=> Building biology/biococoa build started at Mon Sep 18 11:03:18 PDT 2017 port directory: /usr/ports/biology/biococoa building for: DragonFly pkgbox64.dragonflybsd.org 4.9-DEVELOPMENT DragonFly v4.9.0.503.g33553-DEVELOPMENT #21: Fri Aug 4 16:51:32 PDT 2017 marino@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/../10//usr/ports/biology/biococoa/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400908 Jail OSVERSION: 400801 ---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_3 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" OBJC="/usr/local/bin/clang40" 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_INSTALLATION_DOMAIN=SYSTEM OBJC="/usr/local/bin/clang40" 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/clang40" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="/usr/local/bin/clang-cpp40" CPPFLAGS="" LDFLAGS=" -L/usr/local/lib" LIBS="" CXX="/usr/local/bin/clang++40" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- GNU_ARCH=x86_64 VERSION=2.2.2 MAJORVERSION=2 LIBVERSION=0.0.1 MAJORLIBVERSION=0 OSREL=4.8 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_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz Installing pkg-1.10.1... Extracting pkg-1.10.1: .......... done ===> biococoa-2.2.2_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of biococoa-2.2.2_3 =========================================================================== =================================================== =========================================================================== =================================================== ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by biococoa-2.2.2_3 for building =========================================================================== =================================================== ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by biococoa-2.2.2_3 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_3 for building ===> Extracting for biococoa-2.2.2_3 => SHA256 Checksum OK for biococoa-2.2.2-src.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for biococoa-2.2.2_3 =========================================================================== =================================================== ===> biococoa-2.2.2_3 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_3 depends on executable: gmake - found ===> Returning to build of biococoa-2.2.2_3 ===> biococoa-2.2.2_3 depends on package: gnustep-make>0 - not found ===> Installing existing package /packages/All/gnustep-make-2.7.0.txz Installing gnustep-make-2.7.0... `-- Installing libobjc2-1.8.1... `-- Extracting libobjc2-1.8.1: .......... done Extracting gnustep-make-2.7.0: ......... done ===> biococoa-2.2.2_3 depends on package: gnustep-make>0 - found ===> Returning to build of biococoa-2.2.2_3 ===> biococoa-2.2.2_3 depends on file: /usr/local/bin/clang40 - not found ===> Installing existing package /packages/All/llvm40-4.0.1_1.txz Installing llvm40-4.0.1_1... `-- Installing libedit-3.1.20170329_2,1... | `-- Installing ncurses-6.0_3... | `-- Extracting ncurses-6.0_3: .......... done `-- Extracting libedit-3.1.20170329_2,1: .......... done `-- Installing libxml2-2.9.4... `-- Extracting libxml2-2.9.4: .......... done `-- Installing perl5-5.24.2... `-- Extracting perl5-5.24.2: .......... done Extracting llvm40-4.0.1_1: .......... 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 perl5-5.24.2: 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_3 depends on file: /usr/local/bin/clang40 - found ===> Returning to build of biococoa-2.2.2_3 ===> biococoa-2.2.2_3 depends on package: gnustep-back>0 - not found ===> Installing existing package /packages/All/gnustep-back-0.25.1.txz Installing gnustep-back-0.25.1... `-- Installing cairo-1.14.8_1,2... | `-- Installing dri2proto-2.8... | `-- Extracting dri2proto-2.8: .... done | `-- Installing fontconfig-2.12.1,1... | | `-- Installing expat-2.2.1... | | `-- Extracting expat-2.2.1: .......... done | | `-- Installing freetype2-2.8... | | `-- Extracting freetype2-2.8: .......... 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 glib-2.50.2_4,1... | | `-- Installing libffi-3.2.1... | | `-- Extracting libffi-3.2.1: .......... done | | `-- Installing libiconv-1.14_10... | | `-- Extracting libiconv-1.14_10: .......... done | | `-- Installing pcre-8.40_1... | | `-- Extracting pcre-8.40_1: .......... done | | `-- Installing python27-2.7.13_7... | | `-- Installing libressl-2.5.5... | | `-- Extracting libressl-2.5.5: .......... done | | `-- Installing readline-7.0.3... | | `-- Extracting readline-7.0.3: .......... done | | `-- Extracting python27-2.7.13_7: .......... done | `-- Extracting glib-2.50.2_4,1: .......... done No schema files found: doing nothing. | `-- Installing glproto-1.4.17... | `-- Extracting glproto-1.4.17: ...... done | `-- Installing libX11-1.6.5,1... | | `-- Installing kbproto-1.0.7... | | `-- Extracting kbproto-1.0.7: .......... done | | `-- Installing libXau-1.0.8_3... | | `-- Installing xproto-7.0.31... | | `-- Extracting xproto-7.0.31: .......... done | | `-- Extracting libXau-1.0.8_3: .......... done | | `-- Installing libXdmcp-1.1.2... | | `-- Extracting libXdmcp-1.1.2: ......... done | | `-- Installing libxcb-1.12_2... | | `-- Installing libpthread-stubs-0.4... | | `-- Extracting libpthread-stubs-0.4: . done | | `-- Extracting libxcb-1.12_2: .......... done | `-- Extracting libX11-1.6.5,1: .......... 