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authorHorea Christian <chr@chymera.eu>2020-06-19 01:36:54 -0400
committerHorea Christian <chr@chymera.eu>2020-06-19 01:36:54 -0400
commit1fd30cbfb13b50d1d93269344921505777809459 (patch)
tree6ba02f0972faae2a8081a99854d0dcc34c2030a6
parentsci-biology/fsl: gcc compatibility (diff)
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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 <chr@chymera.eu>
-rw-r--r--sci-biology/fsl/Manifest3
-rw-r--r--sci-biology/fsl/files/fsl-5.0.11-no_xmlpp.patch44
-rw-r--r--sci-biology/fsl/files/fsl-5.0.11-qstring_compat.patch63
-rw-r--r--sci-biology/fsl/files/fsl-5.0.11-setup.patch158
-rw-r--r--sci-biology/fsl/files/fsl-5.0.4-headers.patch32
-rw-r--r--sci-biology/fsl/files/fsl-5.0.4-setup.patch110
-rw-r--r--sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch456
-rw-r--r--sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch452
-rw-r--r--sci-biology/fsl/files/fsl-5.0.8-headers.patch21
-rw-r--r--sci-biology/fsl/files/fsl-5.0.8-setup.patch113
-rw-r--r--sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch456
-rw-r--r--sci-biology/fsl/files/fsl-5.0.9-setup.patch115
-rw-r--r--sci-biology/fsl/fsl-5.0.11.ebuild157
-rw-r--r--sci-biology/fsl/fsl-5.0.8.ebuild148
-rw-r--r--sci-biology/fsl/fsl-5.0.9.ebuild142
15 files changed, 0 insertions, 2470 deletions
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?= <frp.bissey@gmail.com>
-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<float> scratchRow(data.Nrows());//read/write a row at a time
- for (int64_t row=0;row<data.Ncols();row++) {
-diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
-index f310dc7..5e9bc18 100644
---- a/src/melodic/meldata.cc
-+++ b/src/melodic/meldata.cc
-@@ -118,7 +118,7 @@ namespace Melodic{
- tmpData = RawData.matrix(Mask);
- memmsg(" after reshape ");
- } else { //Read in Cifti
-- inputCifti.openFile(fname+".nii");
-+ inputCifti.openFile((fname+".nii").c_str());
- const vector<int64_t>& dims = inputCifti.getDimensions();
- tmpData.ReSize(dims[0],dims[1]); //swapped compared to cifti
- vector<float> 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<char> 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 <stdlib.h> /* 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<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout << reg << endl;
- system(reg);
---- src/feat5/tsplot.cc.orig 2013-10-19 23:48:08.997273362 +1300
-+++ src/feat5/tsplot.cc 2013-10-19 23:50:59.376548902 +1300
-@@ -293,7 +293,7 @@
- ofstream outputFile;
- int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600);
- vector<double> 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 << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
-+ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
- if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
- else outputFile << "\n</BODY></HTML>\n\n";
- outputFile.close();
-@@ -740,7 +739,7 @@
- cerr << "Can't open output report file " << outputName << endl;
- exit(1);
- }
-- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
-+ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << 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<int> G;
- vector<string> 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<float> 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<float> maskvol(refim);
- maskvol=0.0f;
- volume4D<float> 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<float>* immni = new volume<float>();
-
-- 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<float>* immni = new volume<float>();
-
-- 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;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- reconSurface_from_bvars( surf, string(argv[i_arg+1]));
-@@ -612,12 +606,6 @@
-
- }else if (command == "-reconAllFromBvarsAndSave"){
- cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- cout<<"recon "<< string(argv[i_arg+1])<<endl;
---- src/libvis/miscpic.h.orig 2013-10-20 00:11:03.706496109 +1300
-+++ src/libvis/miscpic.h 2013-10-20 00:12:24.515626764 +1300
-@@ -89,12 +89,7 @@
- LR_label_flag = true;
- trans= -10;
- edgethresh = 0.0;
-- if(getenv("FSLDIR")!=0){
-- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
-- }
-- else{
-- lutbase = string("/");
-- }
-+ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
- title = string("");
- cbartype = string("");
- cbarptr = NULL;
