diff --git a/science/afni/Makefile b/science/afni/Makefile index 77ee79023b61..2d66138bd2d1 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,161 +1,161 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 22.1.12 +DISTVERSION= 22.1.13 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org COMMENT= Advanced Functional Neuro Imaging LICENSE= GPLv2 BROKEN_aarch64= fails to build: statement requires expression of scalar type \ ('va_list' (aka '__builtin_va_list') invalid) 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 \ libXm.so:x11-toolkits/open-motif \ libf2c.so:lang/f2c \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ libgsl.so:math/gsl \ libicudata.so:devel/icu \ libnetcdff.so:science/netcdf-fortran \ libnetpbm.so:graphics/netpbm \ libpcre2-8.so:devel/pcre2 \ libpng16.so:graphics/png \ libxml2.so:textproc/libxml2 # Remote execution of suma. Also needed for glxinfo. RUN_DEPENDS= endian:sysutils/endian \ mpeg_encode:multimedia/mpeg_encode \ qhull:math/qhull \ R:math/R \ ${CRAN_DEPENDS} USES= gettext gl gmake gnome iconv jpeg:run motif readline USES+= perl5 python shebangfix tar:xz xorg USE_GITHUB= yes USE_GL= gl glu USE_GNOME= glib20 USE_XORG= ice sm x11 xau xcb xdmcp xext xft xi xmu xrender xt SHEBANG_FILES= scripts_install/* \ python_scripts/afnipy/*.py \ python_scripts/scripts/*.py \ jzosky/*.py \ jzosky/lib_RetroTS/*.py \ discoraj/ClusterExplorer/*.py \ pkundu/*.py \ pkundu/meica.libs/*.py \ pkundu/meica.libs/*/*.py \ pkundu/meica.libs/*/*/*.py MAKE_ENV= CC="${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 0e6dd9d60579..3086d208f678 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1654294063 -SHA256 (afni-afni-AFNI_22.1.12_GH0.tar.gz) = 8af1f43585c19b0b2d4d0d7795a3d2402a0abdd7e31f166b1c038e89d1f802bb -SIZE (afni-afni-AFNI_22.1.12_GH0.tar.gz) = 44031603 +TIMESTAMP = 1654634443 +SHA256 (afni-afni-AFNI_22.1.13_GH0.tar.gz) = 3f328dee372606803bead1c7b3c182cbf8a28de6c58eeb32de76e2c710873305 +SIZE (afni-afni-AFNI_22.1.13_GH0.tar.gz) = 44037156 diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist index b7dcdedd8047..a03ac65de6c3 100644 --- a/science/afni/pkg-plist +++ b/science/afni/pkg-plist @@ -1,1962 +1,1963 @@ bin/1dApar2mat bin/1dAstrip bin/1dBandpass bin/1dBport bin/1dCorrelate bin/1dDW_Grad_o_Mat++ bin/1dFlagMotion bin/1dGC.R bin/1dMarry bin/1dNLfit bin/1dRplot bin/1dRplot.R bin/1dSEM bin/1dSEMr.R bin/1dSVAR.R bin/1dTsort bin/1dUpsample bin/1d_tool.py bin/1dcat bin/1ddot bin/1deval bin/1dfft bin/1dgenARMA11 bin/1dgrayplot bin/1dmatcalc bin/1dnorm bin/1dplot bin/1dplot.py bin/1dsound bin/1dsum bin/1dsvd bin/1dtranspose bin/24swap bin/2dImReg bin/2dcat bin/2perm bin/2swap bin/3dABoverlap bin/3dAFNIto3D bin/3dAFNItoANALYZE bin/3dAFNItoNIFTI bin/3dAFNItoNIML bin/3dAFNItoRaw bin/3dANOVA bin/3dANOVA2 bin/3dANOVA3 bin/3dAcost bin/3dAllineate bin/3dAmpToRSFC 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lib/afni/plug_copy.so lib/afni/plug_crender.so lib/afni/plug_deconvolve.so lib/afni/plug_delay_V2.so lib/afni/plug_drawdset.so lib/afni/plug_edit.so lib/afni/plug_extract.so lib/afni/plug_fourier.so lib/afni/plug_hemisub.so lib/afni/plug_histog.so lib/afni/plug_histog_multi.so lib/afni/plug_imreg.so lib/afni/plug_lsqfit.so lib/afni/plug_maskave.so lib/afni/plug_maskcalc.so lib/afni/plug_maxima.so lib/afni/plug_nlfit.so lib/afni/plug_notes.so lib/afni/plug_nth_dataset.so lib/afni/plug_nudge.so lib/afni/plug_permtest.so lib/afni/plug_power.so lib/afni/plug_realtime.so lib/afni/plug_rename.so lib/afni/plug_reorder.so lib/afni/plug_retroicor.so lib/afni/plug_roiedit.so lib/afni/plug_roiplot.so lib/afni/plug_scatplot.so lib/afni/plug_second_dataset.so lib/afni/plug_stats.so lib/afni/plug_stavg.so lib/afni/plug_tag.so lib/afni/plug_threshold.so lib/afni/plug_ttget.so lib/afni/plug_vol2surf.so lib/afni/plug_volreg.so lib/afni/plug_wavelets.so lib/afni/plug_zeropad.so 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