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 libXrender-0.9.10... | | `-- Installing renderproto-0.11.1... | | `-- Extracting renderproto-0.11.1: .... done | `-- Extracting libXrender-0.9.10: .......... done | `-- Installing mesa-libs-17.1.5... | | `-- Installing libXdamage-1.1.4_3... | | `-- Installing damageproto-1.2.1... | | `-- Extracting damageproto-1.2.1: .... done | | `-- Installing libXfixes-5.0.3... | | | `-- Installing fixesproto-5.0... | | | `-- Extracting fixesproto-5.0: .... done | | `-- Extracting libXfixes-5.0.3: .......... done | | `-- Extracting libXdamage-1.1.4_3: ...... 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 | | `-- Installing libdrm-2.4.82,1... | | `-- Installing libpciaccess-0.13.5... | | | `-- Installing pciids-20170727... | | | `-- Extracting pciids-20170727: ..... done | | `-- Extracting libpciaccess-0.13.5: ...... done | | `-- Extracting libdrm-2.4.82,1: .......... done | | `-- Installing libelf-0.8.13_2... | | `-- Extracting libelf-0.8.13_2: .......... done | | `-- Installing libxshmfence-1.2_2... | | `-- Extracting libxshmfence-1.2_2: ......... done | `-- Extracting mesa-libs-17.1.5: .......... done | `-- Installing pixman-0.34.0... | `-- Extracting pixman-0.34.0: .......... done | `-- Installing png-1.6.31... | `-- Extracting png-1.6.31: .......... 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 `-- Extracting cairo-1.14.8_1,2: .......... done `-- Installing giflib-5.1.4... `-- Extracting giflib-5.1.4: .......... done `-- Installing gnustep-base-1.25.0... | `-- Installing avahi-app-0.6.31_5... | | `-- Installing dbus-glib-0.108... | | `-- Installing dbus-1.10.16_1... | | | `-- 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-1.10.16_1: ......... done | | `-- Extracting dbus-glib-0.108: .......... done | | `-- Installing gdbm-1.13_1... | | `-- Extracting gdbm-1.13_1: .......... done | | `-- Installing gnome_subr-1.0... | | `-- Extracting gnome_subr-1.0: . done | | `-- Installing gobject-introspection-1.50.0,1... | | `-- Installing python2-2_3... | | `-- Extracting python2-2_3: ...... done | | `-- Extracting gobject-introspection-1.50.0,1: .......... done | | `-- Installing libdaemon-0.14_1... | | `-- Extracting libdaemon-0.14_1: .......... 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 gmp-6.1.2... | `-- Extracting gmp-6.1.2: .......... done | `-- Installing gnutls-3.5.13... | | `-- Installing ca_root_nss-3.32... | | `-- Extracting ca_root_nss-3.32: ........ done | | `-- Installing libidn2-2.0.3... | | `-- Installing libunistring-0.9.7... | | `-- Extracting libunistring-0.9.7: .......... done | | `-- Extracting libidn2-2.0.3: .......... done | | `-- Installing libtasn1-4.12... | | `-- Extracting libtasn1-4.12: .......... done | | `-- Installing nettle-3.3... | | `-- Extracting nettle-3.3: .......... done | | `-- Installing p11-kit-0.23.7... | | `-- Extracting p11-kit-0.23.7: .......... done | | `-- Installing trousers-0.3.14_1... | | `-- Installing tpm-emulator-0.7.4_2... ===> Creating groups. Creating group '_tss' with gid '601'. ===> Creating users Creating user '_tss' with uid '601'. | | `-- Extracting tpm-emulator-0.7.4_2: ......... done ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | `-- Extracting trousers-0.3.14_1: .......... done | `-- Extracting gnutls-3.5.13: .......... done | `-- Installing icu-58.2_3,1... | `-- Extracting icu-58.2_3,1: .......... done | `-- Installing libgcrypt-1.8.0... | | `-- Installing libgpg-error-1.27... | | `-- Extracting libgpg-error-1.27: .......... done | `-- Extracting libgcrypt-1.8.0: .......... done | `-- Installing libxslt-1.1.29_1... | `-- Extracting libxslt-1.1.29_1: .......... done `-- Extracting gnustep-base-1.25.0: .......... done `-- Installing gnustep-gui-0.25.1... | `-- Installing cups-2.2.3... | | `-- 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-2.2.3: .......... done | `-- Installing flite-1.4_1... | `-- Extracting flite-1.4_1: .......... done | `-- Installing jpeg-turbo-1.5.2... | `-- Extracting jpeg-turbo-1.5.2: .......... 