---- src/melodic/melreport.cc.orig 2013-10-20 00:13:01.475686492 +1300
-+++ src/melodic/melreport.cc 2013-10-20 00:15:02.795882687 +1300
-@@ -85,7 +85,7 @@
-
- {//start IC page
- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
-@@ -488,7 +488,7 @@
- {//start IC2 page
- IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
-@@ -666,8 +666,8 @@
- IChtml << "<HTML> " << endl
- << "<TITLE>MELODIC Component " << num2str(cnum)
- << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
- << "</H1>"<< endl;
-
---- src/melodic/meloptions.cc.orig 2013-10-20 00:15:46.755953769 +1300
-+++ src/melodic/meloptions.cc 2013-10-20 00:18:26.176211442 +1300
-@@ -93,14 +93,6 @@
- explicitnums = false;
- logfname = string("log.txt");
-
-- // work out the path to the $FSLDIR/bin directory
-- if(getenv("FSLDIR")!=0){
-- binpath = (string) getenv("FSLDIR") + "/bin/";
-- } else{
-- binpath = argv[0];
-- binpath = binpath.substr(0,binpath.length()-7);
-- }
--
- // parse once to establish log directory name
- for(int a = options.parse_command_line(argc, argv); a < argc; a++);
-
---- src/melodic/meloptions.h.orig 2013-10-20 00:19:32.176318206 +1300
-+++ src/melodic/meloptions.h 2013-10-20 00:19:53.455352701 +1300
-@@ -93,7 +93,6 @@
- ~MelodicOptions() { delete gopt; }
-
- string version;
-- string binpath;
- string logfname;
- bool filtermode;
- bool explicitnums;
---- src/melodic/meldata.cc.orig 2013-10-20 00:20:45.856437466 +1300
-+++ src/melodic/meldata.cc 2013-10-20 00:21:48.655538924 +1300
-@@ -921,7 +921,7 @@
- void MelodicData::est_smoothness()
- {
- if(Resels == 0){
-- string SM_path = opts.binpath + "smoothest";
-+ string SM_path = "smoothest";
- string Mask_fname = logger.appendDir("mask");
-
- if(opts.segment.value().length()>0){
-@@ -1086,7 +1086,7 @@
- // set up all strings
- string BET_outputfname = string(Mean_fname)+"_brain";
-
-- string BET_path = opts.binpath + "bet";
-+ string BET_path = "bet";
- string BET_optarg = "-m -f 0.4"; // see man bet
- string Mask_fname = BET_outputfname+"_mask";
-
---- src/melodic/melreport.h.orig 2013-10-20 00:22:41.816624872 +1300
-+++ src/melodic/melreport.h 2013-10-20 00:24:25.555792499 +1300
-@@ -105,20 +105,20 @@
- system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
- report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- loghtml.setDir(report.getDir(),"log.html");
- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- navigator.setDir(report.getDir(),"nav.html");
- head.setDir(report.getDir(),"head.html");
- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-+ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
- head << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-+ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
- head <<"<TABLE BORDER=0><TR>" << endl
- <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
- <<"<TABLE BORDER=0>"<< endl
-@@ -130,8 +130,8 @@
- << "</tr></table>" << endl
- << "<TD ALIGN=RIGHT>" << endl
- << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
-- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
-- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
-+ << "<IMG BORDER=0 SRC=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
- << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
- if(opts.guireport.value()==""){
- report <<"<OBJECT data=head.html></OBJECT>" << endl;
---- src/mm/mixture_model.cc.orig 2013-10-20 00:25:00.355848878 +1300
-+++ src/mm/mixture_model.cc 2013-10-20 00:25:32.185900186 +1300
-@@ -2224,8 +2224,8 @@
-
- htmllog << "<HTML> " << endl
- << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
-
- htmllog << "<hr><p>" << endl;
---- src/siena/siena_diff.cc.orig 2013-10-20 00:26:13.215966685 +1300
-+++ src/siena/siena_diff.cc 2013-10-20 00:28:03.925145734 +1300
-@@ -107,7 +107,7 @@
- {
- // {{{ vars
-
--char thestring[10000], segoptions[10000], fsldir[10000];
-+char thestring[10000], segoptions[10000];
- int x_size, y_size, z_size, size, x, y, z, i, count,
- seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
- ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
-@@ -124,8 +124,6 @@
-
- string argv1(argv[1]), argv2(argv[2]);
-
--sprintf(fsldir,"%s",getenv("FSLDIR"));
--
- for (i = 3; i < argc; i++) {
- if (!strcmp(argv[i], "-i"))
- ignore_z=1;
-@@ -209,26 +207,26 @@
- // }}}
- // {{{ transform images and masks
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
- if (edge_masking)
- {
-- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
