svn commit: r502158 - in head/science/afni: . files
Jason W. Bacon
jwb at FreeBSD.org
Mon May 20 19:36:00 UTC 2019
Author: jwb
Date: Mon May 20 19:35:57 2019
New Revision: 502158
URL: https://svnweb.freebsd.org/changeset/ports/502158
Log:
science/afni: Upgrade to 19.1.08
Switch from personal dist snapshots to Github releases
Improve staging procedure to preserve results of build phase
Temporarily use bundled GLw pending fix of libglw port
Added:
head/science/afni/files/patch-crorden_dcm2niix__console_makefile (contents, props changed)
head/science/afni/files/patch-prf__common__circular.c (contents, props changed)
Deleted:
head/science/afni/files/patch-misc_math.c
Modified:
head/science/afni/Makefile
head/science/afni/distinfo
head/science/afni/files/Makefile
head/science/afni/files/patch-Makefile.INCLUDE
head/science/afni/files/patch-netcdf-3.5.0_src_configure
head/science/afni/pkg-descr
head/science/afni/pkg-plist
Modified: head/science/afni/Makefile
==============================================================================
--- head/science/afni/Makefile Mon May 20 18:10:55 2019 (r502157)
+++ head/science/afni/Makefile Mon May 20 19:35:57 2019 (r502158)
@@ -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
+DISTVERSIONPREFIX= AFNI_
+DISTVERSION= 19.1.08
+CATEGORIES= science biology graphics perl5 python
-PORTNAME= afni
-PORTVERSION= 2015.11.13
-PORTREVISION= 8
-CATEGORIES= science biology graphics
-MASTER_SITES= http://www.acadix.biz/Ports/distfiles/
-
MAINTAINER= jwb at 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
+ qhull:math/qhull5 \
+ R:math/R
-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'
+USES= compiler:openmp gettext gl gmake gnome iconv jpeg:run motif \
+ perl5 python shebangfix tar:xz
+USE_GNOME= glib20
+USE_GITHUB= yes
-CONFLICTS= im-[0-9]* \
- nifticlib-[0-9]* \
- open-usp-tukubai-[0-9]*
-
-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 \
+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/mdp/test/run_tests.py
-USE_GNOME= glib20
+ 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>
Modified: head/science/afni/distinfo
==============================================================================
--- head/science/afni/distinfo Mon May 20 18:10:55 2019 (r502157)
+++ head/science/afni/distinfo Mon May 20 19:35:57 2019 (r502158)
@@ -1,2 +1,3 @@
-SHA256 (afni-2015.11.13.tar.xz) = b8647ed2f522a520d90cbfd3da70d34849cec421678ff3baf0ecbb6e9e72414b
-SIZE (afni-2015.11.13.tar.xz) = 48722840
+TIMESTAMP = 1557698397
+SHA256 (afni-afni-AFNI_19.1.08_GH0.tar.gz) = 15dcb04412c68e3ca2673eaf90cdd9bb26c1d23c09ed3346bf330ecbf18c4269
+SIZE (afni-afni-AFNI_19.1.08_GH0.tar.gz) = 38767080
Modified: head/science/afni/files/Makefile
==============================================================================
--- head/science/afni/files/Makefile Mon May 20 18:10:55 2019 (r502157)
+++ head/science/afni/files/Makefile Mon May 20 19:35:57 2019 (r502158)
@@ -100,11 +100,15 @@ LLIBS = -lmri -lf2c -lXm -lXp -lXpm -lXext -lXmu -lXt
# vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
# For suma (NO STATIC LINKING OF GL libs)
-SUMA_INCLUDE_PATH = -I${LOCALBASE}/include/glib-2.0 -I${LOCALBASE}/lib/glib-2.0/include -I${LOCALBASE}/include -I./ -I../ -I../niml/ -Igts/src
+# Use -IGLw_local and -lGLws to avert the following suma runtime error due
+# to lack of extern modifier in GLwDrawA.h:
+# ** ERROR: glwMDrawingAreaWidgetClass is NULL
+# This may break if bundled GLw is not kept up-to-date,
+SUMA_INCLUDE_PATH = -IGLw_local -I${LOCALBASE}/include/glib-2.0 -I${LOCALBASE}/lib/glib-2.0/include -I${LOCALBASE}/include -I./ -I../ -I../niml/ -Igts/src
SUMA_LINK_PATH = -L/usr/lib -L${LOCALBASE}/lib -L../
#use -lGLw if you have libGLw.a or libGLw.so* or
# -lMesaGLw if you have Mesa's version (libMesaGLw*) of libGLw
-SUMA_LINK_LIB = -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm $(LZLIB) -lxml2 -lexpat
+SUMA_LINK_LIB = -lXm -lGLws -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm $(LZLIB) -lxml2 -lexpat
SUMA_MAKEFILE_NAME = SUMA_Makefile
SUMA_BIN_ARCHIVE = SUMA_FreeBSD.tar
SUMA_GLIB_VER = -2.0
Modified: head/science/afni/files/patch-Makefile.INCLUDE
==============================================================================
--- head/science/afni/files/patch-Makefile.INCLUDE Mon May 20 18:10:55 2019 (r502157)
+++ head/science/afni/files/patch-Makefile.INCLUDE Mon May 20 19:35:57 2019 (r502158)
@@ -1,16 +1,16 @@
---- Makefile.INCLUDE.orig 2015-11-06 21:25:04 UTC
+--- Makefile.INCLUDE.orig 2019-05-10 21:23:56 UTC
+++ Makefile.INCLUDE
-@@ -50,7 +50,7 @@ MISC = AFNI_atlas_spaces.niml AFNI.Xd
+@@ -64,7 +64,7 @@ MISC = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a
## AFNI package, but included because they are useful. Some of
## them are Open Source programs, not from the AFNI group at all.
-EXTRAS = cjpeg djpeg whirlgif mpeg_encode myget Xphace rmz aiv mycat quotize $(EXPROGS)
-+EXTRAS = 3dClustBust whirlgif myget Xphace rmz aiv mycat quotize $(EXPROGS)
++EXTRAS = whirlgif myget Xphace rmz aiv mycat quotize $(EXPROGS)
# mpegtoppm in above list
-@@ -60,7 +60,7 @@ EXTRAS = cjpeg djpeg whirlgif mpeg_enc
- PROGRAMS = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge count \
+@@ -77,7 +77,7 @@ EXTRAS = cjpeg djpeg whirlgif mpeg_encode myget Xpha
+ PROGS_1 = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge count \
sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals \
fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3daxialize \
- cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
@@ -18,7 +18,7 @@
waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \
3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \
3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
-@@ -72,7 +72,7 @@ PROGRAMS = afni to3d from3d abut 3dclust
+@@ -90,7 +90,7 @@ PROGS_2 = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn
3dWavelets 3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign \
3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid \
3dEntropy 3ddelay ent16 3dRowFillin 1dgrayplot 3dToutcount 1dsum \
@@ -27,8 +27,8 @@
3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dMINCtoAFNI 3dCM fdrval \
3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI \
