From 1fd30cbfb13b50d1d93269344921505777809459 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 19 Jun 2020 01:36:54 -0400 Subject: sci-biology/fsl: dropped deprecated versions no longer compatible with current GCC and fslpy unbundling Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: Horea Christian --- sci-biology/fsl/Manifest | 3 - sci-biology/fsl/files/fsl-5.0.11-no_xmlpp.patch | 44 -- .../fsl/files/fsl-5.0.11-qstring_compat.patch | 63 --- sci-biology/fsl/files/fsl-5.0.11-setup.patch | 158 ------- sci-biology/fsl/files/fsl-5.0.4-headers.patch | 32 -- sci-biology/fsl/files/fsl-5.0.4-setup.patch | 110 ----- sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch | 456 --------------------- sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch | 452 -------------------- sci-biology/fsl/files/fsl-5.0.8-headers.patch | 21 - sci-biology/fsl/files/fsl-5.0.8-setup.patch | 113 ----- sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch | 456 --------------------- sci-biology/fsl/files/fsl-5.0.9-setup.patch | 115 ------ sci-biology/fsl/fsl-5.0.11.ebuild | 157 ------- sci-biology/fsl/fsl-5.0.8.ebuild | 148 ------- sci-biology/fsl/fsl-5.0.9.ebuild | 142 ------- 15 files changed, 2470 deletions(-) delete mode 100644 sci-biology/fsl/files/fsl-5.0.11-no_xmlpp.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.11-qstring_compat.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.11-setup.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.4-headers.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.4-setup.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.8-headers.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.8-setup.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.9-setup.patch delete mode 100644 sci-biology/fsl/fsl-5.0.11.ebuild delete mode 100644 sci-biology/fsl/fsl-5.0.8.ebuild delete mode 100644 sci-biology/fsl/fsl-5.0.9.ebuild diff --git a/sci-biology/fsl/Manifest b/sci-biology/fsl/Manifest index b38299817..ce2b4be84 100644 --- a/sci-biology/fsl/Manifest +++ b/sci-biology/fsl/Manifest @@ -1,4 +1 @@ -DIST fsl-5.0.11.tar.gz 1507525689 BLAKE2B 212941aa6fb74c1c42f8b11d8e6803f1dfba50f1cdcb4092bfdf98d6832c552fcad59843a8db9e8887b98f86ce255fd9e80e3219a48286d7defe4544f0344225 SHA512 6f859723f8e4bd7e381761983f6423364180f5d3300cb165a3e57f3535d5301624ecb30c1796dae9579da5dd16e80a8a62d9994fec1caebf0835c2f6795ca055 -DIST fsl-5.0.8-sources.tar.gz 1420879532 BLAKE2B fab46d286b9c083f31408e885235a72a195f14a1e863264e8cbff2b6cfb8c70ef335cafe58dff38141b1d027aef301e94212da4c9b6d3f4306ba60c81e19cec7 SHA512 8dedf13d633d71fa28c5dd6591fab4adda4893b76467affa6f58aee917ee3fdc83da07d8f505feb61ac2733de1bfb84f7f9ff74589756946be21cdb9f057f0f0 -DIST fsl-5.0.9-sources.tar.gz 1491426239 BLAKE2B 310c4eb131856120f803d67f18e4d4e97df1ff22143bffa45be5f8abe31a01ce3df5a64abf5d065670b95394249a2f569a66a9cc22cd004b03e868e823d4555d SHA512 86a33084cf880ea1341ff8622eb13a364a462018a0fac55ee291dd8917e8453701db57f35529e144d419ea744397906b586b88acaf9a2dea0291fa3101ebb27d DIST fsl-6.0.2.tar.gz 2505331864 BLAKE2B 0fbc23c788e0960e41a895f8eddd346e8facfae448c637eca18d39b142f8aabd9531427ce4ff97c634fdc5d16a74163947c7bade219a8900722815321144b41e SHA512 fe308393076c51c50b086f9bf7ff5ddebcf8b1284128e734b9d9e501019917ceba7c0ee5cd5aa1ed44452bcd042ad72653c1a8693f94eab9b83a80fe508a56ca diff --git a/sci-biology/fsl/files/fsl-5.0.11-no_xmlpp.patch b/sci-biology/fsl/files/fsl-5.0.11-no_xmlpp.patch deleted file mode 100644 index bccf0e238..000000000 --- a/sci-biology/fsl/files/fsl-5.0.11-no_xmlpp.patch +++ /dev/null @@ -1,44 +0,0 @@ -diff --git a/src/flameo/Makefile b/src/flameo/Makefile -index 5389e2f..52785c3 100644 ---- a/src/flameo/Makefile -+++ b/src/flameo/Makefile -@@ -2,7 +2,7 @@ include ${FSLCONFDIR}/default.mk - - PROJNAME = flame - --USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio -+USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio - USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} - - UNAME := $(shell uname) -@@ -10,7 +10,7 @@ ifeq (${UNAME},Darwin) - LIBS = -liconv - endif - --LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lfslio -lniftiio -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lprob -lz -+LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lfslio -lniftiio ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lprob -lz - - XFILES = flameo - -diff --git a/src/melodic/Makefile b/src/melodic/Makefile -index 53b951a..803c39e 100644 ---- a/src/melodic/Makefile -+++ b/src/melodic/Makefile -@@ -7,7 +7,7 @@ OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui - - PROJNAME = melodic - --USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio -+USRINCFLAGS = -fPIC -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -I${FSLEXTINC} ${CIFTICFLAGS} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio - USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB} - - UNAME := $(shell uname) -@@ -15,7 +15,7 @@ ifeq (${UNAME},Darwin) - LIBS = -liconv - endif - --LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lfslio -lniftiio -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm -lgdc -lgd -lpng -lz -+LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lfslio -lniftiio ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm -lgdc -lgd -lpng -lz - - TEST_OBJS = test.o - diff --git a/sci-biology/fsl/files/fsl-5.0.11-qstring_compat.patch b/sci-biology/fsl/files/fsl-5.0.11-qstring_compat.patch deleted file mode 100644 index 78aa020c6..000000000 --- a/sci-biology/fsl/files/fsl-5.0.11-qstring_compat.patch +++ /dev/null @@ -1,63 +0,0 @@ -From bbd60f634cdcdfbbb3eb8f3b6d00f366d9f34bf9 Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?Fran=C3=A7ois=20Bissey?= -Date: Thu, 18 Oct 2018 11:21:05 +1300 -Subject: [PATCH] Basic compatibility between for AString built with either - glib ustring or QString - ---- - src/flameo/gsa.cc | 4 ++-- - src/melodic/meldata.cc | 2 +- - src/melodic/meldata.h | 2 +- - 3 files changed, 4 insertions(+), 4 deletions(-) - -diff --git a/src/flameo/gsa.cc b/src/flameo/gsa.cc -index 6a477f9..0860d46 100644 ---- a/src/flameo/gsa.cc -+++ b/src/flameo/gsa.cc -@@ -74,7 +74,7 @@ namespace GSA { - sourceType=mode; - if ( sourceType.compare("CIFTI") == 0 ) { - cifti::CiftiFile inputCifti; -- inputCifti.openFile(fslbasename(filename)+".nii"); -+ inputCifti.openFile((fslbasename(filename)+".nii").c_str()); - ciftiExemplar=inputCifti.getCiftiXML(); - cerr << "ndim " << ciftiExemplar.getNumberOfDimensions() << endl; - cerr << "type1 " << ciftiExemplar.getMappingType(0) << endl; -@@ -194,7 +194,7 @@ namespace GSA { - scalarsMap.setLength(data.Nrows()); - ciftiExemplar.setMap(0, scalarsMap); - CiftiFile outputFile; -- outputFile.setWritingFile(fslbasename(filename)+extension+".nii");//sets up on-disk writing with default writing version -+ outputFile.setWritingFile((fslbasename(filename)+extension+".nii").c_str());//sets up on-disk writing with default writing version - outputFile.setCiftiXML(ciftiExemplar,false); - vector scratchRow(data.Nrows());//read/write a row at a time - for (int64_t row=0;row& dims = inputCifti.getDimensions(); - tmpData.ReSize(dims[0],dims[1]); //swapped compared to cifti - vector scratchRow(dims[0]);//read/write a row at a time -diff --git a/src/melodic/meldata.h b/src/melodic/meldata.h -index 1e1adfc..d898152 100644 ---- a/src/melodic/meldata.h -+++ b/src/melodic/meldata.h -@@ -109,7 +109,7 @@ namespace Melodic{ - message(" " << logger.appendDir(fname) << endl); - } else { //Process CIFTI save ICs as float - cifti::CiftiFile outputFile; -- outputFile.setWritingFile(logger.appendDir(fname)+".nii");//sets up on-disk writing with default writing version -+ outputFile.setWritingFile((logger.appendDir(fname)+".nii").c_str());//sets up