Index: head/science/afni/Makefile =================================================================== --- head/science/afni/Makefile (revision 504495) +++ head/science/afni/Makefile (revision 504496) @@ -1,168 +1,168 @@ # $FreeBSD$ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 19.1.18 +DISTVERSION= 19.1.20 CATEGORIES= science biology graphics perl5 python MAINTAINER= jwb@FreeBSD.org COMMENT= Advanced Functional Neuro Imaging LICENSE= GPLv2 BROKEN_sparc64= Does not compile: "undefined reference to '_mcount'" BUILD_DEPENDS= gm4:devel/m4 \ R:math/R LIB_DEPENDS= libexpat.so:textproc/expat2 \ libf2c.so:lang/f2c \ libgsl.so:math/gsl \ libnetcdff.so:science/netcdf-fortran \ libxml2.so:textproc/libxml2 \ libXm.so:x11-toolkits/open-motif \ libnetpbm.so:graphics/netpbm RUN_DEPENDS= endian:sysutils/endian \ mpeg_encode:multimedia/mpeg_encode \ qhull:math/qhull5 \ R:math/R USES= compiler:openmp gettext gl gmake gnome iconv jpeg:run motif \ perl5 python shebangfix tar:xz USE_GNOME= glib20 USE_GITHUB= yes SHEBANG_FILES= scripts_install/* \ python_scripts/afni_python/*.py \ jzosky/*.py \ jzosky/lib_RetroTS/*.py \ discoraj/ClusterExplorer/*.py \ roopchansinghv/PsychoPy-NeuroFeedback-Demo/*.py \ roopchansinghv/PsychoPy-NeuroFeedback-Demo/*/*.py \ pkundu/*.py \ pkundu/meica.libs/*.py \ pkundu/meica.libs/*/*.py \ pkundu/meica.libs/*/*/*.py USE_GL= gl glu USE_XORG= x11 xext xi xmu xp xt MAKE_ENV= CC="${CC}" R_SHARE_DIR=${LOCALBASE}/lib/R/share MAKE_JOBS_UNSAFE=yes WRKSRC_SUBDIR= src ALL_TARGET= vastness suma ########################################################################### # Install parameters SUB_FILES= pkg-message afni.cshrc afni.profile INSTALL_WRKSRC= ${WRKSRC}/BSD INSTALL_TMP= ${INSTALL_WRKSRC}-temp PRESTAGE= ${WRKSRC}/prestage OPTIONS_DEFINE= DOCS .include CONFLICTS= im-[0-9]* \ nifticlib-[0-9]* \ open-usp-tukubai-[0-9]* X11R6_FILES= coxplot/Makefile \ coxplot/Makefile.f2c \ 3DEdge/src/Makefile \ SUMA/SUMA_Makefile \ edt_blur.c \ suma_datasets.c \ SUMA/SUMA_Load_Surface_Object.c \ SUMA/SUMA_MiscFunc.c \ SUMA/SUMA_ParseCommands.c \ SUMA/GLUT/libglut/glut_event.c \ SUMA/SUMA_Surface_IO.c post-extract: .for f in ${X11R6_FILES} @${REINPLACE_CMD} \ -e 's|/usr/X11R6|$${LOCALBASE}|g' ${WRKSRC}/${f} .endfor @${REINPLACE_CMD} \ -E 's|AFNI_[0-9_]+|${PORTVERSION}|g' ${WRKSRC}/AFNI_label.h @${CP} ${FILESDIR}/Makefile ${WRKSRC} @${RM} ${WRKSRC}/3DEdge/src/Makefile.orig # shebangfix misses /bin/python on 10.1 # @${REINPLACE_CMD} -e "s|/bin/python|${PYTHON_CMD}|g" \ # ${WRKSRC}/python_scripts/afni_python/lib_fat_Rfactor.py pre-configure: @${REINPLACE_CMD} -e "s|-lglib|-lglib-2.0|g" \ ${WRKSRC}/SUMA/SUMA_Makefile @${REINPLACE_CMD} \ -e 's|os\.path\.dirname(sys\.argv\[0\])|"${DATADIR}"|g' \ ${WRKSRC}/pkundu/meica.py @${REINPLACE_CMD} \ -e 's|g_info|afni_g_info|g' \ ${WRKSRC}/rickr/Dimon.c \ ${WRKSRC}/rickr/Dimon1.c \ ${WRKSRC}/afni_history_rickr.c \ ${WRKSRC}/mri_dicom_stuff.c \ ${WRKSRC}/mri_process_siemens.c \ ${WRKSRC}/mri_read_dicom.c \ ${WRKSRC}/to3d.c \ ${WRKSRC}/mri_dicom_stuff.h do-install: # AFNI install just dumps everything into one flat directory # Preserve original install dir and make a sacrificial temp copy # to be pruned and rearranged for easy staging @${RM} -r ${INSTALL_TMP} @${CP} -R ${INSTALL_WRKSRC} ${INSTALL_TMP} # Clean up and organize files into ${PRESTAGE}, destroying # temp copy in the process @${RM} -rf ${PRESTAGE} @${MKDIR} ${PRESTAGE}/bin \ ${PRESTAGE}/scripts \ ${PRESTAGE}/lib \ ${PRESTAGE}/include \ ${PRESTAGE}/trash \ ${PRESTAGE}/doc \ ${PRESTAGE}/share @${RM} ${INSTALL_TMP}/libf2c.a @${MV} ${INSTALL_TMP}/meica.libs \ ${INSTALL_TMP}/shiny \ ${INSTALL_TMP}/lib_RetroTS \ ${INSTALL_TMP}/afniInterfaceRT \ ${INSTALL_TMP}/funstuff \ ${INSTALL_TMP}/AFNI.*rc \ ${INSTALL_TMP}/afnigui* \ ${PRESTAGE}/share @${MV} ${INSTALL_TMP}/*.a \ ${INSTALL_TMP}/*.so \ ${PRESTAGE}/lib @${MV} ${INSTALL_TMP}/*.h ${PRESTAGE}/include @${CP} ${WRKDIR}/afni-AFNI_${PORTVERSION}/doc/README/* ${PRESTAGE}/doc @for binary in `${FILE} ${INSTALL_TMP}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \ ${MV} $${binary} ${PRESTAGE}/bin ; \ done @${MV} ${INSTALL_TMP}/* ${PRESTAGE}/scripts # Install to STAGEDIR using proper ports tools @${MKDIR} \ ${STAGEDIR}${DATADIR} \ ${STAGEDIR}${PREFIX}/lib/afni \ ${STAGEDIR}${PREFIX}/include/afni \ ${STAGEDIR}${DOCSDIR} \ ${STAGEDIR}${PREFIX}/etc/mri ${INSTALL_PROGRAM} ${PRESTAGE}/bin/* ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${PRESTAGE}/scripts/* ${STAGEDIR}${PREFIX}/bin ${INSTALL_DATA} ${PRESTAGE}/lib/* ${STAGEDIR}${PREFIX}/lib/afni ${INSTALL_DATA} ${PRESTAGE}/include/* ${STAGEDIR}${PREFIX}/include/afni (cd ${PRESTAGE}/share && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}) ${INSTALL_SCRIPT} ${WRKDIR}/afni.cshrc ${WRKDIR}/afni.profile \ ${STAGEDIR}${PREFIX}/etc/mri do-install-DOCS-on: ${INSTALL_DATA} ${PRESTAGE}/doc/* ${STAGEDIR}${DOCSDIR} .include Index: head/science/afni/distinfo =================================================================== --- head/science/afni/distinfo (revision 504495) +++ head/science/afni/distinfo (revision 504496) @@ -1,3 +1,3 @@ -TIMESTAMP = 1559998284 -SHA256 (afni-afni-AFNI_19.1.18_GH0.tar.gz) = 73be9fa066ba3da3f035c9935612c6f4254257be4f8b99df29437cdd0ca31b07 -SIZE (afni-afni-AFNI_19.1.18_GH0.tar.gz) = 38927911 +TIMESTAMP = 1560861068 +SHA256 (afni-afni-AFNI_19.1.20_GH0.tar.gz) = d9d63e3c8f4d38b28c4ceb71ee5537e66f400a6f2b2e0443fa58f2cf7a112007 +SIZE (afni-afni-AFNI_19.1.20_GH0.tar.gz) = 