3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dAFNItoMINC 3dBrickStat \
-@@ -92,7 +92,7 @@ PROGRAMS = afni to3d from3d abut 3dclust
- 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip \
+@@ -112,7 +112,7 @@ PROGS_3 = 3dDeconvolve_f 3dAnhist 3dAFNIto3D 3dUnifor
+ PROGS_4 = 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip \
3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D \
3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI \
- niccc rbox qdelaunay 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply \
@@ -36,7 +36,7 @@
1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport \
3dNormalityTest 3dmask_tool FIRdesign help_format 2perm 3dClustCount \
column_cat 3dUnifize 3dNwarpCat 3dQwarp 3dLocalHistog 3dNwarpAdjust \
-@@ -104,7 +104,7 @@ PROGRAMS = afni to3d from3d abut 3dclust
+@@ -138,7 +138,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4)
PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge \
sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnoise count \
fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim imupsam \
@@ -45,7 +45,7 @@
waver 3dnewid 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval \
3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
imstack byteorder 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot \
-@@ -144,7 +144,7 @@ PROGRAMS_NOPLUG = afni to3d from3d abut
+@@ -181,7 +181,7 @@ PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize
PROGRAMS_EXE = afni.exe to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge \
sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals count \
fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3dGetrow \
@@ -54,26 +54,25 @@
waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \
3dAFNItoNIML AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \
3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
-@@ -276,7 +276,7 @@ prog_list:
- echo "$(PROGRAMS) $(SCRIPTS) $(SUMA_PROGS) $(SUMA_GTS_PROGS) \
- $(PY_SCRIPTS)" | tr ' ' '\n' | LC_COLLATE=C sort | uniq \
- > ___prog_list.txt
-- make -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs | \
-+ $(MAKE) -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs | \
- tr ' ' '\n' | LC_COLLATE=C sort | uniq >> ___prog_list.txt
- cat ___prog_list.txt | LC_COLLATE=C sort | uniq >> prog_list.txt
- \rm -f ___prog_list.txt
-@@ -364,6 +364,9 @@ byteorder:byteorder.o
- 3dbuc2fim:3dbuc2fim.o
- $(CC) -o 3dbuc2fim 3dbuc2fim.o $(LFLAGS) $(LLIBS)
+@@ -303,7 +303,7 @@ echo_progs:
+ prog_list_bin:
+ echo "$(PROGRAMS) $(SUMA_PROGS) $(SUMA_GTS_PROGS)" \
+ | tr ' ' '\n' > ___plist_bin.txt
+- make -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs \
++ $(MAKE) -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs \
+ | tr ' ' '\n' >> ___plist_bin.txt
+ cat ___plist_bin.txt | LC_COLLATE=C sort | uniq > prog_list_bin.txt
+ \rm -f ___plist_bin.txt
+@@ -2884,7 +2884,7 @@ r_misc.o: rickr/r_misc.c rickr/r_misc.h
-+3dClustBust:3dClustBust.c
-+ $(CC) -o 3dClustBust 3dClustBust.c $(INFLAGS) $(LFLAGS) $(LLIBS)
-+
- mritopgm:mritopgm.c
- $(CC) -o mritopgm mritopgm.c $(INFLAGS) $(LFLAGS) $(LLIBS)
