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Maintainer: bacon4...@gmail.com Last committer: m...@freebsd.org Ident: $FreeBSD: head/science/afni/Makefile 412349 2016-04-01 14:25:16Z mat $ Log URL: http://beefy2.nyi.freebsd.org/data/93amd64-default/417508/logs/afni-2015.11.13.log Build URL: http://beefy2.nyi.freebsd.org/build.html?mastername=93amd64-default&build=417508 Log: ====>> Building science/afni build started at Sun Jun 26 10:49:56 UTC 2016 port directory: /usr/ports/science/afni building for: FreeBSD 93amd64-default-job-11 9.3-RELEASE-p44 FreeBSD 9.3-RELEASE-p44 amd64 maintained by: bacon4...@gmail.com Makefile ident: $FreeBSD: head/science/afni/Makefile 412349 2016-04-01 14:25:16Z mat $ Poudriere version: 3.1.14 Host OSVERSION: 1100109 Jail OSVERSION: 903000 ---Begin Environment--- SHELL=/bin/csh UNAME_v=FreeBSD 9.3-RELEASE-p44 UNAME_r=9.3-RELEASE-p44 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=amd64 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/93amd64-default/ref UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=afni-2015.11.13 OSREL=9.3 _OSRELEASE=9.3-RELEASE-p44 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=24 PWD=/usr/local/poudriere/data/.m/93amd64-default/ref/.p/pool HAVE_COMPAT_IA32_KERN=YES LINUX_OSRELEASE=2.6.32 MASTERNAME=93amd64-default SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=903000 ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/science/afni/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/afni/work HOME=/wrkdirs/usr/ports/science/afni/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- CC="cc" R_SHARE_DIR=/usr/local/lib/R/share MOTIFLIB="-L/usr/local/lib -lXm -lXp" XDG_DATA_HOME=/wrkdirs/usr/ports/science/afni/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/afni/work HOME=/wrkdirs/usr/ports/science/afni/work TMPDIR="/tmp" NO_PIE=yes WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd9 PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_VER=2.7 PYTHON_VERSION=python2.7 GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" OSREL=9.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.20.3 PERL_VER=5.20 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.20 DOCSDIR="share/doc/afni" EXAMPLESDIR="share/examples/afni" DATADIR="share/afni" WWWDIR="www/afni" ETCDIR="etc/afni" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/afni DOCSDIR=/usr/local/share/doc/afni EXAMPLESDIR=/usr/local/share/examples/afni WWWDIR=/usr/local/www/afni ETCDIR=/usr/local/etc/afni --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> afni-2015.11.13 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.6.txz [93amd64-default-job-11] Installing pkg-1.8.6... [93amd64-default-job-11] Extracting pkg-1.8.6: .......... done ===> afni-2015.11.13 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of afni-2015.11.13 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by afni-2015.11.13 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by afni-2015.11.13 for building => SHA256 Checksum OK for afni-2015.11.13.tar.xz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by afni-2015.11.13 for building ===> Extracting for afni-2015.11.13 => SHA256 Checksum OK for afni-2015.11.13.tar.xz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for afni-2015.11.13 ===> Applying FreeBSD patches for afni-2015.11.13 /usr/bin/sed -i.bak -e "s|-lglib|-lglib-2.0|g" /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/SUMA/SUMA_Makefile /usr/bin/sed -i.bak -e "s|/bin/python|/usr/local/bin/python2.7|g" /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/python_scripts/lib_fat_Rfactor.py /usr/bin/sed -i.bak -e 's|os\.path\.dirname(sys\.argv\[0\])|"/usr/local/libexec"|g' /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/pkundu/meica.py /usr/bin/sed -i.bak -e 