Date: Sun, 4 Dec 2016 05:30:25 GMT From: pkg-fallout@FreeBSD.org To: bacon4000@gmail.com Cc: pkg-fallout@FreeBSD.org Subject: [package - 93i386-default][science/afni] Failed for afni-2015.11.13_1 in package/timeout Message-ID: <201612040530.uB45UPHr001354@beefy3.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: bacon4000@gmail.com Last committer: jrm@FreeBSD.org Ident: $FreeBSD: head/science/afni/Makefile 427397 2016-11-29 21:15:41Z jrm $ Log URL: http://beefy3.nyi.freebsd.org/data/93i386-default/427588/logs/afni-2015.11.13_1.log Build URL: http://beefy3.nyi.freebsd.org/build.html?mastername=93i386-default&build=427588 Log: ====>> Building science/afni build started at Sun Dec 4 04:03:53 UTC 2016 port directory: /usr/ports/science/afni building for: FreeBSD 93i386-default-job-02 9.3-RELEASE-p50 FreeBSD 9.3-RELEASE-p50 i386 maintained by: bacon4000@gmail.com Makefile ident: $FreeBSD: head/science/afni/Makefile 427397 2016-11-29 21:15:41Z jrm $ Poudriere version: 3.1.14 Host OSVERSION: 1200010 Jail OSVERSION: 903000 Job Id: 02 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 UNAME_v=FreeBSD 9.3-RELEASE-p50 UNAME_r=9.3-RELEASE-p50 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=i386 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/93i386-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_1 OSREL=9.3 _OSRELEASE=9.3-RELEASE-p50 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=24 PWD=/usr/local/poudriere/data/.m/93i386-default/ref/.p/pool MASTERNAME=93i386-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 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -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=5.24.1 PERL_VER=5.24 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/5.24 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 MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /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_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.3.txz [93i386-default-job-02] Installing pkg-1.9.3... [93i386-default-job-02] Extracting pkg-1.9.3: .......... done ===> afni-2015.11.13_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of afni-2015.11.13_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by afni-2015.11.13_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by afni-2015.11.13_1 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_1 for building ===> Extracting for afni-2015.11.13_1 => SHA256 Checksum OK for afni-2015.11.13.tar.xz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for afni-2015.11.13_1 ===> Applying FreeBSD patches for afni-2015.11.13_1 /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_1 depends on executable: gm4 - not found ===> Installing existing package /packages/All/m4-1.4.17_1,1.txz [93i386-default-job-02] Installing m4-1.4.17_1,1... [93i386-default-job-02] `-- Installing indexinfo-0.2.6... [93i386-default-job-02] `-- Extracting indexinfo-0.2.6: .... done [93i386-default-job-02] Extracting m4-1.4.17_1,1: .......... done ===> afni-2015.11.13_1 depends on executable: gm4 - found ===> Returning to build of afni-2015.11.13_1 ===> afni-2015.11.13_1 depends on executable: R - not found ===> Installing existing package /packages/All/R-3.3.2_6.txz [93i386-default-job-02] Installing R-3.3.2_6... [93i386-default-job-02] `-- Installing libXt-1.1.5,1... [93i386-default-job-02] | `-- Installing xproto-7.0.31... [93i386-default-job-02] | `-- Extracting xproto-7.0.31: .......... done [93i386-default-job-02] | `-- Installing libSM-1.2.2_3,1... [93i386-default-job-02] | | `-- Installing libICE-1.0.9_1,1... [93i386-default-job-02] | | `-- Extracting libICE-1.0.9_1,1: .......... done [93i386-default-job-02] | `-- Extracting libSM-1.2.2_3,1: .......... done [93i386-default-job-02] | `-- Installing libX11-1.6.4,1... [93i386-default-job-02] | | `-- Installing kbproto-1.0.7... [93i386-default-job-02] | | `-- Extracting kbproto-1.0.7: .......... done [93i386-default-job-02] | | `-- Installing libXdmcp-1.1.2... [93i386-default-job-02] | | `-- Extracting libXdmcp-1.1.2: ......... done [93i386-default-job-02] | | `-- Installing libxcb-1.12... [93i386-default-job-02] | | `-- Installing libxml2-2.9.4... [93i386-default-job-02] | | | `-- Installing