+ dcm2niix_afni:
+ ( cd crorden/dcm2niix_console ; \
+- make ; \
++ $(MAKE) ; \
+ $(MV) dcm2niix ../../dcm2niix_afni ; \
+ cd ../../ ; )
-@@ -2728,8 +2731,8 @@ cjpeg:
+@@ -3108,8 +3108,8 @@ libjpeg.a:
$(MAKE) clean ; $(RM) Makefile )
libXmHTML.a:
@@ -82,18 +81,19 @@
+ ( cd XmHTML ; $(MAKE) lib 'CC=$(CC)' 'II=$(IFLAGS)' ; \
+ $(MV) lib/libXmHTML.a .. ; $(MAKE) clean )
- thd_xwebber.o:thd_xwebber.c
- $(CC) -c thd_xwebber.c -I./XmHTML/include $(INFLAGS)
-@@ -3518,8 +3521,9 @@ toyR: toyR.c AFNI_embeddedRCall.o
+ xutil_webber.o:xutil_webber.c
+ $(CC) -c xutil_webber.c -I./XmHTML/include $(INFLAGS)
+@@ -3920,9 +3920,10 @@ toyR: toyR.c AFNI_embeddedRCall.o
####
- R_io.so:R_io.c libmri.a
+ R_io.so:R_io.c $(LIBMRI_OBJ)
( if which R >/dev/null ; then \
- echo PKG_CPPFLAGS = $(INFLAGS) > Makevars ;\
-- echo PKG_LIBS = $(LFLAGS) $(LLIBS) >> Makevars ;\
-- R CMD SHLIB R_io.c ; \
+- echo PKG_LIBS = $(LFLAGS) $(LLIBS) $(RLIB_CONVERT) >> Makevars ;\
+- R CMD SHLIB -o R_io.so R_io.c ; \
+ echo PKG_CPPFLAGS = $(INFLAGS) -I${LOCALBASE}/lib/R/include > Makevars ;\
-+ echo PKG_LIBS = $(LFLAGS) $(LLIBS) -L${LOCALBASE}/lib/R/lib >> Makevars ;\
-+ # Fails because R uses 'make' instead of gmake R CMD SHLIB -n R_io.c; \
++ echo PKG_LIBS = $(LFLAGS) $(LLIBS) $(RLIB_CONVERT) -L${LOCALBASE}/lib/R/lib >> Makevars ;\
++ # Fails because R uses 'make' instead of gmake: R CMD SHLIB -n R_io.c; \
+ $(MAKE) -f 'Makevars' -f '/usr/local/lib/R/etc/Makeconf' -f '/usr/local/lib/R/share/make/shlib.mk' SHLIB='R_io.so' OBJECTS='R_io.o';\
else echo WARNING: Cannot build R_io.so because R is not installed;\
fi ; )
+
Added: head/science/afni/files/patch-crorden_dcm2niix__console_makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/afni/files/patch-crorden_dcm2niix__console_makefile Mon May 20 19:35:57 2019 (r502158)
@@ -0,0 +1,24 @@
+--- crorden/dcm2niix_console/makefile.orig 2019-05-12 14:54:20 UTC
++++ crorden/dcm2niix_console/makefile
+@@ -1,8 +1,8 @@
+ # Regular use
+-CFLAGS=-s -O3
++CXXFLAGS?=-s -O3
+
+ # Debugging
+-#CFLAGS=-g
++#CXXFLAGS=-g
+
+ #run "make" for default build
+ #run "JPEGLS=1 make" for JPEGLS build
+@@ -14,8 +14,8 @@ endif
+ ifneq ($(OS),Windows_NT)
+ OS = $(shell uname)
+ ifeq "$(OS)" "Darwin"
+- CFLAGS=-dead_strip -O3
++ CXXFLAGS=-dead_strip -O3
+ 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
Modified: head/science/afni/files/patch-netcdf-3.5.0_src_configure
==============================================================================
--- head/science/afni/files/patch-netcdf-3.5.0_src_configure Mon May 20 18:10:55 2019 (r502157)
+++ head/science/afni/files/patch-netcdf-3.5.0_src_configure Mon May 20 19:35:57 2019 (r502158)
@@ -1,6 +1,6 @@
---- netcdf-3.5.0/src/configure.orig 2015-11-06 21:25:09 UTC
+--- netcdf-3.5.0/src/configure.orig 2019-05-10 21:23:56 UTC
+++ netcdf-3.5.0/src/configure
-@@ -933,10 +933,10 @@ echo "configure:928: checking for top-le
+@@ -933,10 +933,10 @@ echo "configure:928: checking for top-level source-dir
Added: head/science/afni/files/patch-prf__common__circular.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/afni/files/patch-prf__common__circular.c Mon May 20 19:35:57 2019 (r502158)
