet.m.o ; clang-3.8: warning: argument unused during compilation: '-pthread' gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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/ /usr/local/bin/clang38 BCSequenceTool.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCTools.obj/BCSequenceTool.m.o /usr/local/bin/clang38 BCToolDigest.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCTools.obj/BCToolDigest.m.o /usr/local/bin/clang38 BCToolHydropathyCalculator.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCTools.obj/BCToolHydropathyCalculator.m.o /usr/local/bin/clang38 BCToolMassCalculator.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCTools.obj/BCToolMassCalculator.m.o /usr/local/bin/clang38 BCToolComplement.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCTools.obj/BCToolComplement.m.o In file included from BCSequenceTool.m:31: In file included from ../BCTools/BCSequenceTool.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCToolComplement.m:31: In file included from ../BCTools/BCToolComplement.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCToolDigest.m:31: In file included from ../BCTools/BCToolDigest.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCToolHydropathyCalculator.m:31: In file included from ../BCTools/BCToolHydropathyCalculator.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. In file included from BCToolMassCalculator.m:31: In file included from ../BCTools/BCToolMassCalculator.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ /usr/local/bin/clang38 BCToolSequenceFinder.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCTools.obj/BCToolSequenceFinder.m.o 2 warnings generated. 2 warnings generated. /usr/local/bin/clang38 BCToolSymbolCounter.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCTools.obj/BCToolSymbolCounter.m.o 2 warnings generated. /usr/local/bin/clang38 BCToolTranslator.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCTools.obj/BCToolTranslator.m.o 2 warnings generated. /usr/local/bin/clang38 BCToolTranslatorDNA.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCTools.obj/BCToolTranslatorDNA.m.o In file included from BCToolSequenceFinder.m:31: In file included from ../BCTools/BCToolSequenceFinder.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCToolSymbolCounter.m:31: In file included from ../BCTools/BCToolSymbolCounter.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCToolTranslator.m:32: In file included from ../BCTools/BCToolTranslator.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCToolTranslatorDNA.m:31: In file included from ../BCTools/BCToolTranslatorDNA.h:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. /usr/local/bin/clang38 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./obj/subproject.o obj/BCTools.obj/BCSequenceTool.m.o obj/BCTools.obj/BCToolDigest.m.o obj/BCTools.obj/BCToolHydropathyCalculator.m.o obj/BCTools.obj/BCToolMassCalculator.m.o obj/BCTools.obj/BCToolComplement.m.o obj/BCTools.obj/BCToolSequenceFinder.m.o obj/BCTools.obj/BCToolSymbolCounter.m.o obj/BCTools.obj/BCToolTranslator.m.o obj/BCTools.obj/BCToolTranslatorDNA.m.o ; clang-3.8: warning: argument unused during compilation: '-pthread' gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCTools' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/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/ /usr/local/bin/clang38 BCDataMatrix.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCUtils.obj/BCDataMatrix.m.o /usr/local/bin/clang38 BCUtilData.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCUtils.obj/BCUtilData.m.o /usr/local/bin/clang38 BCUtilStrings.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -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 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCUtils.obj/BCUtilStrings.m.o In file included from BCDataMatrix.m:32: In file included from ../BCUtils/BCDataMatrix.h:32: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCUtilStrings.m:32: In file included from ../BCUtils/BCUtilStrings.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCUtilData.m:31: In file included from ../BCUtils/BCUtilData.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ BCDataMatrix.m:261:93: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat] 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] NSLog(@"Invalid list format for data matrix, expected 3 items, got %d", [a count]); ~~ ^~~~~~~~~ %lu BCUtilStrings.m:98:23: warning: incompatible pointer types sending 'id' to parameter of type 'int *' [-Wincompatible-pointer-types] if ([scanner scanInt:nil]) ^~~ /usr/local/include/objc/runtime.h:207:14: note: expanded from macro 'nil' # define nil ((id)_OBJC_NULL_PTR) ^~~~~~~~~~~~~~~~~~~~ /usr/local/GNUstep/System/Library/Headers/Foundation/NSScanner.h:94:25: note: passing argument to parameter 'value' here - (BOOL) scanInt: (int*)value; ^ BCUtilStrings.m:100:24: warning: incompatible pointer types sending 'id' to parameter of type 'int *' [-Wincompatible-pointer-types] if ([scanner scanInt:nil]) ^~~ /usr/local/include/objc/runtime.h:207:14: note: expanded from macro 'nil' # define nil ((id)_OBJC_NULL_PTR) ^~~~~~~~~~~~~~~~~~~~ /usr/local/GNUstep/System/Library/Headers/Foundation/NSScanner.h:94:25: note: passing argument to parameter 'value' here - (BOOL) scanInt: (int*)value; ^ 2 warnings generated. 4 warnings generated. 4 warnings generated. /usr/local/bin/clang38 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./obj/subproject.o obj/BCUtils.obj/BCDataMatrix.m.o obj/BCUtils.obj/BCUtilData.m.o obj/BCUtils.obj/BCUtilStrings.m.o ; clang-3.8: warning: argument unused during compilation: '-pthread' gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... cd .; \ /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs ./obj/BCFoundation.obj/ /usr/local/bin/clang38 BCStringDefinitions.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCFoundation.obj/BCStringDefinitions.m.o /usr/local/bin/clang38 BCPreferences.m -c \ -MMD -MP -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -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/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers \ -o obj/BCFoundation.obj/BCPreferences.m.o In file included from BCStringDefinitions.m:31: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ In file included from BCPreferences.m:31: In file included from ./BCPreferences.h:36: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/Foundation.h:30: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. 