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 libsndfile-1.0.28... | | `-- 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-1.0.28: .......... done | `-- Installing tiff-4.0.8... | | `-- Installing jbigkit-2.1_1... | | `-- Extracting jbigkit-2.1_1: .......... done | `-- Extracting tiff-4.0.8: .......... done `-- Extracting gnustep-gui-0.25.1: .......... done `-- Installing libGLU-9.0.0_3... `-- Extracting libGLU-9.0.0_3: ...... done `-- Installing libXcursor-1.1.14_4... `-- Extracting libXcursor-1.1.14_4: .......... done `-- Installing libXft-2.3.2_1... `-- Extracting libXft-2.3.2_1: ......... done `-- Installing libXmu-1.1.2_3,1... `-- Extracting libXmu-1.1.2_3,1: .......... done Extracting gnustep-back-0.25.1: .......... done Message from freetype2-2.8: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). Message from python27-2.7.13_7: =========================================================================== 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 ca_root_nss-3.32: ********************************* 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_3 depends on package: gnustep-back>0 - found ===> Returning to build of biococoa-2.2.2_3 =========================================================================== =================================================== ===> biococoa-2.2.2_3 depends on shared library: libobjc.so.4.6 - found (/usr/local/lib/libobjc.so.4.6) =========================================================================== =================================================== ===> Configuring for biococoa-2.2.2_3 =========================================================================== =================================================== ===> Building for biococoa-2.2.2_3 gmake[1]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2' This is gnustep-make 2.7.0. Type 'gmake print-gnustep-make-help' for help. Running in gnustep-make version 2 strict mode. Making build-headers in subprojects of framework BioCocoa... gmake[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/clang40 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/clang40 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/clang40 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 /usr/local/bin/clang40 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -o ./obj/subproject.o obj/BCAlignment.obj/BCPairwiseAlignment.m.o obj/BCAlignment.obj/BCScoreMatrix.m.o obj/BCAlignment.obj/BCSequenceAlignment.m.o ; clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] 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/clang40 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/clang40 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 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) ^~~~~~~~~ 1 warning generated. /usr/local/bin/clang40 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -o ./obj/subproject.o obj/BCAnalysis.obj/BCMCP.m.o obj/BCAnalysis.obj/BCSuffixArray.m.o ; clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] 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/clang40 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/clang40 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/clang40 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/clang40 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 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 4 warnings generated. /usr/local/bin/clang40 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -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-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] 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/clang40 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/clang40 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/clang40 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/clang40 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 /usr/local/bin/clang40 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -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-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] 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/clang40 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/clang40 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/clang40 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/clang40 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/clang40 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 /usr/local/bin/clang40 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 /usr/local/bin/clang40 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -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-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] 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/clang40 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/clang40 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/clang40 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/clang40 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 /usr/local/bin/clang40 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -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-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] 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/clang40 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/clang40 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/clang40 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/clang40 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 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 3 warnings generated. 