@@ -0,0 +1,18 @@
+--- 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 <stdlib.h>
++ #include <malloc_np.h>
++ malloc_stats_print(NULL, NULL, "g");
++#else
++ fprintf(stderr, "No malloc_stats() on this platform.\n");
+ #endif
+ }
+
Modified: head/science/afni/pkg-descr
==============================================================================
--- head/science/afni/pkg-descr Mon May 20 18:10:55 2019 (r502157)
+++ head/science/afni/pkg-descr Mon May 20 19:35:57 2019 (r502158)
@@ -1,5 +1,5 @@
-This is a port of AFNI, Analysis of Functional Neuro Imaging. AFNI is
-a tool for analyzing 3 dimensional images, especially functional MRI
-images used in brain mapping research.
+AFNI (Analysis of Functional Neuro Imaging) is a tool for analyzing
+3-dimensional images, especially functional MRI images used in brain mapping
+research.
WWW: http://afni.nimh.nih.gov/afni/
Modified: head/science/afni/pkg-plist
==============================================================================
--- head/science/afni/pkg-plist Mon May 20 18:10:55 2019 (r502157)
+++ head/science/afni/pkg-plist Mon May 20 19:35:57 2019 (r502158)
@@ -1,11 +1,12 @@
+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
@@ -23,6 +24,8 @@ bin/1dgrayplot
bin/1dmatcalc
bin/1dnorm
bin/1dplot
+bin/1dplot.py
+bin/1dsound
bin/1dsum
bin/1dsvd
bin/1dtranspose
@@ -54,11 +57,11 @@ bin/3dBRAIN_VOYAGERtoAFNI
bin/3dBandpass
bin/3dBlurInMask
bin/3dBlurToFWHM
+bin/3dBrainSync
bin/3dBrickStat
bin/3dCM
bin/3dCRUISEtoAFNI
bin/3dClipLevel
-bin/3dClustBust
bin/3dClustCount
bin/3dClustSim
bin/3dConformist
@@ -67,17 +70,17 @@ bin/3dCountSpikes
bin/3dDFT
bin/3dDTeig
bin/3dDTtoDWI
-bin/3dDTtoNoisyDWI
bin/3dDWItoDT
-bin/3dDWUncert
bin/3dDeconvolve
bin/3dDeconvolve_f
+bin/3dDegreeCentrality
bin/3dDespike
bin/3dDetrend
-bin/3dEigsToDT
+bin/3dECM
bin/3dEmpty
bin/3dEntropy
bin/3dErrtsCormat
+bin/3dExtractGroupInCorr
bin/3dExtrema
bin/3dFDR
bin/3dFFT
@@ -89,6 +92,7 @@ bin/3dGC.R
bin/3dGenFeatureDist
bin/3dGenPriors
bin/3dGetrow
+bin/3dGrayplot
bin/3dGroupInCorr
bin/3dHist
bin/3dICA.R
@@ -98,10 +102,12 @@ bin/3dIntracranial
bin/3dInvFMRI
bin/3dKS.R
bin/3dKruskalWallis
+bin/3dLFCD
bin/3dLME
bin/3dLME.R
bin/3dLRflip
bin/3dLSS
+bin/3dLocalACF
bin/3dLocalBistat
bin/3dLocalHistog
bin/3dLocalPV
@@ -109,17 +115,20 @@ bin/3dLocalSVD
bin/3dLocalstat
bin/3dMEMA
bin/3dMEMA.R
+bin/3dMEPFM
+bin/3dMEPFM.R
bin/3dMINCtoAFNI
+bin/3dMSE
bin/3dMVM
bin/3dMVM.R
+bin/3dMVM_validator
bin/3dMannWhitney
bin/3dMaskToASCII
-bin/3dMatch
bin/3dMax
bin/3dMean
bin/3dMedianFilter
+bin/3dMultiThresh
bin/3dNLfim
-bin/3dNetCorr
bin/3dNormalityTest
bin/3dNotes
bin/3dNwarpAdjust
@@ -132,18 +141,16 @@ bin/3dOverlap
bin/3dPAR2AFNI.pl
bin/3dPFM
bin/3dPFM.R
+bin/3dPVmap
bin/3dPeriodogram
bin/3dPolyfit
bin/3dProbTrackID
bin/3dPval
bin/3dQwarp
bin/3dREMLfit
-bin/3dROIMaker
bin/3dROIstats
-bin/3dRSFC
bin/3dRank
bin/3dRankizer
-bin/3dReHo
bin/3dRegAna
bin/3dRetinoPhase
bin/3dRowFillin
@@ -151,6 +158,7 @@ bin/3dRprogDemo
bin/3dRprogDemo.R
bin/3dSeg
bin/3dSetupGroupInCorr
+bin/3dSharpen
bin/3dSignatures