libiconv-1.14_9... [93i386-default-job-02] | | | `-- Extracting libiconv-1.14_9: .......... done [93i386-default-job-02] | | `-- Extracting libxml2-2.9.4: .......... done [93i386-default-job-02] | | `-- Installing libpthread-stubs-0.3_6... [93i386-default-job-02] | | `-- Extracting libpthread-stubs-0.3_6: ..... done [93i386-default-job-02] | | `-- Installing libXau-1.0.8_3... [93i386-default-job-02] | | `-- Extracting libXau-1.0.8_3: .......... done [93i386-default-job-02] | | `-- Extracting libxcb-1.12: .......... done [93i386-default-job-02] | `-- Extracting libX11-1.6.4,1: .......... done [93i386-default-job-02] `-- Extracting libXt-1.1.5,1: .......... done [93i386-default-job-02] `-- Installing pango-1.38.0_1... <snip> libSUMA.a libglut.a libply.a -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat /bin/rm -f SurfDist cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o SurfDist ../xutil.o ../LiteClue.o ../parser.o ../parser_int.o \ SUMA_SurfDist.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ libSUMA.a libglut.a libply.a -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat /bin/rm -f SpharmReco cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o SpharmReco ../afni_warp.o ../afni_slice_byte.o ../afni_slice_short.o ../afni_slice_float.o ../afni_slice_complex.o ../afni_slice_rgbyte.o ../xutil.o ../LiteClue.o SUMA_SpharmReco.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ ../parser.o ../parser_int.o \ libSUMA.a libglut.a libply.a -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat /bin/rm -f SpharmDeco cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o SpharmDeco ../afni_warp.o ../afni_slice_byte.o ../afni_slice_short.o ../afni_slice_float.o ../afni_slice_complex.o ../afni_slice_rgbyte.o ../xutil.o ../LiteClue.o SUMA_SpharmDeco.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ ../parser.o ../parser_int.o \ libSUMA.a libglut.a libply.a -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat /bin/rm -f prompt_user cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o prompt_user ../afni_warp.o ../afni_slice_byte.o ../afni_slice_short.o ../afni_slice_float.o ../afni_slice_complex.o ../afni_slice_rgbyte.o ../xutil.o ../LiteClue.o SUMA_prompt_user.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ ../parser.o ../parser_int.o MarchingCubes/debug/MarchingCubes.o \ libSUMA.a libglut.a libply.a -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat /bin/rm -f SurfRetinoMap cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o SurfRetinoMap ../afni_warp.o ../afni_slice_byte.o ../afni_slice_short.o ../afni_slice_float.o ../afni_slice_complex.o ../afni_slice_rgbyte.o \ ../xutil.o ../LiteClue.o SUMA_SurfRetinoMap.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ ../parser.o ../parser_int.o MarchingCubes/debug/MarchingCubes.o \ libSUMA.a libglut.a libply.a -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat /bin/rm -f ParseName cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o ParseName ../xutil.o ../LiteClue.o ../parser.o ../parser_int.o \ SUMA_ParseName.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ libSUMA.a libglut.a libply.a -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat /bin/rm -f 3dGenPriors cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o 3dGenPriors ../afni_warp.o ../afni_slice_byte.o ../afni_slice_short.o ../afni_slice_float.o ../afni_slice_complex.o ../afni_slice_rgbyte.o \ ../xutil.o ../LiteClue.o SUMA_3dGenPriors.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ ../parser.o ../parser_int.o MarchingCubes/debug/MarchingCubes.o \ -I../3DEdge/src -l3DEdge -I../avovk libSUMA.a libglut.a libply.a libSUMAseg.a\ -lsegtools -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat -lgsl -lgslcblas /bin/rm -f 3dGenFeatureDist cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o 3dGenFeatureDist ../afni_warp.o ../afni_slice_byte.o ../afni_slice_short.o ../afni_slice_float.o ../afni_slice_complex.o ../afni_slice_rgbyte.o \ ../xutil.o ../LiteClue.o SUMA_3dGenFeatureDist.