on-disk writing with default writing version - cifti::CiftiXML xml(inputCifti.getCiftiXML()); - cifti::CiftiScalarsMap scalarsMap; - std::vector foo = xml.writeXMLToVector(); --- -2.18.1 - diff --git a/sci-biology/fsl/files/fsl-5.0.11-setup.patch b/sci-biology/fsl/files/fsl-5.0.11-setup.patch deleted file mode 100644 index cf9cb785d..000000000 --- a/sci-biology/fsl/files/fsl-5.0.11-setup.patch +++ /dev/null @@ -1,158 +0,0 @@ -diff --git a/build b/build -index 6827443..19b2002 100755 ---- a/build -+++ b/build -@@ -3,7 +3,7 @@ - if [ $# -ge 1 ] ; then - PROJECTS="$@"; - else -- MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ -+ MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ - meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \ - DiscreteOpt FastPDlib MSMRegLib \ - misc_c avwutils basil bet2 cluster dpm copain tissue fast4 feat5 film filmbabe flirt fabber baycest \ -@@ -25,8 +25,8 @@ flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp verbena MSM bianca - done - fi - --echo "Building projects - see build.log file for progress..." --./config/common/buildproj $PROJECTS > ./build.log 2>&1 -+echo "Building projects" -+./config/common/buildproj $PROJECTS - finalStatus=$? - if [ $finalStatus -eq 0 ]; then - echo "Build completed successfully."; -diff --git a/config/common/buildproj b/config/common/buildproj -index 3450bda..ec3edc1 100755 ---- a/config/common/buildproj -+++ b/config/common/buildproj -@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then - fi - PROJECTS="$@" ; export PROJECTS ; - --FSLDIR=`pwd` -+#FSLDIR=`pwd` - FSLDEVDIR=${FSLDIR} - FSLCONFDIR=${FSLDIR}/config --FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` -+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` - export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE - - buildmessages="" ; export buildmessages ; -@@ -66,7 +66,7 @@ for projname in $PROJECTS; do - if [ -x ./fslconfig ] ; then - . ./fslconfig ; - fi -- if ${MAKE} -k ${MAKEOPTIONS} ; then -+ if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then - if ${MAKE} ${MAKEOPTIONS} install ; then - installok=true; - # Clean up after ourselves -@@ -81,6 +81,7 @@ for projname in $PROJECTS; do - if [ $installok = false ] ; then - echo " " - echo "ERROR::Could not install $projname successfully" ; -+ exit 1 - fi - else - echo " " -@@ -89,6 +90,7 @@ for projname in $PROJECTS; do - echo " " - echo " " - errorprojs="$errorprojs $projname" ; export errorprojs ; -+ exit 1 - fi - fi - done -diff --git a/config/common/vars.mk b/config/common/vars.mk -index 53754be..ff7a117 100755 ---- a/config/common/vars.mk -+++ b/config/common/vars.mk -@@ -24,15 +24,15 @@ USRINCFLAGS = - USRCFLAGS = - USRCXXFLAGS = - --LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} -+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS} - --AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} -+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS} - - CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ -- ${AccumulatedIncFlags} -+ ${AccumulatedIncFlags} ${USERCFLAGS} - --CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ -- ${AccumulatedIncFlags} -+CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ -+ ${AccumulatedIncFlags} ${USERCXXFLAGS} - - HFILES = *.h - AFILES = *.a -diff --git a/config/generic/systemvars.mk b/config/generic/systemvars.mk -index e40e3d6..ddb5bfe 100755 ---- a/config/generic/systemvars.mk -+++ b/config/generic/systemvars.mk -@@ -4,20 +4,20 @@ SHELL = /bin/sh - - # System dependent commands (NB: the first two are the most platform dependent) - --INSTALL = ginstall -p --RANLIB = ranlib -+INSTALL = install -p -+RANLIB = @@GENTOO_RANLIB@@ - - RM = /bin/rm - CP = /bin/cp - MV = /bin/mv - CHMOD = /bin/chmod - MKDIR = /bin/mkdir --TCLSH = ${FSLDIR}/bin/fsltclsh -+TCLSH = tclsh - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC = @@GENTOO_CC@@ -+CXX = @@GENTOO_CXX@@ - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -25,7 +25,7 @@ ARCHFLAGS = - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS = - MACHDBGFLAGS = - GNU_ANSI_FLAGS = -Wall -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn -diff --git a/extras/build b/extras/build -index 6133a1b..caeae2d 100755 ---- a/extras/build -+++ b/extras/build -@@ -104,8 +104,8 @@ PROJECTS="${PROJECTS} libpng" - if [ ${BUILDICONV} -eq 1 ]; then - PROJECTS="${PROJECTS} libiconv" - fi --PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw" --PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxml++-2.34.0 libsqlite libnlopt ../include/armawrap/dummy_newmat" -+PROJECTS="libgdc libprob libcprob newmat cprob newran" -+PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat" - for projname in $PROJECTS; do - if [ -d $FSLESRCDIR/$projname ] ; then - buildIt $FSLESRCDIR $projname 1 -diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile -index b3a32fc..e949ba1 100755 ---- a/src/mist-clean/Makefile -+++ b/src/mist-clean/Makefile -@@ -52,7 +52,7 @@ installpython: - cp -r python/* ${DESTDIR}/python/mist - - clean: -- rm ${OBJS} mist/mist.o mist/mist -+ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion." - - .PHONY: all clean installdata - diff --git a/sci-biology/fsl/files/fsl-5.0.4-headers.patch b/sci-biology/fsl/files/fsl-5.0.4-headers.patch deleted file mode 100644 index 803151bb7..000000000 --- a/sci-biology/fsl/files/fsl-5.0.4-headers.patch +++ /dev/null @@ -1,32 +0,0 @@ ---- src/avwutils/fslmaths.cc.orig 2013-10-19 00:17:44.765129309 +1300 -+++ src/avwutils/fslmaths.cc 2013-10-19 00:18:02.975157728 +1300 -@@ -71,7 +71,7 @@ - #include "newimage/newimageall.h" - #include "miscmaths/miscmaths.h" - #include "utils/fsl_isfinite.h" --#include "libprob/libprob.h" -+#include "libprob.h" - - using namespace MISCMATHS; - using namespace NEWIMAGE; ---- src/miscvis/writepng.c.orig 2013-10-19 00:18:32.415203592 +1300 -+++ src/miscvis/writepng.c 2013-10-19 00:19:05.414255132 +1300 -@@ -32,6 +32,7 @@ - - #include /* for exit() prototype */ - -+#include "zlib.h" - #include "png.h" /* libpng header; includes zlib.h and setjmp.h */ - #include "writepng.h" /* typedefs, common macros, public prototypes */ - ---- src/ptx2/surfmaths.cc.orig 2013-10-19 00:19:51.595327317 +1300 -+++ src/ptx2/surfmaths.cc 2013-10-19 00:20:09.284354805 +1300 -@@ -72,7 +72,7 @@ - #include "csv_mesh.h" - #include "miscmaths/miscmaths.h" - #include "utils/fsl_isfinite.h" --#include "libprob/libprob.h" -+#include "libprob.h" - - using namespace MISCMATHS; - diff --git a/sci-biology/fsl/files/fsl-5.0.4-setup.patch b/sci-biology/fsl/files/fsl-5.0.4-setup.patch deleted file mode 100644 index 0b961492a..000000000 --- a/sci-biology/fsl/files/fsl-5.0.4-setup.patch +++ /dev/null @@ -1,110 +0,0 @@ ---- extras/build.orig 2013-10-18 21:37:53.533939550 +1300 -+++ extras/build 2013-10-18 21:40:42.283158471 +1300 -@@ -41,7 +41,7 @@ - - errorprojs="" ; export errorprojs ; - --PROJECTS="tcl tk zlib libpng libiconv libgd libgdc libprob libcprob newmat cprob newran cephes fftw" -+PROJECTS="libgdc libprob libcprob newmat cprob newran cephes" - - for projname in $PROJECTS; do - ---- build.orig 2013-10-18 22:24:22.312777248 +1300 -+++ build 2013-10-18 22:24:59.161835107 +1300 -@@ -11,8 +11,7 @@ - ifit load_varian load_dicom misc_scripts fdt first possum sgeutils flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp"; - fi - --echo "Building projects - see build.log file for progress..." --./config/common/buildproj $PROJECTS > ./build.log 2>&1 --echo "Finished build : end of log file shows ..." --tail -10 build.log -+echo "Building projects" -+./config/common/buildproj $PROJECTS -+echo "Finished build" - ---- config/common/buildproj.orig 2013-10-18 22:28:40.683182435 +1300 -+++ config/common/buildproj 2013-10-18 22:29:09.612227825 +1300 -@@ -11,10 +11,10 @@ - fi - PROJECTS="$@" ; export PROJECTS ; - --FSLDIR=`pwd` -+#FSLDIR=`pwd` - FSLDEVDIR=${FSLDIR} - FSLCONFDIR=${FSLDIR}/config --FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` -+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` - export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE - - buildmessages="" ; export buildmessages ; ---- config/generic/systemvars.mk.orig 2007-07-13 23:00:20.000000000 +1200 -+++ config/generic/systemvars.mk 2013-10-18 23:13:06.472693414 +1300 -@@ -4,20 +4,20 @@ - - # System dependent commands (NB: the first two are the most platform dependent) - --INSTALL = ginstall -p --RANLIB = ranlib -+INSTALL = install -p -+RANLIB = @@GENTOO_RANLIB@@ - - RM = /bin/rm - CP = /bin/cp - MV = /bin/mv - CHMOD = /bin/chmod - MKDIR = /bin/mkdir --TCLSH = ${FSLDIR}/bin/fsltclsh -+TCLSH = tclsh - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC = @@GENTOO_CC@@ -+CXX = @@GENTOO_CXX@@ - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -25,7 +25,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS = - MACHDBGFLAGS = - GNU_ANSI_FLAGS = -Wall -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn ---- config/common/vars.mk.orig 2013-10-18 23:39:26.384029157 +1300 -+++ config/common/vars.mk 2013-10-18 23:40:49.489145387 +1300 -@@ -24,15 +24,15 @@ - USRCFLAGS = - USRCXXFLAGS = - --LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} -+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS} - --AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} -+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS} - - CFLAGS = ${ANSI_FLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ -- ${AccumulatedIncFlags} -+ ${AccumulatedIncFlags} ${USERCFLAGS} - - CXXFLAGS = ${ANSI_FLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ -- ${AccumulatedIncFlags} -+ ${AccumulatedIncFlags} ${USERCXXFLAGS} - - HFILES = *.h - AFILES = *.a ---- config/common/buildproj.orig 2013-10-19 23:27:10.477238469 +1300 -+++ config/common/buildproj 2013-10-19 23:28:32.207370622 +1300 -@@ -66,7 +66,7 @@ - if [ -x fslconfig ] ; then - ./fslconfig ; - fi -- if ${MAKE} -k ${MAKEOPTIONS} ; then -+ if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then - if ${MAKE} install ; then - installok=true; - # Clean up after ourselves diff --git a/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch deleted file mode 100644 index a4fff260f..000000000 --- a/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch +++ /dev/null @@ -1,456 +0,0 @@ ---- src/fast4/fast_two.cc.orig 2013-10-19 23:45:02.636971888 +1300 -+++ src/fast4/fast_two.cc 2013-10-19 23:46:45.436138299 +1300 -@@ -166,7 +166,7 @@ - string csfPriorName, grayPriorName, whitePriorName; - if(alternatePriors.unset()) - { -- string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_"; -+ string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_"; - csfPriorName = priorRootName+"csf"; - grayPriorName = priorRootName+"gray"; - whitePriorName = priorRootName+"white"; -@@ -215,15 +215,15 @@ - if(bapused>0) - { - char reg[1024]; -- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str()); -+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str()); - if(verbose.value()) - cout< normalisedContrasts, model, triggers; -- string fmriFileName, fslPath, featdir, vType, indexText; -+ string fmriFileName, featdir, vType, indexText; - ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4); - bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false); - bool zWeightClusters(true); -@@ -307,7 +307,6 @@ - if (argc<2) usage(""); - featdir=string(argv[1]); - fmriFileName=featdir+"/filtered_func_data"; -- fslPath=string(getenv("FSLDIR")); - - string outputName(featdir); - -@@ -725,7 +724,7 @@ - cerr << "Can't open output report file " << outputName << endl; - exit(1); - } -- outputFile << "\n"<< statType << num2str(i) <<"\n\n
\n