- }
-
-@@ -287,8 +285,8 @@
- cout << "saving image 1 to disk prior to segmentation" << endl;
- save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
- in1.destroy();
-- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
-+ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-+ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
- cout << thestring << endl;
- system(thestring);
- }
---- src/topup/topupfns.cpp.orig 2013-10-20 00:28:36.456198320 +1300
-+++ src/topup/topupfns.cpp 2013-10-20 00:29:37.905297565 +1300
-@@ -463,8 +463,7 @@
- if (TOPUP::check_exist(ecfname)) return(ecfname);
- }
- if (!TOPUP::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 (TOPUP::check_exist(ecfname)) return(ecfname);
- else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
- ecfname += string(".cnf");
---- etc/matlab/call_fsl.m.orig 2013-10-20 23:17:58.626045346 +1300
-+++ etc/matlab/call_fsl.m 2013-10-20 23:20:06.556252150 +1300
-@@ -8,7 +8,7 @@
- % Debian/Ubuntu users should uncomment as
- % indicated
-
--fsldir=getenv('FSLDIR');
-+%fsldir=getenv('FSLDIR');
-
- % Debian/Ubuntu - uncomment the following
- %fsllibdir=sprintf('%s/%s', fsldir, 'bin');
---- etc/js/label-div.html.orig 2013-10-20 23:22:04.906443685 +1300
-+++ etc/js/label-div.html 2013-10-20 23:23:35.006589232 +1300
-@@ -2,12 +2,12 @@
- <head>
- <title>label-div</title>
- <!--[if IE]>
-- <script type="text/javascript" src="FSLDIR/etc/js/excanvas.js"></script>
-+ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/excanvas.js"></script>
- <![endif]-->
-- <script type="text/javascript" src="FSLDIR/etc/js/strftime-min.js"></script>
-- <script type="text/javascript" src="FSLDIR/etc/js/rgbcolor.js"></script>
-- <script type="text/javascript" src="FSLDIR/etc/js/dygraph-canvas.js"></script>
-- <script type="text/javascript" src="FSLDIR/etc/js/dygraph.js"></script>
-+ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/strftime-min.js"></script>
-+ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/rgbcolor.js"></script>
-+ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/dygraph-canvas.js"></script>
-+ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/dygraph.js"></script>
- <script type="text/javascript" src="PNMDATA.js"></script>
- </head>
- <body>
diff --git a/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch
deleted file mode 100644
index 593c1c807..000000000
--- a/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch
+++ /dev/null
@@ -1,452 +0,0 @@
-diff -Naur src.orig/fast4/fast_two.cc src/fast4/fast_two.cc
---- src.orig/fast4/fast_two.cc 2015-03-30 11:54:10.522550233 +1300
-+++ src/fast4/fast_two.cc 2015-03-30 11:54:18.412569892 +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<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout << reg << endl;
- system(reg);
-diff -Naur src.orig/feat5/feat_model.cc src/feat5/feat_model.cc
---- src.orig/feat5/feat_model.cc 2015-03-30 11:54:10.502550183 +1300
-+++ src/feat5/feat_model.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -741,7 +741,7 @@
- vector<int> G;
- vector<string> titles;
- float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
-- char fl[10000], *FSLDIR;
-+ char fl[10000];
- string fn, filename;
- FONT_DATA *font_data = new FONT_DATA[1];
-
-@@ -760,8 +760,6 @@
- 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));
-@@ -1491,7 +1489,7 @@
- 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);
-@@ -2134,6 +2132,6 @@
-
- fclose(outputfile);
-
-- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename;
-+ filename="wpng -q -overwrite " + filename;
- system(filename.c_str());
- }
-diff -Naur src.orig/feat5/tsplot.cc src/feat5/tsplot.cc
---- src.orig/feat5/tsplot.cc 2015-03-30 11:54:10.502550183 +1300
-+++ src/feat5/tsplot.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -293,7 +293,7 @@
- ofstream outputFile;
- int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600);
- vector<double> 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 << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
-+ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
- if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
- else outputFile << "\n</BODY></HTML>\n\n";
- outputFile.close();
-@@ -740,7 +739,7 @@
- cerr << "Can't open output report file " << outputName << endl;
- exit(1);
- }
-- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
-+ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