3 warnings generated. /usr/local/bin/clang40 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -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-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] 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/clang40 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/clang40 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/clang40 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/clang40 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/clang40 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 BCNucleotideRNA.m:454:43: warning: 'BCNucleotideRNA' may not respond to 'initWithDictionary:' aBase = [[[BCNucleotideRNA alloc] initWithDictionary: aBase] autorelease]; ~~~~~~~~~~~~~~~~~~~~~~~ ^ 1 warning generated. /usr/local/bin/clang40 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 BCNucleotideDNA.m:445:43: warning: 'BCNucleotideDNA' may not respond to 'initWithDictionary:' aBase = [[[BCNucleotideDNA alloc] initWithDictionary: aBase] autorelease]; ~~~~~~~~~~~~~~~~~~~~~~~ ^ 1 warning generated. /usr/local/bin/clang40 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -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-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] 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/clang40 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/clang40 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/clang40 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/clang40 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/clang40 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 /usr/local/bin/clang40 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 /usr/local/bin/clang40 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 /usr/local/bin/clang40 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 /usr/local/bin/clang40 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 /usr/local/bin/clang40 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -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-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] 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/clang40 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/clang40 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/clang40 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 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; ^ 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 2 warnings generated. 2 warnings generated. /usr/local/bin/clang40 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -o ./obj/subproject.o obj/BCUtils.obj/BCDataMatrix.m.o obj/BCUtils.obj/BCUtilData.m.o obj/BCUtils.obj/BCUtilStrings.m.o ; clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] 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/clang40 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/clang40 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 /usr/local/bin/clang40 -nostdlib -Wl,-r -L/usr/local/lib -pthread -fexceptions -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-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] 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 "$classarray" > ./derived_src/BioCocoa-class-list; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "@interface NSFramework_BioCocoa : NSObject" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses;" >> derived_src/NSFramework_BioCocoa.m; \ echo "@end" >> derived_src/NSFramework_BioCocoa.m; \ echo "@implementation NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion { return @\"2\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "static NSString *allClasses[] = {$classlist};" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses { return allClasses; }" >> derived_src/NSFramework_BioCocoa.m;\ echo "@end" >> derived_src/NSFramework_BioCocoa.m /usr/local/bin/clang40 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 \ /usr/local/bin/clang40 -shared -Wl,-soname,libBioCocoa.so.2 -L/usr/local/lib -rdynamic -rdynamic -rdynamic -L/usr/local/lib -pthread -fexceptions -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_3 depends on package: gnustep-back>0 - found =========================================================================== =================================================== ===> Staging for biococoa-2.2.2_3 ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/biology/biococoa/biococoa-2.2.2' This is gnustep-make 2.7.0. Type 'gmake print-gnustep-make-help' for help. Running in gnustep-make version 2 strict mode. Making build-headers in subprojects of framework BioCocoa... gmake[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 (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/2/./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/2/./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/2/./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_3 file sizes/checksums [68]: . done packing files [68]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for biococoa-2.2.2_3 build of biology/biococoa ended at Mon Sep 18 11:07:03 PDT 2017 build time: 00:03:45