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ ../parser.o ../parser_int.o MarchingCubes/debug/MarchingCubes.o \ -I../3DEdge/src -l3DEdge -I../avovk libSUMA.a libglut.a libply.a libSUMAseg.a \ -lsegtools -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat -lgsl -lgslcblas /bin/rm -f 3dSeg cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o 3dSeg ../afni_warp.o ../afni_slice_byte.o ../afni_slice_short.o ../afni_slice_float.o ../afni_slice_complex.o ../afni_slice_rgbyte.o \ ../xutil.o ../LiteClue.o SUMA_3dSeg.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ ../parser.o ../parser_int.o MarchingCubes/debug/MarchingCubes.o \ -I../3DEdge/src -l3DEdge -I../avovk \ libSUMA.a libglut.a libply.a libSUMAseg.a -lsegtools -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat \ -lgsl -lgslcblas /bin/rm -f SurfExtrema cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o SurfExtrema ../afni_warp.o ../afni_slice_byte.o ../afni_slice_short.o ../afni_slice_float.o ../afni_slice_complex.o ../afni_slice_rgbyte.o ../xutil.o ../LiteClue.o SUMA_SurfExtrema.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ ../parser.o ../parser_int.o MarchingCubes/debug/MarchingCubes.o \ libSUMA.a libglut.a libply.a -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat /bin/rm -f 3dinfill cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o 3dinfill ../afni_warp.o ../afni_slice_byte.o ../afni_slice_short.o ../afni_slice_float.o ../afni_slice_complex.o ../afni_slice_rgbyte.o \ ../xutil.o ../LiteClue.o SUMA_3dinfill.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ ../parser.o ../parser_int.o MarchingCubes/debug/MarchingCubes.o \ -I../3DEdge/src -l3DEdge -I../avovk \ libSUMA.a libglut.a libply.a libSUMAseg.a -lsegtools -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat \ -lgsl -lgslcblas /bin/rm -f 3dHist cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o 3dHist ../afni_warp.o ../afni_slice_byte.o ../afni_slice_short.o ../afni_slice_float.o ../afni_slice_complex.o ../afni_slice_rgbyte.o \ ../xutil.o ../LiteClue.o SUMA_3dHist.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ ../parser.o ../parser_int.o MarchingCubes/debug/MarchingCubes.o \ -I../3DEdge/src -l3DEdge -I../avovk libSUMA.a libglut.a libply.a libSUMAseg.a \ -lsegtools -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat -lgsl -lgslcblas /bin/rm -f HalloSuma cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o HalloSuma \ SUMA_HalloSuma.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ libSUMA.a libglut.a libply.a -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat /bin/rm -f InstaTract cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o InstaTract \ SUMA_InstaTract.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ libSUMA.a libglut.a libply.a -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat SUMA_InstaTract.c: In function 'SendToSuma': SUMA_InstaTract.c:351: warning: passing argument 1 of 'SUMA_Wait_Till_Stream_Goes_Bad' from incompatible pointer type /bin/rm -f niprobe cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED -o niprobe ../xutil.o ../LiteClue.o ../parser.o ../parser_int.o \ SUMA_niprobe.c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ libSUMA.a libglut.a libply.a -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat gmake[1]: 'SUMA_glxdino' is up to date. gmake[1]: 'SUMA_paperplane' is up to date. gmake[1]: 'SUMA_pixmap2eps' is up to date. /bin/rm -f BrainSkin cc -O2 -pipe -fno-strict-aliasing -Wno-return-type -Wno-switch -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -DSUMA_COMPILED \ -o BrainSkin SUMA_BrainSkin.c \ -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src -I../nifti/nifti2 -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr -L/usr/lib -L/usr/local/lib -L../ \ ../parser.o ../parser_int.o MarchingCubes/debug/MarchingCubes.o \ ../xutil.o ../LiteClue.o -I../avovk -lf2c \ libSUMAGTS.a libSUMA.a libglut.a libply.a libSUMAseg.a -lglib-2.0 \ -lsegtools -lmrix -lcoxplot -lmri -ltracktools -lf2c -l3DEdge \ -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm -lz -lxml2 -lexpat -lgsl -lgslcblas libgts.a gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/SUMA' ( if [ ! -d ./BSD ]; then /bin/mkdir -p ./BSD; echo WARNING: directory ./BSD has been created. ; fi ;\ /bin/cp -f SUMA/suma SUMA/MakeColorMap SUMA/ROI2dataset SUMA/3dVol2Surf \ SUMA/3dSurf2Vol SUMA/SurfMeasures SUMA/SurfFWHM \ SUMA/ScaleToMap SUMA/MapIcosahedron