diff options
Diffstat (limited to 'science/afni/Makefile')
| -rw-r--r-- | science/afni/Makefile | 159 |
1 files changed, 82 insertions, 77 deletions
diff --git a/science/afni/Makefile b/science/afni/Makefile index 8744258258fe..393a627ad67e 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,28 +1,21 @@ # $FreeBSD$ -############################################################################ -# http://www.neuro.mcw.edu/Ports has the latest source distribution from -# which this port is built. It will be updated as time permits. -# -# afni.nimh.nih.gov is the ultimate source for AFNI, and will always -# contain the latest source release. If this port is not up to date, -# you can download the latest sources and build manually. - -PORTNAME= afni -PORTVERSION= 2015.11.13 -PORTREVISION= 8 -CATEGORIES= science biology graphics -MASTER_SITES= http://www.acadix.biz/Ports/distfiles/ +PORTNAME= afni +DISTVERSIONPREFIX= AFNI_ +DISTVERSION= 19.1.08 +CATEGORIES= science biology graphics perl5 python MAINTAINER= jwb@FreeBSD.org COMMENT= Advanced Functional Neuro Imaging LICENSE= GPLv2 -BUILD_DEPENDS= gm4:devel/m4 +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 \ - libR.so:math/R \ libgsl.so:math/gsl \ libnetcdff.so:science/netcdf-fortran \ libxml2.so:textproc/libxml2 \ @@ -30,33 +23,32 @@ LIB_DEPENDS= libexpat.so:textproc/expat2 \ RUN_DEPENDS= endian:sysutils/endian \ mpeg_encode:multimedia/mpeg_encode \ ppmtogif:graphics/netpbm \ - qhull:math/qhull5 - -BROKEN_aarch64= fails to compile: suma_utils.c:3043:10: statement requires expression of scalar type -BROKEN_sparc64= fails to compile: undefined reference to '_mcount' - -CONFLICTS= im-[0-9]* \ - nifticlib-[0-9]* \ - open-usp-tukubai-[0-9]* + qhull:math/qhull5 \ + R:math/R -USES= gettext gmake iconv jpeg:run motif perl5 python shebangfix tar:xz -SHEBANG_FILES= suma_change_spec \ - 3dPAR2AFNI.pl \ - python_scripts/*.py \ - pkundu/meica.py \ - pkundu/meica.libs/*.py \ - pkundu/meica.libs/mdp/test/run_tests.py +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 -OPTIONS_DEFINE= DOCS - -.include <bsd.port.options.mk> - -USE_GL= gl glu glw +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 ########################################################################### @@ -65,8 +57,17 @@ ALL_TARGET= vastness suma SUB_FILES= pkg-message afni.cshrc afni.profile INSTALL_WRKSRC= ${WRKSRC}/BSD +INSTALL_TMP= ${INSTALL_WRKSRC}-temp PRESTAGE= ${WRKSRC}/prestage +OPTIONS_DEFINE= DOCS + +.include <bsd.port.options.mk> + +CONFLICTS= im-[0-9]* \ + nifticlib-[0-9]* \ + open-usp-tukubai-[0-9]* + X11R6_FILES= coxplot/Makefile \ coxplot/Makefile.f2c \ 3DEdge/src/Makefile \ @@ -86,21 +87,20 @@ post-extract: .endfor @${REINPLACE_CMD} \ -E 's|AFNI_[0-9_]+|${PORTVERSION}|g' ${WRKSRC}/AFNI_label.h - @${REINPLACE_CMD} \ - -e "s|%%PREFIX%%|${PREFIX}|g" ${WRKSRC}/afni.1 @${CP} ${FILESDIR}/Makefile ${WRKSRC} @${RM} ${WRKSRC}/3DEdge/src/Makefile.orig # shebangfix misses /bin/python on 10.1 -post-patch: - ${REINPLACE_CMD} -e "s|-lglib|-lglib-2.0|g" \ +# @${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 - ${REINPLACE_CMD} -e "s|/bin/python|${PYTHON_CMD}|g" \ - ${WRKSRC}/python_scripts/lib_fat_Rfactor.py - ${REINPLACE_CMD} \ - -e 's|os\.path\.dirname(sys\.argv\[0\])|"${PREFIX}/libexec"|g' \ + @${REINPLACE_CMD} \ + -e 's|os\.path\.dirname(sys\.argv\[0\])|"${DATADIR}"|g' \ ${WRKSRC}/pkundu/meica.py - ${REINPLACE_CMD} \ + @${REINPLACE_CMD} \ -e 's|g_info|afni_g_info|g' \ ${WRKSRC}/rickr/Dimon.c \ ${WRKSRC}/rickr/Dimon1.c \ @@ -111,53 +111,58 @@ post-patch: ${WRKSRC}/to3d.c \ ${WRKSRC}/mri_dicom_stuff.h -post-build: - ${MKDIR} ${PRESTAGE}/bin \ +do-install: + # AFNI install just dumps everything into one flat directory + # Preserve original install dir and make a sacrificial temp copy + # to be pruned and rearranged for easy staging + @${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 - ${MV} ${INSTALL_WRKSRC}/libf2c.a \ - ${PRESTAGE}/trash - ${MV} ${INSTALL_WRKSRC}/*.a \ - ${INSTALL_WRKSRC}/*.so \ - ${PRESTAGE}/lib - ${MV} ${INSTALL_WRKSRC}/funstuff \ - ${INSTALL_WRKSRC}/AFNI.*rc \ - ${INSTALL_WRKSRC}/afnigui* \ + @${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_WRKSRC}/*.h \ - ${PRESTAGE}/include - ${MV} ${INSTALL_WRKSRC}/README* \ - ${PRESTAGE}/doc - for binary in `${FILE} ${INSTALL_WRKSRC}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \ + @${MV} ${INSTALL_TMP}/*.a \ + ${INSTALL_TMP}/*.so \ + ${PRESTAGE}/lib + @${MV} ${INSTALL_TMP}/*.h ${PRESTAGE}/include + @${CP} ${WRKDIR}/afni-AFNI_${PORTVERSION}/doc/README/* ${PRESTAGE}/doc + @for binary in `${FILE} ${INSTALL_TMP}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \ ${MV} $${binary} ${PRESTAGE}/bin ; \ done - ${MV} ${INSTALL_WRKSRC}/* \ - ${PRESTAGE}/scripts - ${MV} ${PRESTAGE}/scripts/meica.libs ${PRESTAGE} + @${MV} ${INSTALL_TMP}/* ${PRESTAGE}/scripts -do-install: - ${MKDIR} ${STAGEDIR}${DATADIR} \ + # Install to STAGEDIR using proper ports tools + @${MKDIR} \ + ${STAGEDIR}${DATADIR} \ ${STAGEDIR}${PREFIX}/lib/afni \ - ${STAGEDIR}${PREFIX}/include/afni - for f in ${PRESTAGE}/lib/*; do \ - ${STRIP_CMD} $${f}; \ - done - ${INSTALL_DATA} ${PRESTAGE}/lib/* ${STAGEDIR}${PREFIX}/lib/afni - ${INSTALL_DATA} ${PRESTAGE}/include/* ${STAGEDIR}${PREFIX}/include/afni - cd ${PRESTAGE}/share && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR} + ${STAGEDIR}${PREFIX}/include/afni \ + ${STAGEDIR}${DOCSDIR} \ + ${STAGEDIR}${PREFIX}/etc/mri ${INSTALL_PROGRAM} ${PRESTAGE}/bin/* ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${PRESTAGE}/scripts/* ${STAGEDIR}${PREFIX}/bin - cd ${PRESTAGE} && ${COPYTREE_BIN} meica.libs \ - ${STAGEDIR}${PREFIX}/libexec - ${INSTALL_DATA} ${WRKSRC}/Atlases/* ${STAGEDIR}${DATADIR} - ${INSTALL_MAN} ${WRKSRC}/afni.1 ${STAGEDIR}${MAN1PREFIX}/man/man1 - ${MKDIR} ${STAGEDIR}${DOCSDIR} ${STAGEDIR}${PREFIX}/etc/mri - ${INSTALL_DATA} ${PRESTAGE}/doc/* ${STAGEDIR}${DOCSDIR} + ${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 <bsd.port.mk> |