's|g_info|afni_g_info|g' /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/rickr/Dimon.c /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/rickr/Dimon1.c /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/afni_history_rickr.c /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/mri_dicom_stuff.c /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/mri_process_siemens.c /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/mri_read_dicom.c /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/to3d.c /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/mri_dicom_stuff.h =========================================================================== =======================<phase: build-depends >============================ ===> afni-2015.11.13 depends on executable: gm4 - not found ===> Installing existing package /packages/All/m4-1.4.17_1,1.txz [93amd64-default-job-11] Installing m4-1.4.17_1,1... [93amd64-default-job-11] `-- Installing indexinfo-0.2.4... [93amd64-default-job-11] `-- Extracting indexinfo-0.2.4: .... done [93amd64-default-job-11] Extracting m4-1.4.17_1,1: .......... done ===> afni-2015.11.13 depends on executable: gm4 - found ===> Returning to build of afni-2015.11.13 ===> afni-2015.11.13 depends on executable: msgfmt - not found ===> Installing existing package /packages/All/gettext-tools-0.19.8.1.txz [93amd64-default-job-11] Installing gettext-tools-0.19.8.1... [93amd64-default-job-11] `-- Installing libiconv-1.14_9... [93amd64-default-job-11] `-- Extracting libiconv-1.14_9: .......... done [93amd64-default-job-11] `-- Installing gettext-runtime-0.19.8.1... [93amd64-default-job-11] `-- Extracting gettext-runtime-0.19.8.1: .......... done [93amd64-default-job-11] Extracting gettext-tools-0.19.8.1: .......... done ===> afni-2015.11.13 depends on executable: msgfmt - found ===> Returning to build of afni-2015.11.13 ===> afni-2015.11.13 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1.txz [93amd64-default-job-11] Installing gmake-4.2.1... [93amd64-default-job-11] Extracting gmake-4.2.1: .......... done ===> afni-2015.11.13 depends on executable: gmake - found ===> Returning to build of afni-2015.11.13 ===> afni-2015.11.13 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.11_3.txz [93amd64-default-job-11] Installing python27-2.7.11_3... [93amd64-default-job-11] `-- Installing libffi-3.2.1... [93amd64-default-job-11] `-- Extracting libffi-3.2.1: .......... done [93amd64-default-job-11] Extracting python27-2.7.11_3: .......... done Message from python27-2.7.11_3: =========================================================================== 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 <snip> [93amd64-default-job-11] | | `-- Installing png-1.6.21... [93amd64-default-job-11] | | `-- Extracting png-1.6.21: .......... done [93amd64-default-job-11] | | `-- Installing libGL-11.2.2... [93amd64-default-job-11] | | | `-- Installing libXxf86vm-1.1.4_1... [93amd64-default-job-11] | | | `-- Installing xf86vidmodeproto-2.3.1... [93amd64-default-job-11] | | | `-- Extracting xf86vidmodeproto-2.3.1: .... done [93amd64-default-job-11] | | | `-- Extracting libXxf86vm-1.1.4_1: .......... done [93amd64-default-job-11] | | `-- Extracting libGL-11.2.2: .......... done [93amd64-default-job-11] | | `-- Installing pixman-0.34.0... [93amd64-default-job-11] | | `-- Extracting pixman-0.34.0: .......... done [93amd64-default-job-11] | | `-- Installing xcb-util-renderutil-0.3.9_1... [93amd64-default-job-11] | | | `-- Installing xcb-util-0.4.0_1,1... [93amd64-default-job-11] | | | `-- Extracting xcb-util-0.4.0_1,1: .......... done [93amd64-default-job-11] | | `-- Extracting xcb-util-renderutil-0.3.9_1: ...... done [93amd64-default-job-11] | | `-- Installing glib-2.46.2... [93amd64-default-job-11] | | | `-- Installing