bin/3dSignatures.R
bin/3dSkullStrip
@@ -159,7 +167,6 @@ bin/3dStatClust
bin/3dSurf2Vol
bin/3dSurfMask
bin/3dSynthesize
-bin/3dTORTOISEtoHere
bin/3dTRfix
bin/3dTSgen
bin/3dTagalign
@@ -167,6 +174,7 @@ bin/3dTcat
bin/3dTcorr1D
bin/3dTcorrMap
bin/3dTcorrelate
+bin/3dTfilter
bin/3dTfitter
bin/3dThreetoRGB
bin/3dTnorm
@@ -178,7 +186,9 @@ bin/3dTrackID
bin/3dTshift
bin/3dTsmooth
bin/3dTsort
+bin/3dTsplit4D
bin/3dTstat
+bin/3dTto1D
bin/3dTwotoComplex
bin/3dUndump
bin/3dUnifize
@@ -190,6 +200,7 @@ bin/3dWarpDrive
bin/3dWavelets
bin/3dWilcoxon
bin/3dWinsor
+bin/3dXClustSim
bin/3dXYZcat
bin/3dZcat
bin/3dZcutup
@@ -232,6 +243,8 @@ bin/3dresample
bin/3dretroicor
bin/3drotate
bin/3dsvm
+bin/3dsvm_linpredict
+bin/3dtoXdataset
bin/3dttest
bin/3dttest++
bin/3dvolreg
@@ -249,6 +262,8 @@ bin/@Align_Centers
bin/@Atlasize
bin/@Center_Distance
bin/@CheckForAfniDset
+bin/@ClustExp_CatLab
+bin/@ClustExp_run_shiny
bin/@CommandGlobb
bin/@DO.examples
bin/@DTI_studio_reposition
@@ -271,14 +286,18 @@ bin/@GetAfniOrient
bin/@GetAfniPrefix
bin/@GetAfniRes
bin/@GetAfniView
+bin/@GradFlipTest
bin/@Install_3dPFM_Demo
bin/@Install_AfniRetinoDemo
bin/@Install_ClustScat_Demo
+bin/@Install_D99_macaque
bin/@Install_DBSproc
bin/@Install_FATCAT_DEMO
+bin/@Install_FATCAT_DEMO2
bin/@Install_FATMVM_DEMO
bin/@Install_InstaCorr_Demo
bin/@Install_MEICA_Demo
+bin/@Install_NIH_Marmoset
bin/@Install_RSFMRI_Motion_Group_Demo
bin/@Install_TSrestMovieDemo
bin/@IsoMasks
@@ -293,15 +312,18 @@ bin/@R_funclist
bin/@RenamePanga
bin/@Reorder
bin/@RetinoProc
+bin/@SSwarper
bin/@SUMA_AlignToExperiment
bin/@SUMA_FSvolToBRIK
bin/@SUMA_Make_Spec_Caret
bin/@SUMA_Make_Spec_FS
bin/@SUMA_Make_Spec_SF
+bin/@SUMA_renumber_FS
bin/@ScaleVolume
bin/@ScriptCheck
bin/@Shift_Volume
bin/@ShowDynamicRange
+bin/@SkullStrip_TouchUp
bin/@Spharm.examples
bin/@SurfSmooth.HEAT_07.examples
bin/@T1scale
@@ -310,42 +332,77 @@ bin/@ToRAI
bin/@UpdateAfni
bin/@VolCenter
bin/@afni.run.me
+bin/@afni_R_package_install
+bin/@afni_refacer_make_master
+bin/@afni_refacer_make_onebigA12
+bin/@afni_refacer_run
bin/@align_partial_oblique
bin/@auto_align
bin/@auto_tlrc
bin/@build_afni_Xlib
+bin/@chauffeur_afni
bin/@clean_help_dir
bin/@clip_volume
+bin/@compute_OC_weights
bin/@compute_gcor
bin/@demo_prompt
bin/@diff.files
bin/@diff.tree
+bin/@djunct_4d_imager
+bin/@djunct_4d_slices_to_3d_vol
+bin/@djunct_calc_mont_dims.py
+bin/@djunct_combine_str.py
+bin/@djunct_dwi_selector.tcsh
+bin/@djunct_edgy_align_check
+bin/@djunct_is_label.py
+bin/@djunct_montage_coordinator
+bin/@djunct_select_str.py
+bin/@djunct_slice_space
+bin/@djunct_vol_3slice_select
bin/@escape-
+bin/@extract_meica_ortvec
bin/@fast_roi
+bin/@fat_tract_colorize
bin/@fix_FSsphere
bin/@float_fix
+bin/@get.afni.version
bin/@global_parse
+bin/@grayplot
bin/@help.AFNI
bin/@isOblique
bin/@make_plug_diff
bin/@make_stim_file
+bin/@measure_bb_thick
+bin/@measure_erosion_thick
+bin/@measure_in2out
bin/@move.to.series.dirs
bin/@np
bin/@parse_afni_name
bin/@parse_name
bin/@radial_correlate
bin/@simulate_motion
+bin/@snapshot_volreg
+bin/@snapshot_volreg3
bin/@statauxcode
+bin/@suma_reprefixize_spec