2 warnings generated. /usr/local/bin/clang38 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./obj/subproject.o obj/BCFoundation.obj/BCStringDefinitions.m.o obj/BCFoundation.obj/BCPreferences.m.o BCAlignment/obj/subproject.o BCAnalysis/obj/subproject.o BCGeneExpression/obj/subproject.o BCGeneticCode/obj/subproject.o BCProteinStructure/obj/subproject.o BCSequence/obj/subproject.o BCSequenceIO/obj/subproject.o BCSymbol/obj/subproject.o BCTools/obj/subproject.o BCUtils/obj/subproject.o ; clang-3.8: warning: argument unused during compilation: '-pthread' gmake[2]: Leaving directory '/wrkdirs/biology/biococoa/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/subproject.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;}'`; \ 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 "$classarray" > ./derived_src/BioCocoa-class-list; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "@interface NSFramework_BioCocoa : NSObject" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses;" >> derived_src/NSFramework_BioCocoa.m; \ echo "@end" >> derived_src/NSFramework_BioCocoa.m; \ echo "@implementation NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv { return nil; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath { return @\"/usr/local/GNUstep/System/Library/Frameworks\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion { return @\"2\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "static NSString *allClasses[] = {$classlist};" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses { return allClasses; }" >> derived_src/NSFramework_BioCocoa.m;\ echo "@end" >> derived_src/NSFramework_BioCocoa.m /usr/local/bin/clang38 derived_src/NSFramework_BioCocoa.m -c -MMD -MP -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_LIBRARY=1 -DGNU_RUNTIME=1 -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions -D_NATIVE_OBJC_EXCEPTIONS -fobjc-nonfragile-abi -D_NONFRAGILE_ABI -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -Wall -DGSWARN -DGSDIAGNOSE -Wno-import -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fgnu-runtime -pipe -O2 -fno-strict-aliasing -Wno-import -I/usr/local/include -fconstant-string-class=NSConstantString -I./derived_src -I. -I/wrkdirs/biology/biococoa/GNUstep/Library/Headers -I/usr/local/GNUstep/Local/Library/Headers -I/usr/local/GNUstep/System/Library/Headers -o obj/BioCocoa.obj/NSFramework_BioCocoa.o In file included from derived_src/NSFramework_BioCocoa.m:1: In file included from /usr/local/GNUstep/System/Library/Headers/Foundation/NSString.h:87: In file included from /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSVersionMacros.h:219: /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:416:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __strong ^ /usr/local/GNUstep/System/Library/Headers/GNUstepBase/GSConfig.h:417:13: warning: ignoring redefinition of Objective-C qualifier macro [-Wobjc-macro-redefinition] # define __weak ^ 2 warnings generated. \ /usr/local/bin/clang38 -shared -Wl,-soname,libBioCocoa.so.2 -L/usr/local/lib -rdynamic -rdynamic -rdynamic -L/usr/local/lib -pthread -fexceptions -fobjc-nonfragile-abi -o ./BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 obj/BioCocoa.obj/NSFramework_BioCocoa.o BCFoundation/obj/subproject.o -L/wrkdirs/biology/biococoa/GNUstep/Library/Libraries -L/usr/local/GNUstep/Local/Library/Libraries -L/usr/local/GNUstep/System/Library/Libraries && (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) \ BCFoundation/obj/subproject.o:BCSuffixArray.m:function _i_BCSuffixArray__constructFromSequenceArray_strand_: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() BCFoundation/obj/subproject.o:BCSuffixArray.m:function _i_BCSuffixArray__constructFromSequenceArray_strand_: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() 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 gmake[1]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2' =========================================================================== =================================================== ===> biococoa-2.2.2_2 depends on package: gnustep-back>0 - found =========================================================================== =================================================== ===> Staging for biococoa-2.2.2_2 ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2' This is gnustep-make 2.6.7. Type 'gmake print-gnustep-make-help' for help. Making build-headers in subprojects of framework BioCocoa... gmake[2]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... gmake[4]: Nothing to be done for 'internal-subproject-build-headers'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... gmake[4]: Nothing to be done for 'internal-subproject-build-headers'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... gmake[4]: Nothing to be done for 'internal-subproject-build-headers'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... gmake[4]: Nothing to be done for 'internal-subproject-build-headers'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... gmake[4]: Nothing to be done for 'internal-subproject-build-headers'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... gmake[4]: Nothing to be done for 'internal-subproject-build-headers'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... gmake[4]: Nothing to be done for 'internal-subproject-build-headers'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... gmake[4]: Nothing to be done for 'internal-subproject-build-headers'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCTools' Making build-headers for subproject BCTools... gmake[4]: Nothing to be done for 'internal-subproject-build-headers'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCTools' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... gmake[4]: Nothing to be done for 'internal-subproject-build-headers'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... gmake[3]: Nothing to be done for 