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diff --git a/science/afni/Makefile b/science/afni/Makefile
index 4e81f12f071d..18c24c20453e 100644
--- a/science/afni/Makefile
+++ b/science/afni/Makefile
@@ -1,163 +1,163 @@
PORTNAME= afni
DISTVERSIONPREFIX= AFNI_
-DISTVERSION= 25.1.08
+DISTVERSION= 25.1.09
CATEGORIES= science biology graphics perl5 python
MAINTAINER= fernape@FreeBSD.org
COMMENT= Advanced Functional Neuro Imaging
WWW= https://afni.nimh.nih.gov/afni/
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
# Remote execution of suma. Also needed for glxinfo.
RUN_DEPENDS= endian:sysutils/endian \
ffmpeg:multimedia/ffmpeg \
qhull:math/qhull \
R:math/R \
${CRAN_DEPENDS}
USES= gettext gl gmake gnome iconv jpeg:run motif readline
USES+= perl5 python shebangfix tar:xz xorg
USE_GITHUB= yes
USE_GL= gl glu
USE_GNOME= glib20 libxml2
USE_XORG= ice sm x11 xau xcb xdmcp xext xft xi xmu xrender xt
SHEBANG_FILES= scripts_install/* \
python_scripts/afnipy/*.py \
python_scripts/scripts/*.py \
jzosky/*.py \
jzosky/lib_RetroTS/*.py \
discoraj/ClusterExplorer/*.py \
pkundu/*.py \
pkundu/meica.libs/*.py \
pkundu/meica.libs/*/*.py \
pkundu/meica.libs/*/*/*.py
MAKE_ENV= CC="${CC}" R_SHARE_DIR=${LOCALBASE}/lib/R/share
MAKE_JOBS_UNSAFE=yes
ALL_TARGET= vastness suma
CFLAGS+= -fcommon -Wno-incompatible-function-pointer-types
###########################################################################
# 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 <bsd.port.options.mk>
CONFLICTS= im \
nifticlib \
open-usp-tukubai
X11R6_FILES= coxplot/Makefile \
coxplot/Makefile.f2c
PKG_COMPRESSION_LEVEL= 6
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 <bsd.port.mk>
diff --git a/science/afni/distinfo b/science/afni/distinfo
index cc36808f49c4..d1105a46c5eb 100644
--- a/science/afni/distinfo
+++ b/science/afni/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1746597097
-SHA256 (afni-afni-AFNI_25.1.08_GH0.tar.gz) = 300b83cee2f9e1bb3943a3eb5a2dcb18fecca9cb33f22bc2407789ca5c1631b6
-SIZE (afni-afni-AFNI_25.1.08_GH0.tar.gz) = 53278260
+TIMESTAMP = 1747516527
+SHA256 (afni-afni-AFNI_25.1.09_GH0.tar.gz) = baec767861a8a4e191d1181976bf89e50ca3eaed06f44ba07a43d9bdafc90ff1
+SIZE (afni-afni-AFNI_25.1.09_GH0.tar.gz) = 53281164

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