+bin/@surf_to_vol_spackle
+bin/@thickness_master
bin/@toMNI_Awarp
bin/@toMNI_Qwarpar
bin/@update.afni.binaries
+bin/@xyz_to_ijk
bin/AFNI_Batch_R
bin/AFNI_atlas_spaces.niml
+bin/AFNI_version.txt
bin/AFNIio.R
bin/AFNIplot.R
bin/AlphaSim
bin/AnalyzeTrace
+bin/BayesianGroupAna.R
+bin/BayesianGroupAna.py
bin/BrainSkin
+bin/ClustExp_HistTable.py
+bin/ClustExp_StatParse.py
bin/CompareSurfaces
bin/ConvertDset
bin/ConvertSurface
@@ -357,6 +414,7 @@ bin/Dimon1
bin/DriveSuma
bin/ExamineXmat
bin/ExamineXmat.R
+bin/FATCAT_matplot
bin/FD2
bin/FIRdesign
bin/FSread_annot
@@ -366,12 +424,17 @@ bin/Ifile
bin/InstaTract
bin/IsoSurface
bin/Level2.R
+bin/MBA
+bin/MBA.R
bin/MakeColorMap
bin/MapIcosahedron
bin/ParseName
+bin/RBA
+bin/RBA.R
bin/ROI2dataset
bin/ROIgrow
bin/RSFgen
+bin/RetroTS.py
bin/SUMA_glxdino
bin/SUMA_paperplane
bin/SUMA_pixmap2eps
@@ -396,10 +459,17 @@ bin/SurfToSurf
bin/SurfaceMetrics
bin/Vecwarp
bin/Xphace
+bin/abids_json_info.py
+bin/abids_json_tool.py
+bin/abids_lib.py
+bin/abids_tool.py
bin/abut
bin/adwarp
bin/afni
bin/afni_base.py
+bin/afni_check_omp
+bin/afni_fs_aparc+aseg_2000.txt
+bin/afni_fs_aparc+aseg_2009.txt
bin/afni_history
bin/afni_open
bin/afni_proc.py
@@ -412,6 +482,8 @@ bin/afni_vcheck
bin/afni_xmat.py
bin/aiv
bin/align_epi_anat.py
+bin/apqc_make_html.py
+bin/apqc_make_tcsh.py
bin/apsearch
bin/ask_me.py
bin/auto_warp.py
@@ -422,8 +494,10 @@ bin/cifti_tool
bin/column_cat
bin/count
bin/db_mod.py
+bin/dcm2niix_afni
bin/demo.fixed.niml.do
bin/demo.mobile.niml.do
+bin/demoExpt.py
bin/dicom_hdr
bin/dicom_hinfo
bin/dicom_to_raw
@@ -435,6 +509,18 @@ bin/fat_mvm_gridconv.py
bin/fat_mvm_prep.py
bin/fat_mvm_review.py
bin/fat_mvm_scripter.py
+bin/fat_proc_align_anat_pair
+bin/fat_proc_axialize_anat
+bin/fat_proc_connec_vis
+bin/fat_proc_convert_dcm_anat
+bin/fat_proc_convert_dcm_dwis
+bin/fat_proc_decmap
+bin/fat_proc_dwi_to_dt
+bin/fat_proc_filter_dwis
+bin/fat_proc_grad_plot
+bin/fat_proc_imit2w_from_t1w
+bin/fat_proc_map_to_dti
+bin/fat_proc_select_vols
bin/fat_roi_row.py
bin/fdrval
bin/fftest
@@ -448,6 +534,9 @@ bin/gen_epi_review.py
bin/gen_group_command.py
bin/gen_ss_review_scripts.py
bin/gen_ss_review_table.py
+bin/get_afni_model_PRF
+bin/get_afni_model_PRF_6
+bin/get_afni_model_PRF_6_BAD
bin/gifti_tool
bin/gui_uber_align_test.py
bin/gui_uber_skel.py
@@ -472,12 +561,22 @@ bin/imupsam
bin/inspec
bin/lib_RR_plot.py
bin/lib_afni1D.py
+bin/lib_apqc_html.py
+bin/lib_apqc_html_css.py
+bin/lib_apqc_html_helps.py
+bin/lib_apqc_io.py
+bin/lib_apqc_tcsh.py
+bin/lib_decay_timing.py
+bin/lib_dti_sundry.py
bin/lib_fat_Rfactor.py
bin/lib_fat_funcs.py
bin/lib_fat_plot_sel.py
bin/lib_matplot.py
+bin/lib_plot_1D.py
bin/lib_qt_gui.py
+bin/lib_rand_timing.py
bin/lib_realtime.py
+bin/lib_ss_review.py
bin/lib_subjects.py
bin/lib_surf_clustsim.py
bin/lib_system_check.py
@@ -493,7 +592,6 @@ bin/lpc_align.py
bin/make_pq_script.py
bin/make_random_timing.py
bin/make_stim_times.py
-bin/map_TrackID
bin/mayo_analyze
bin/meica.py
bin/module_test_lib.py
@@ -503,17 +601,19 @@ bin/myget
bin/neuro_deconvolve.py
bin/nicat
bin/niccc
-bin/nifti1_test
bin/nifti1_tool
bin/nifti_tool