pcre-8.38_1... [93amd64-default-job-11] | | | `-- Extracting pcre-8.38_1: .......... done [93amd64-default-job-11] | | `-- Extracting glib-2.46.2: .......... done No schema files found: doing nothing. [93amd64-default-job-11] | | `-- Extracting cairo-1.14.6,2: .......... done [93amd64-default-job-11] | | `-- Installing icu-55.1... [93amd64-default-job-11] | | `-- Extracting icu-55.1: .......... done [93amd64-default-job-11] | | `-- Installing graphite2-1.3.8... [93amd64-default-job-11] | | `-- Extracting graphite2-1.3.8: .......... done [93amd64-default-job-11] | `-- Extracting harfbuzz-1.2.3: .......... done [93amd64-default-job-11] | `-- Installing xorg-fonts-truetype-7.7_1... [93amd64-default-job-11] | | `-- Installing font-misc-meltho-1.0.3_3... [93amd64-default-job-11] | | `-- Installing mkfontdir-1.0.7... [93amd64-default-job-11] | | | `-- Installing mkfontscale-1.1.2... [93amd64-default-job-11] | | | `-- Installing libfontenc-1.1.3... [93amd64-default-job-11] | | | `-- Extracting libfontenc-1.1.3: ...... done [93amd64-default-job-11] | | | `-- Extracting mkfontscale-1.1.2: .. done [93amd64-default-job-11] | | `-- Extracting mkfontdir-1.0.7: .. done [93amd64-default-job-11] | | `-- Extracting font-misc-meltho-1.0.3_3: .......... done [93amd64-default-job-11] | | `-- Installing font-bh-ttf-1.0.3_3... [93amd64-default-job-11] | | `-- Extracting font-bh-ttf-1.0.3_3: .......... done [93amd64-default-job-11] | | `-- Installing font-misc-ethiopic-1.0.3_3... [93amd64-default-job-11] | | `-- Extracting font-misc-ethiopic-1.0.3_3: ... done [93amd64-default-job-11] | | `-- Installing dejavu-2.35... [93amd64-default-job-11] | | `-- Extracting dejavu-2.35: .......... done [93amd64-default-job-11] `-- Extracting pango-1.38.0_1: .......... done [93amd64-default-job-11] `-- Installing gsed-4.2.2... [93amd64-default-job-11] `-- Extracting gsed-4.2.2: .......... done [93amd64-default-job-11] `-- Installing openblas-0.2.18_1,1... [93amd64-default-job-11] `-- Extracting openblas-0.2.18_1,1: ......... done [93amd64-default-job-11] `-- Installing curl-7.49.0... [93amd64-default-job-11] | `-- Installing ca_root_nss-3.25... [93amd64-default-job-11] | `-- Extracting ca_root_nss-3.25: ....... done [93amd64-default-job-11] `-- Extracting curl-7.49.0: .......... done [93amd64-default-job-11] `-- Installing ghostscript9-agpl-base-9.16_5... [93amd64-default-job-11] | `-- Installing jbig2dec-0.13... [93amd64-default-job-11] | `-- Extracting jbig2dec-0.13: .......... done [93amd64-default-job-11] | `-- Installing libpaper-1.1.24.4... [93amd64-default-job-11] | `-- Extracting libpaper-1.1.24.4: .......... done [93amd64-default-job-11] | `-- Installing svgalib-1.4.3_7... [93amd64-default-job-11] | `-- Extracting svgalib-1.4.3_7: .......... done [93amd64-default-job-11] | `-- Installing libidn-1.31... [93amd64-default-job-11] | `-- Extracting libidn-1.31: .......... done [93amd64-default-job-11] | `-- Installing cups-2.1.4... [93amd64-default-job-11] | | `-- Installing avahi-app-0.6.31_5... [93amd64-default-job-11] | | `-- Installing gnome_subr-1.0... [93amd64-default-job-11] | | `-- Extracting gnome_subr-1.0: . done [93amd64-default-job-11] | | `-- Installing gobject-introspection-1.46.0... [93amd64-default-job-11] | | | `-- Installing python2-2_3... [93amd64-default-job-11] | | | `-- Extracting python2-2_3: ...... done [93amd64-default-job-11] | | `-- Extracting gobject-introspection-1.46.0: .......... done [93amd64-default-job-11] | | `-- Installing gdbm-1.12... [93amd64-default-job-11] | | `-- Extracting gdbm-1.12: .......... done [93amd64-default-job-11] | | `-- Installing libdaemon-0.14_1... [93amd64-default-job-11] | | `-- Extracting libdaemon-0.14_1: .......... done [93amd64-default-job-11] | | `-- Installing dbus-glib-0.104... [93amd64-default-job-11] | | | `-- Installing dbus-1.8.20... ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. [93amd64-default-job-11] | | | `-- Extracting dbus-1.8.20: ......... done [93amd64-default-job-11] | | `-- Extracting dbus-glib-0.104: .......... done ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. [93amd64-default-job-11] | | `-- Extracting avahi-app-0.6.31_5: .......... done [93amd64-default-job-11] | | `-- Installing gnutls-3.4.13... [93amd64-default-job-11] | | `-- Installing nettle-3.2... [93amd64-default-job-11] | | `-- Extracting nettle-3.2: .......... done [93amd64-default-job-11] | | `-- Installing libtasn1-4.8... [93amd64-default-job-11] | | `-- Extracting libtasn1-4.8: .......... done [93amd64-default-job-11] | | `-- Installing trousers-0.3.13... [93amd64-default-job-11] | | | `-- Installing tpm-emulator-0.7.4_1... ===> Creating groups. Creating group '_tss' with gid '601'. ===> Creating users Creating user '_tss' with uid '601'. [93amd64-default-job-11] | | | `-- Extracting tpm-emulator-0.7.4_1: ......... done ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. [93amd64-default-job-11] | | `-- Extracting trousers-0.3.13: .......... done [93amd64-default-job-11] | | `-- Installing p11-kit-0.23.2... [93amd64-default-job-11] | | `-- Extracting p11-kit-0.23.2: .......... done [93amd64-default-job-11] | | `-- Extracting gnutls-3.4.13: .......... done ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. [93amd64-default-job-11] | `-- Extracting cups-2.1.4: .......... done [93amd64-default-job-11] | `-- Installing lcms2-2.7_2... [93amd64-default-job-11] | | `-- Installing tiff-4.0.6_1... [93amd64-default-job-11] | | `-- Installing jbigkit-2.1_1... [93amd64-default-job-11] | | `-- Extracting jbigkit-2.1_1: .......... done [93amd64-default-job-11] | | `-- Extracting tiff-4.0.6_1: .......... done [93amd64-default-job-11] | `-- Extracting lcms2-2.7_2: .......... done [93amd64-default-job-11] | `-- Installing gsfonts-8.11_6... [93amd64-default-job-11] | `-- Extracting gsfonts-8.11_6: .......... done [93amd64-default-job-11] `-- Extracting ghostscript9-agpl-base-9.16_5: .......... done [93amd64-default-job-11] `-- Installing tk86-8.6.5... [93amd64-default-job-11] | `-- Installing tcl86-8.6.5_1... [93amd64-default-job-11] | `-- Extracting tcl86-8.6.5_1: .......... done [93amd64-default-job-11] | `-- Installing libXScrnSaver-1.2.2_3... [93amd64-default-job-11] | | `-- Installing scrnsaverproto-1.2.2... [93amd64-default-job-11] | | `-- Extracting scrnsaverproto-1.2.2: ... done [93amd64-default-job-11] | `-- Extracting libXScrnSaver-1.2.2_3: .......... done [93amd64-default-job-11] `-- Extracting tk86-8.6.5: .......... done [93amd64-default-job-11] Extracting R-3.3.0_1: .......... done ldconfig: warning: /usr/local/lib/R/lib: No such file or directory Message from gcc-4.8.5_2: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc48 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from dejavu-2.35: Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. Message from ca_root_nss-3.25: ********************************* 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-0.3.13: 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 groupadd _tss -m your_account Message from ghostscript9-agpl-base-9.16_5: Note: in order to use the script "dvipdf", dvips must be installed. This program is provided by another package print/tex-dvipsk. FAPIfontmap and FAPIcidfmap in /usr/local/share/ghostscript/9.16/Resource/Init have to be configured if you want to use FAPI feature. ===> afni-2015.11.13 depends on shared library: libR.so - not found *** [lib-depends] Error code 1 Stop in /usr/ports/science/afni. _______________________________________________ freebsd-pkg-fallout@freebsd.org mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "freebsd-pkg-fallout-unsubscr...@freebsd.org"