FEAT Time Series Report - "<< statType << num2str(i) <<"

\n
\n
Full plots

\n"<< graphText; -+ outputFile << "\n"<< statType << num2str(i) <<"\n\n

\n

FEAT Time Series Report - "<< statType << num2str(i) <<"

\n
\n
Full plots

\n"<< graphText; - if (useTriggers) outputFile << "\n

Peristimulus plots

\n"<< peristimulusText <<"\n

\n\n"; - else outputFile << "\n\n\n"; - outputFile.close(); -@@ -740,7 +739,7 @@ - cerr << "Can't open output report file " << outputName << endl; - exit(1); - } -- outputFile << "\nFEAT Time Series Report\n\n
\n

FEAT Time Series Report

\n
\n
" << indexText << "
" << endl << endl; -+ outputFile << "\nFEAT Time Series Report\n\n
\n

FEAT Time Series Report

\n
\n
" << indexText << "
" << endl << endl; - outputFile.close(); - - /* now output same thing without start and end, for inclusion in feat report */ ---- src/feat5/feat_model.cc.orig 2013-10-19 23:52:13.456668655 +1300 -+++ src/feat5/feat_model.cc 2013-10-19 23:53:31.655795065 +1300 -@@ -734,7 +734,6 @@ - vector G; - vector titles; - float tr, mult, trmult, nltffwhm=0, maxconvwin=0; -- char fl[10000], *FSLDIR; - string fn, filename; - FONT_DATA *font_data = new FONT_DATA[1]; - -@@ -753,8 +752,6 @@ - if (argc==3) - motionparams=remmean(read_ascii_matrix(argv[2])); - -- FSLDIR=getenv("FSLDIR"); -- - fn = string(argv[1])+".fsf"; - - level = atoi(find_line(fn, "fmri(level)", fl)); -@@ -1479,7 +1476,7 @@ - writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE); - writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G); - -- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite "+string(argv[1])+".ppm "; -+ filename="wpng -q -overwrite "+string(argv[1])+".ppm "; - system(filename.c_str()); - - return(0); -@@ -2122,6 +2119,6 @@ - - fclose(outputfile); - -- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename; -+ filename="wpng -q -overwrite " + filename; - system(filename.c_str()); - } ---- src/first/first_utils.cc.orig 2013-10-19 23:54:30.375890034 +1300 -+++ src/first/first_utils.cc 2013-10-19 23:59:11.706344887 +1300 -@@ -1954,8 +1954,8 @@ - if (!surfaceVAout.value()) { - // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise) - volume refim; -- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } -- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } -+ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } -+ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } - volume maskvol(refim); - maskvol=0.0f; - volume4D volnormals; ---- src/fnirt/fnirtfns.cpp.orig 2013-10-20 00:00:18.106452166 +1300 -+++ src/fnirt/fnirtfns.cpp 2013-10-20 00:04:56.005901533 +1300 -@@ -1203,8 +1203,7 @@ - return(string(ref_fname)); - } - else { -- const char *fsldir_ptr = getenv("FSLDIR"); -- string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname; -+ string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname; - if (NEWIMAGE::fsl_imageexists(eref_fname)) return(eref_fname); - else return(string("")); - } -@@ -1230,9 +1229,8 @@ - NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist - eref_fname = ref_fname; - } -- catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard -- const char *fsldir_ptr = getenv("FSLDIR"); -- eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname; -+ catch(...) { // Didn't exist in current directory, try in .../data/standard -+ eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname; - try { - cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl; - NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist -@@ -1267,8 +1265,7 @@ - if (check_exist(ecfname)) return(ecfname); - } - if (!FNIRT::path(cfname).length()) { // If no path explicitly given -- const char *fsldir_ptr = getenv("FSLDIR"); -- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname; -+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname; - if (check_exist(ecfname)) return(ecfname); - else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given - ecfname += string(".cnf"); ---- src/fslsurface/fslsurface_first.cc.orig 2013-10-20 00:05:35.495965454 +1300 -+++ src/fslsurface/fslsurface_first.cc 2013-10-20 00:06:54.346092913 +1300 -@@ -500,8 +500,7 @@ - - volume* immni = new volume(); - -- char* fsldir = getenv("FSLDIR"); -- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm"); -+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); - - //read_volume_hdr_only(*immni, template_name); - -@@ -699,8 +698,7 @@ - - volume* immni = new volume(); - -- char* fsldir = getenv("FSLDIR"); -- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm"); -+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); - - //read_volume_hdr_only(*immni, template_name); - ---- src/fslsurface/fslsurfacemaths.cpp.orig 2013-10-20 00:07:39.457165850 +1300 -+++ src/fslsurface/fslsurfacemaths.cpp 2013-10-20 00:09:28.396341998 +1300 -@@ -598,12 +598,6 @@ - - }else if (command == "-reconFromBvars"){ - cout<<"do recon "<" << endl -+ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl - << "" - << "FSL" << endl - << "