bin/niml_feedme
bin/niprobe
bin/nsize
bin/option_list.py
+bin/p2dsetstat
+bin/parse_fs_lt_log.py
bin/plugout_drive
bin/plugout_ijk
bin/plugout_tt
bin/plugout_tta
+bin/prompt_popup
bin/prompt_user
bin/python_module_test.py
bin/quick.alpha.vals.py
@@ -532,18 +632,22 @@ bin/siemens_vision
bin/slow_surf_clustsim.py
bin/smooth.R
bin/sqwave
+bin/stimband
bin/strblast
bin/suma
bin/suma_change_spec
+bin/tedana_wrapper.py
bin/tfim
bin/timing_tool.py
bin/to3d
+bin/tokens
bin/uber_align_test.py
bin/uber_proc.py
bin/uber_skel.py
bin/uber_subject.py
bin/uber_ttest.py
bin/ui_xmat.py
+bin/unWarpEPI.py
bin/uniq_images
bin/waver
bin/whereami
@@ -577,7 +681,7 @@ include/afni/mri_warpfield.h
include/afni/mrilib.h
include/afni/multivector.h
include/afni/nifti1.h
-include/afni/nifti1_io.h
+include/afni/nifti2_io.h
include/afni/nifticdf.h
include/afni/niml.h
include/afni/r_idisp.h
@@ -593,7 +697,6 @@ include/afni/thd_ttatlas_CA_EZ.h
include/afni/thd_ttatlas_query.h
include/afni/vecmat.h
include/afni/vol2surf.h
-include/afni/volpack.h
include/afni/znzlib.h
lib/afni/R_io.so
lib/afni/libGLws.a
@@ -601,11 +704,12 @@ lib/afni/libSUMA.a
lib/afni/libcoxplot.a
lib/afni/libmri.a
lib/afni/libmrix.a
-lib/afni/libvolpack.a
lib/afni/model_beta.so
lib/afni/model_constant.so
lib/afni/model_conv_PRF.so
lib/afni/model_conv_PRF_6.so
+lib/afni/model_conv_PRF_6_BAD.so
+lib/afni/model_conv_PRF_DOG.so
lib/afni/model_conv_cosine4.so
lib/afni/model_conv_diffgamma.so
lib/afni/model_convgamma.so
@@ -666,7 +770,6 @@ lib/afni/plug_permtest.so
lib/afni/plug_power.so
lib/afni/plug_realtime.so
lib/afni/plug_rename.so
-lib/afni/plug_render.so
lib/afni/plug_reorder.so
lib/afni/plug_retroicor.so
lib/afni/plug_roiedit.so
@@ -682,330 +785,13 @@ lib/afni/plug_vol2surf.so
lib/afni/plug_volreg.so
lib/afni/plug_wavelets.so
lib/afni/plug_zeropad.so
-libexec/meica.libs/alignp_mepi_anat.py
-libexec/meica.libs/mdp/__init__.py
-libexec/meica.libs/mdp/caching/__init__.py
-libexec/meica.libs/mdp/caching/caching_extension.py
-libexec/meica.libs/mdp/classifier_node.py
-libexec/meica.libs/mdp/configuration.py
-libexec/meica.libs/mdp/extension.py
-libexec/meica.libs/mdp/graph/__init__.py
-libexec/meica.libs/mdp/graph/graph.py
-libexec/meica.libs/mdp/helper_funcs.py
-libexec/meica.libs/mdp/hinet/__init__.py
-libexec/meica.libs/mdp/hinet/flownode.py
-libexec/meica.libs/mdp/hinet/hinet.css
-libexec/meica.libs/mdp/hinet/htmlvisitor.py
-libexec/meica.libs/mdp/hinet/layer.py
-libexec/meica.libs/mdp/hinet/switchboard.py
-libexec/meica.libs/mdp/hinet/switchboard_factory.py
-libexec/meica.libs/mdp/linear_flows.py
-libexec/meica.libs/mdp/nodes/__init__.py
-libexec/meica.libs/mdp/nodes/classifier_nodes.py
-libexec/meica.libs/mdp/nodes/convolution_nodes.py
-libexec/meica.libs/mdp/nodes/em_nodes.py
-libexec/meica.libs/mdp/nodes/expansion_nodes.py
-libexec/meica.libs/mdp/nodes/fda_nodes.py
-libexec/meica.libs/mdp/nodes/ica_nodes.py
-libexec/meica.libs/mdp/nodes/ica_nodes.py~
-libexec/meica.libs/mdp/nodes/ica_nodes_old.py
*** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
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