'internal-subproject-build-headers'. gmake[2]: Leaving directory '/wrkdirs/biology/biococoa/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[2]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation' Making all in subprojects of subproject BCFoundation... gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' Making all for subproject BCAlignment... gmake[5]: Nothing to be done for 'internal-subproject-compile'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' Making all for subproject BCAnalysis... gmake[5]: Nothing to be done for 'internal-subproject-compile'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making all for subproject BCGeneExpression... gmake[5]: Nothing to be done for 'internal-subproject-compile'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making all for subproject BCGeneticCode... gmake[5]: Nothing to be done for 'internal-subproject-compile'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making all for subproject BCProteinStructure... gmake[5]: Nothing to be done for 'internal-subproject-compile'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' Making all for subproject BCSequence... gmake[5]: Nothing to be done for 'internal-subproject-compile'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making all for subproject BCSequenceIO... gmake[5]: Nothing to be done for 'internal-subproject-compile'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' Making all for subproject BCSymbol... gmake[5]: Nothing to be done for 'internal-subproject-compile'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCTools' Making all for subproject BCTools... gmake[5]: Nothing to be done for 'internal-subproject-compile'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCTools' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCUtils... gmake[5]: Nothing to be done for 'internal-subproject-compile'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... gmake[4]: Nothing to be done for 'internal-subproject-compile'. gmake[2]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation' Making all for framework BioCocoa... gmake[3]: 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[2]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation' Making install in subprojects of subproject BCFoundation... gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' Making install for subproject BCAlignment... gmake[4]: Nothing to be done for 'internal-subproject-install'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' Making install for subproject BCAnalysis... gmake[4]: Nothing to be done for 'internal-subproject-install'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making install for subproject BCGeneExpression... gmake[4]: Nothing to be done for 'internal-subproject-install'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making install for subproject BCGeneticCode... gmake[4]: Nothing to be done for 'internal-subproject-install'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making install for subproject BCProteinStructure... gmake[4]: Nothing to be done for 'internal-subproject-install'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' Making install for subproject BCSequence... gmake[4]: Nothing to be done for 'internal-subproject-install'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making install for subproject BCSequenceIO... gmake[4]: Nothing to be done for 'internal-subproject-install'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' Making install for subproject BCSymbol... gmake[4]: Nothing to be done for 'internal-subproject-install'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCTools' Making install for subproject BCTools... gmake[4]: Nothing to be done for 'internal-subproject-install'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCTools' gmake[3]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCUtils... gmake[4]: Nothing to be done for 'internal-subproject-install'. gmake[3]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCFoundation... gmake[3]: Nothing to be done for 'internal-subproject-install'. gmake[2]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2/BCFoundation' Making install for framework BioCocoa... /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Frameworks /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Libraries/. /usr/local/GNUstep/System/Library/Makefiles/mkinstalldirs /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Headers rm -rf /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Frameworks/BioCocoa.framework; \ (cd .; tar cfX - /usr/local/GNUstep/System/Library/Makefiles/tar-exclude-list BioCocoa.framework) | (cd /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Frameworks; tar xf -) cd /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Headers; \ rm -f BioCocoa; \ ln -s `/usr/local/GNUstep/System/Library/Makefiles/relative_path.sh /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Headers /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Frameworks/BioCocoa.framework/Headers short` BioCocoa; \ cd /wrkdirs/biology/biococoa/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/biology/biococoa/stage//usr/local/GNUstep/System/Library/Libraries/. /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so short` libBioCocoa.so; \ if test -r "/wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2"; then \ ln -s `/usr/local/GNUstep/System/Library/Makefiles/relative_path.sh /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Libraries/. /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2 short` libBioCocoa.so.2; \ fi; \ ln -s `/usr/local/GNUstep/System/Library/Makefiles/relative_path.sh /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Libraries/. /wrkdirs/biology/biococoa/stage//usr/local/GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2.2.2 short` libBioCocoa.so.2.2.2 gmake[1]: Leaving directory '/wrkdirs/biology/biococoa/biococoa-2.2.2' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for biococoa-2.2.2_2 file sizes/checksums [68]: . done packing files [68]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for biococoa-2.2.2_2 build of biology/biococoa ended at Mon Mar 13 03:42:06 PDT 2017 build time: 00:01:51