SUMA/CreateIcosahedron \ SUMA/CompareSurfaces \ SUMA/ConvertSurface SUMA/ConvertDset SUMA/SurfClust SUMA/IsoSurface \ SUMA/ConvexHull SUMA/SUMA_glxdino SUMA/SUMA_pixmap2eps SUMA/SurfaceMetrics \ SUMA/inspec SUMA/quickspec SUMA/FSread_annot SUMA/SurfPatch SUMA/SurfQual \ SUMA/SurfSmooth SUMA/SUMA_paperplane \ SUMA/SampBias SUMA/3dSkullStrip SUMA/3dCRUISEtoAFNI \ SUMA/3dBRAIN_VOYAGERtoAFNI SUMA/3dSurfMask \ SUMA/SurfToSurf SUMA/Surf2VolCoord SUMA/ROIgrow SUMA/SurfDsetInfo \ SUMA/SurfInfo SUMA/AnalyzeTrace SUMA/DriveSuma SUMA/SurfDist \ SUMA/SpharmReco SUMA/SpharmDeco SUMA/prompt_user SUMA/SurfRetinoMap \ SUMA/ParseName SUMA/3dGenPriors SUMA/3dGenFeatureDist SUMA/3dSeg \ SUMA/SurfExtrema SUMA/3dinfill \ SUMA/3dHist SUMA/HalloSuma SUMA/InstaTract SUMA/niprobe SUMA/BrainSkin \ ./BSD ; \ if [ -f SUMA/SurfMesh ]; then /bin/cp -f SUMA/SurfMesh ./BSD ; fi; \ /bin/cp -f @SUMA_* ./BSD ;) /bin/mkdir -p /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/bin /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/scripts /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/lib /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/include /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/trash /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/doc /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/share /bin/mv /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/BSD/libf2c.a /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/trash /bin/mv /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/BSD/*.a /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/BSD/*.so /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/lib /bin/mv /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/BSD/funstuff /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/BSD/AFNI.*rc /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/BSD/afnigui* /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/share /bin/mv /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/BSD/*.h /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/include /bin/mv /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/BSD/README* /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/doc for binary in `/usr/bin/file /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/BSD/* | fgrep 'ELF' | /usr/bin/awk -F ':' ' { print $1 }'` ; do /bin/mv ${binary} /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/bin ; done /bin/mv /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/BSD/* /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/scripts /bin/mv /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/scripts/meica.libs /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage =========================================================================== =======================<phase: run-depends >============================ ===> afni-2015.11.13_1 depends on executable: endian - not found ===> Installing existing package /packages/All/endian-1.1.txz [93i386-default-job-02] Installing endian-1.1... [93i386-default-job-02] Extracting endian-1.1: ..... done ===> afni-2015.11.13_1 depends on executable: endian - found ===> Returning to build of afni-2015.11.13_1 ===> afni-2015.11.13_1 depends on executable: mpeg_encode - not found ===> Installing existing package /packages/All/mpeg_encode-1.5b.txz [93i386-default-job-02] Installing mpeg_encode-1.5b... [93i386-default-job-02] Extracting mpeg_encode-1.5b: .... done ===> afni-2015.11.13_1 depends on executable: mpeg_encode - found ===> Returning to build of afni-2015.11.13_1 ===> afni-2015.11.13_1 depends on executable: ppmtogif - not found ===> Installing existing package /packages/All/netpbm-10.35.98.txz [93i386-default-job-02] Installing netpbm-10.35.98... [93i386-default-job-02] `-- Installing jasper-1.900.1_16... [93i386-default-job-02] `-- Extracting jasper-1.900.1_16: .......... done [93i386-default-job-02] Extracting netpbm-10.35.98: .......... done Message from jasper-1.900.1_16: ===> NOTICE: The jasper 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 netpbm-10.35.98: ===> NOTICE: The netpbm 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 ===> afni-2015.11.13_1 depends on executable: ppmtogif - found ===> Returning to build