diff --git a/science/afni/Makefile b/science/afni/Makefile index 8ccabcd8b7fe..8f59165aa8f3 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,152 +1,152 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 21.3.00 +DISTVERSION= 21.3.05 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org COMMENT= Advanced Functional Neuro Imaging LICENSE= GPLv2 CRAN_DEPENDS= R-cran-lme4>0:math/R-cran-lme4 \ R-cran-snow>0:science/R-cran-snow \ R-cran-psych>0:math/R-cran-psych BUILD_DEPENDS= gm4:devel/m4 \ R:math/R \ ${CRAN_DEPENDS} 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 # Remote execution of suma. Also needed for glxinfo. RUN_DEPENDS= endian:sysutils/endian \ mpeg_encode:multimedia/mpeg_encode \ qhull:math/qhull \ R:math/R \ ${CRAN_DEPENDS} USES= gettext gl gmake gnome iconv jpeg:run motif USES+= perl5 python shebangfix tar:xz xorg USE_GITHUB= yes USE_GL= gl glu USE_GNOME= glib20 USE_XORG= x11 xext xi xmu xt SHEBANG_FILES= scripts_install/* \ python_scripts/afnipy/*.py \ python_scripts/scripts/*.py \ jzosky/*.py \ jzosky/lib_RetroTS/*.py \ discoraj/ClusterExplorer/*.py \ pkundu/*.py \ pkundu/meica.libs/*.py \ pkundu/meica.libs/*/*.py \ pkundu/meica.libs/*/*/*.py MAKE_ENV= CC="${CC}" R_SHARE_DIR=${LOCALBASE}/lib/R/share MAKE_JOBS_UNSAFE=yes CFLAGS+= -fcommon ALL_TARGET= vastness suma ########################################################################### # Install parameters SUB_FILES= pkg-message afni.cshrc afni.profile INSTALL_WRKSRC= ${WRKSRC}/BSD WRKSRC_SUBDIR= src OPTIONS_DEFINE= DOCS INSTALL_TMP= ${INSTALL_WRKSRC}-temp PRESTAGE= ${WRKSRC}/prestage .include CONFLICTS= im \ nifticlib \ open-usp-tukubai X11R6_FILES= coxplot/Makefile \ coxplot/Makefile.f2c 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} ${WRKSRC}/3DEdge/src/Makefile.orig pre-configure: @${REINPLACE_CMD} -e "s|-lglib|-lglib-2.0|g" \ ${WRKSRC}/SUMA/SUMA_Makefile @${REINPLACE_CMD} \ -e 's|os\.path\.dirname(os\.path\.abspath(os\.path\.expanduser(sys\.argv\[0\])))|"${DATADIR}"|g' \ ${WRKSRC}/pkundu/meica.py do-install: # AFNI install just dumps everything into one flat directory # ${WRKSRC}/BSD == ${INSTALL_WRKSRC}. # Preserve ${INSTALL_WRKSRC} and make a sacrificial temp copy # to be pruned and rearranged for easy staging @${RM} -r ${INSTALL_TMP} @${CP} -R ${INSTALL_WRKSRC} ${INSTALL_TMP} # Clean up and organize files into ${PRESTAGE}, destroying # ${INSTALL_TMP} in the process @${RM} -rf ${PRESTAGE} @${MKDIR} ${PRESTAGE}/bin \ ${PRESTAGE}/scripts \ ${PRESTAGE}/lib \ ${PRESTAGE}/include \ ${PRESTAGE}/trash \ ${PRESTAGE}/doc \ ${PRESTAGE}/share \ ${PRESTAGE}/pylib @${RM} ${INSTALL_TMP}/libf2c.a @${MV} ${INSTALL_TMP}/meica.libs \ ${INSTALL_TMP}/shiny \ ${INSTALL_TMP}/lib_RetroTS \ ${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 ${PRESTAGE}/include @${MV} ${INSTALL_TMP}/afnipy ${PRESTAGE}/pylib @${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 (cd ${PRESTAGE}/pylib && \ ${COPYTREE_SHARE} . ${STAGEDIR}${PYTHON_SITELIBDIR}) ${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 diff --git a/science/afni/distinfo b/science/afni/distinfo index 9f1bdd01f641..232f36f8c254 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1633707047 -SHA256 (afni-afni-AFNI_21.3.00_GH0.tar.gz) = b1d5f18eb8f741af8389796cce7dc8bc37d4c868624ea251ed1e7b9d2d421508 -SIZE (afni-afni-AFNI_21.3.00_GH0.tar.gz) = 43819613 +TIMESTAMP = 1636477646 +SHA256 (afni-afni-AFNI_21.3.05_GH0.tar.gz) = ef8f4bc206aba23a2af8afad38d54ebde1766d0eb9eedc48131745df9b962ba4 +SIZE (afni-afni-AFNI_21.3.05_GH0.tar.gz) = 43844406 diff --git a/science/afni/files/patch-crorden_dcm2niix__console_makefile b/science/afni/files/patch-crorden_dcm2niix__console_makefile index 7816c4ff42c5..5c34e38e062f 100644 --- a/science/afni/files/patch-crorden_dcm2niix__console_makefile +++ b/science/afni/files/patch-crorden_dcm2niix__console_makefile @@ -1,28 +1,28 @@ ---- crorden/dcm2niix_console/makefile.orig 2021-06-15 02:26:33 UTC +--- crorden/dcm2niix_console/makefile.orig 2021-11-08 00:47:00 UTC +++ crorden/dcm2niix_console/makefile @@ -1,8 +1,8 @@ # Regular use -CFLAGS=-s -O3 +CXXFLAGS?=-s -O3 # Debugging -#CFLAGS=-g +#CXXFLAGS=-g #Leak tests: # https://clang.llvm.org/docs/AddressSanitizer.html -@@ -23,7 +23,7 @@ ifneq ($(OS),Windows_NT) +@@ -21,7 +21,7 @@ ifneq ($(OS),Windows_NT) + ifeq "$(OS)" "Darwin" + #CFLAGS=-dead_strip -O3 #CFLAGS= -O3 - # CFLAGS=-O3 -sectcreate __TEXT __info_plist Info.plist - # rickr - ponder -sectcreate later -- CFLAGS=-O3 -+ CXXFLAGS=-O3 +- CFLAGS=-O3 -sectcreate __TEXT __info_plist Info.plist ++ CXXFLAGS=-O3 -sectcreate __TEXT __info_plist Info.plist #Apple notarization requires a Info.plist # For .app bundles, the Info.plist is a separate file, for executables it is appended as a section #you can check that the Info.plist section has been inserted with either of these commands -@@ -33,4 +33,4 @@ ifneq ($(OS),Windows_NT) +@@ -31,4 +31,4 @@ ifneq ($(OS),Windows_NT) endif endif all: - g++ $(CFLAGS) -I. $(JFLAGS) main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG + $(CXX) $(CXXFLAGS) -I. $(JFLAGS) main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -o dcm2niix -DmyDisableOpenJPEG