38939294 Index: head/science/afni/files/patch-prf__common__circular.c =================================================================== --- head/science/afni/files/patch-prf__common__circular.c (revision 504495) +++ head/science/afni/files/patch-prf__common__circular.c (nonexistent) @@ -1,18 +0,0 @@ ---- prf_common_circular.c.orig 2019-05-10 21:23:56 UTC -+++ prf_common_circular.c -@@ -318,8 +318,14 @@ static int show_malloc_stats(char * mesg) - - if( show_stats ) { - fprintf(stderr,"\n----- malloc stats: %s\n", mesg); --#ifndef DARWIN -+#if defined(__linux__) - malloc_stats(); -+#elif defined(__FreeBSD__) -+ #include -+ #include -+ malloc_stats_print(NULL, NULL, "g"); -+#else -+ fprintf(stderr, "No malloc_stats() on this platform.\n"); - #endif - } - Property changes on: head/science/afni/files/patch-prf__common__circular.c ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/science/afni/files/patch-nifti_cifti_afni__xml.h =================================================================== --- head/science/afni/files/patch-nifti_cifti_afni__xml.h (revision 504495) +++ head/science/afni/files/patch-nifti_cifti_afni__xml.h (nonexistent) @@ -1,10 +0,0 @@ ---- nifti/cifti/afni_xml.h.orig 2015-11-06 21:25:14 UTC -+++ nifti/cifti/afni_xml.h -@@ -5,6 +5,7 @@ - #define AXML_MAX_ELEN 128 /* maximum element length */ - - #include -+#include - - /* ---------------------------------------------------------------------- - This code is for generic reading of xml into structures. Property changes on: head/science/afni/files/patch-nifti_cifti_afni__xml.h ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/science/afni/files/patch-ptaylor_Makefile.ptaylor.INCLUDE =================================================================== --- head/science/afni/files/patch-ptaylor_Makefile.ptaylor.INCLUDE (revision 504495) +++ head/science/afni/files/patch-ptaylor_Makefile.ptaylor.INCLUDE (nonexistent) @@ -1,16 +0,0 @@ ---- ptaylor/Makefile.ptaylor.INCLUDE.orig 2019-05-21 17:27:32 UTC -+++ ptaylor/Makefile.ptaylor.INCLUDE -@@ -228,11 +228,11 @@ map_TrackID:map_TrackID.o ${AFNI_3dOBJS} ${PTAYLORLIB} - - 3dDWUncert.o: 3dDWUncert.c - $(RM) $@ -- $(CCOMP_PT) -c 3dDWUncert.c $(PTAYLOR_INCLUDE_PATH) -+ $(CCOMP_PT) -c -fopenmp 3dDWUncert.c $(PTAYLOR_INCLUDE_PATH) - - 3dDWUncert:3dDWUncert.o ${AFNI_3dOBJS} ${PTAYLORLIB} - $(RM) $@ -- $(CCOMP_PT) -o 3dDWUncert 3dDWUncert.o ${AFNI_3dOBJS} \ -+ $(CCOMP_PT) -fopenmp -o 3dDWUncert 3dDWUncert.o ${AFNI_3dOBJS} \ - ${PTAYLOR_INCLUDE_PATH} ${PTAYLOR_LINK_PATH} \ - $(LFLAGS) ${PTAYLORLIB} $(LLIBS) \ - -lgsl -lgslcblas -lm Property changes on: head/science/afni/files/patch-ptaylor_Makefile.ptaylor.INCLUDE ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property