of afni-2015.11.13_1 ===> afni-2015.11.13_1 depends on executable: qhull - not found ===> Installing existing package /packages/All/qhull5-1.0_3.txz [93i386-default-job-02] Installing qhull5-1.0_3... [93i386-default-job-02] Extracting qhull5-1.0_3: .......... done ===> afni-2015.11.13_1 depends on executable: qhull - found ===> Returning to build of afni-2015.11.13_1 ===> afni-2015.11.13_1 depends on executable: R - found ===> afni-2015.11.13_1 depends on executable: cjpeg - found ===> afni-2015.11.13_1 depends on file: /usr/local/bin/python2.7 - found ===> afni-2015.11.13_1 depends on package: libGL>0 - found ===> afni-2015.11.13_1 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> afni-2015.11.13_1 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> afni-2015.11.13_1 depends on file: /usr/local/libdata/pkgconfig/xi.pc - found ===> afni-2015.11.13_1 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> afni-2015.11.13_1 depends on file: /usr/local/libdata/pkgconfig/xp.pc - found ===> afni-2015.11.13_1 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> afni-2015.11.13_1 depends on file: /usr/local/libdata/pkgconfig/xpm.pc - found ===> afni-2015.11.13_1 depends on package: perl5>=5.24<5.25 - found =========================================================================== =======================<phase: stage >============================ ===> Staging for afni-2015.11.13_1 ===> Generating temporary packing list /bin/mkdir -p /wrkdirs/usr/ports/science/afni/work/stage/usr/local/share/afni /wrkdirs/usr/ports/science/afni/work/stage/usr/local/lib/afni /wrkdirs/usr/ports/science/afni/work/stage/usr/local/include/afni for f in /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/lib/*; do /usr/bin/strip ${f}; done install -m 0644 /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/lib/* /wrkdirs/usr/ports/science/afni/work/stage/usr/local/lib/afni install -m 0644 /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/include/* /wrkdirs/usr/ports/science/afni/work/stage/usr/local/include/afni cd /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/share && /bin/sh -c '(/usr/bin/find -Ed $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null 2>&1) && /usr/bin/find -Ed $0 $2 \( -type d -exec /bin/sh -c '\''cd '\''$1'\'' && chmod 755 "$@"'\'' -- . {} + -o -type f -exec /bin/sh -c '\''cd '\''$1'\'' && chmod 444 "$@"'\'' -- . {} + \)' -- . /wrkdirs/usr/ports/science/afni/work/stage/usr/local/share/afni install -s -m 555 /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/bin/* /wrkdirs/usr/ports/science/afni/work/stage/usr/local/bin install -m 555 /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/scripts/* /wrkdirs/usr/ports/science/afni/work/stage/usr/local/bin cd /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage && /bin/sh -c '(/usr/bin/find -Ed $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null 2>&1) && /usr/bin/find -Ed $0 $2 \( -type d -exec /bin/sh -c '\''cd '\''$1'\'' && chmod 755 "$@"'\'' -- . {} + -o -type f -exec /bin/sh -c '\''cd '\''$1'\'' && chmod 555 "$@"'\'' -- . {} + \)' -- meica.libs /wrkdirs/usr/ports/science/afni/work/stage/usr/local/libexec install -m 0644 /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/Atlases/* /wrkdirs/usr/ports/science/afni/work/stage/usr/local/share/afni install -m 444 /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/afni.1 /wrkdirs/usr/ports/science/afni/work/stage/usr/local/man/man1 /bin/mkdir -p /wrkdirs/usr/ports/science/afni/work/stage/usr/local/share/doc/afni /wrkdirs/usr/ports/science/afni/work/stage/usr/local/etc/mri install -m 0644 /wrkdirs/usr/ports/science/afni/work/afni-2015.11.13/prestage/doc/* /wrkdirs/usr/ports/science/afni/work/stage/usr/local/share/doc/afni install -m 555 /wrkdirs/usr/ports/science/afni/work/afni.cshrc /wrkdirs/usr/ports/science/afni/work/afni.profile /wrkdirs/usr/ports/science/afni/work/stage/usr/local/etc/mri ====> Compressing man pages (compress-man) =========================================================================== =======================<phase: package >============================ ===> Building package for afni-2015.11.13_1 ====>> Killing timed out build after 3600 seconds
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