- outputFile.close();
-
- /* now output same thing without start and end, for inclusion in feat report */
-diff -Naur src.orig/first/first_utils.cc src/first/first_utils.cc
---- src.orig/first/first_utils.cc 2015-03-30 11:54:10.482550135 +1300
-+++ src/first/first_utils.cc 2015-03-30 11:54:18.412569892 +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<float> 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<float> maskvol(refim);
- maskvol=0.0f;
- volume4D<float> volnormals;
-diff -Naur src.orig/fnirt/fnirtfns.cpp src/fnirt/fnirtfns.cpp
---- src.orig/fnirt/fnirtfns.cpp 2015-03-30 11:54:10.522550233 +1300
-+++ src/fnirt/fnirtfns.cpp 2015-03-30 11:54:18.412569892 +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");
-diff -Naur src.orig/fslsurface/fslsurface_first.cc src/fslsurface/fslsurface_first.cc
---- src.orig/fslsurface/fslsurface_first.cc 2015-03-30 11:54:10.522550233 +1300
-+++ src/fslsurface/fslsurface_first.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -500,8 +500,7 @@
-
- volume<float>* immni = new volume<float>();
-
-- 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<float>* immni = new volume<float>();
-
-- 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);
-
-diff -Naur src.orig/fslsurface/fslsurfacemaths.cpp src/fslsurface/fslsurfacemaths.cpp
---- src.orig/fslsurface/fslsurfacemaths.cpp 2015-03-30 11:54:10.522550233 +1300
-+++ src/fslsurface/fslsurfacemaths.cpp 2015-03-30 11:54:18.412569892 +1300
-@@ -598,12 +598,6 @@
-
- }else if (command == "-reconFromBvars"){
- cout<<"do recon "<<endl;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- reconSurface_from_bvars( surf, string(argv[i_arg+1]));
-@@ -612,12 +606,6 @@
-
- }else if (command == "-reconAllFromBvarsAndSave"){
- cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- cout<<"recon "<< string(argv[i_arg+1])<<endl;
-diff -Naur src.orig/libvis/miscpic.h src/libvis/miscpic.h
---- src.orig/libvis/miscpic.h 2015-03-30 11:54:10.482550135 +1300
-+++ src/libvis/miscpic.h 2015-03-30 11:54:18.412569892 +1300
-@@ -89,12 +89,7 @@
- LR_label_flag = true;
- trans= -10;
- edgethresh = 0.0;
-- if(getenv("FSLDIR")!=0){
-- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
-- }
-- else{
-- lutbase = string("/");
-- }
-+ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
- title = string("");
- cbartype = string("");
- cbarptr = NULL;
-diff -Naur src.orig/melodic/meldata.cc src/melodic/meldata.cc
---- src.orig/melodic/meldata.cc 2015-03-30 11:54:10.502550183 +1300
-+++ src/melodic/meldata.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -971,7 +971,7 @@
- void MelodicData::est_smoothness()
- {
- if(Resels == 0){
-- string SM_path = opts.binpath + "smoothest";
-+ string SM_path = "smoothest";
- string Mask_fname = logger.appendDir("mask");
-
- if(opts.segment.value().length()>0){
-@@ -1136,7 +1136,7 @@
- // set up all strings
- string BET_outputfname = string(Mean_fname)+"_brain";
-
-- string BET_path = opts.binpath + "bet";
-+ string BET_path = "bet";
- string BET_optarg = "-m -f 0.4"; // see man bet
- string Mask_fname = BET_outputfname+"_mask";
-
-diff -Naur src.orig/melodic/meloptions.cc src/melodic/meloptions.cc
---- src.orig/melodic/meloptions.cc 2015-03-30 11:54:10.502550183 +1300
-+++ src/melodic/meloptions.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -93,14 +93,6 @@
- explicitnums = false;
- logfname = string("log.txt");
-
-- // work out the path to the $FSLDIR/bin directory
-- if(getenv("FSLDIR")!=0){
-- binpath = (string) getenv("FSLDIR") + "/bin/";
-- } else{
-- binpath = argv[0];
-- binpath = binpath.substr(0,binpath.length()-7);
-- }
--
- // parse once to establish log directory name
- for(int a = options.parse_command_line(argc, argv); a < argc; a++);
-
-diff -Naur src.orig/melodic/meloptions.h src/melodic/meloptions.h
---- src.orig/melodic/meloptions.h 2015-03-30 11:54:10.502550183 +1300
-+++ src/melodic/meloptions.h 2015-03-30 11:54:18.412569892 +1300
-@@ -93,7 +93,6 @@
- ~MelodicOptions() { delete gopt; }
-
- string version;
-- string binpath;
- string logfname;
- bool filtermode;
- bool explicitnums;
-diff -Naur src.orig/melodic/melreport.cc src/melodic/melreport.cc
---- src.orig/melodic/melreport.cc 2015-03-30 11:54:10.502550183 +1300
-+++ src/melodic/melreport.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -84,8 +84,8 @@
- IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
-
- {//start IC page
-- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
-@@ -487,8 +487,8 @@
-
- {//start IC2 page
- IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
-- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
-@@ -666,8 +666,8 @@
- IChtml << "<HTML> " << endl
- << "<TITLE>MELODIC Component " << num2str(cnum)
- << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
- << "</H1>"<< endl;
-
-diff -Naur src.orig/melodic/melreport.h src/melodic/melreport.h
---- src.orig/melodic/melreport.h 2015-03-30 11:54:10.502550183 +1300
-+++ src/melodic/melreport.h 2015-03-30 12:11:17.995116883 +1300
-@@ -104,21 +104,21 @@
- const time_t tmptime = time(NULL);
- system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
- report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
-- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- loghtml.setDir(report.getDir(),"log.html");
-- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- navigator.setDir(report.getDir(),"nav.html");
- head.setDir(report.getDir(),"head.html");
-- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-- head << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-+ navigator << "<link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
-+ head << "<link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
- head <<"<TABLE BORDER=0><TR>" << endl
- <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
- <<"<TABLE BORDER=0>"<< endl
-@@ -130,8 +130,8 @@
- << "</tr></table>" << endl
- << "<TD ALIGN=RIGHT>" << endl
- << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
-- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
-- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
-+ << "<IMG BORDER=0 SRC=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
- << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
- if(opts.guireport.value()==""){
- report <<"<OBJECT data=head.html></OBJECT>" << endl;
-diff -Naur src.orig/mm/mixture_model.cc src/mm/mixture_model.cc
---- src.orig/mm/mixture_model.cc 2015-03-30 11:54:10.522550233 +1300
-+++ src/mm/mixture_model.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -2224,8 +2224,8 @@
-
- htmllog << "<HTML> " << endl
- << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
-
- htmllog << "<hr><p>" << endl;
-diff -Naur src.orig/siena/siena_diff.cc src/siena/siena_diff.cc
---- src.orig/siena/siena_diff.cc 2015-03-30 11:54:10.482550135 +1300
-+++ src/siena/siena_diff.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -107,7 +107,7 @@
- {
- // {{{ vars
-
--char thestring[10000], segoptions[10000], fsldir[10000];
-+char thestring[10000], segoptions[10000];
- int x_size, y_size, z_size, size, x, y, z, i, count,
- seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
- ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
-@@ -124,8 +124,6 @@
-
- string argv1(argv[1]), argv2(argv[2]);
-
--sprintf(fsldir,"%s",getenv("FSLDIR"));
--
- for (i = 3; i < argc; i++) {
- if (!strcmp(argv[i], "-i"))
- ignore_z=1;
-@@ -209,26 +207,26 @@
- // }}}
- // {{{ transform images and masks
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
- if (edge_masking)
- {
-- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
- }
-
-@@ -287,8 +285,8 @@
- cout << "saving image 1 to disk prior to segmentation" << endl;
- save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
- in1.destroy();
-- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
-+ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-+ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
- cout << thestring << endl;
- system(thestring);
- }
-diff -Naur src.orig/topup/topupfns.cpp src/topup/topupfns.cpp
---- src.orig/topup/topupfns.cpp 2015-03-30 11:54:10.522550233 +1300
-+++ src/topup/topupfns.cpp 2015-03-30 11:54:18.412569892 +1300
-@@ -463,8 +463,7 @@
- if (TOPUP::check_exist(ecfname)) return(ecfname);
- }
- if (!TOPUP::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 (TOPUP::check_exist(ecfname)) return(ecfname);
- else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
- ecfname += string(".cnf");
-
diff --git a/sci-biology/fsl/files/fsl-5.0.8-headers.patch b/sci-biology/fsl/files/fsl-5.0.8-headers.patch
deleted file mode 100644
index ab2ab3da3..000000000
--- a/sci-biology/fsl/files/fsl-5.0.8-headers.patch
+++ /dev/null
@@ -1,21 +0,0 @@
---- 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 <stdlib.h> /* 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-5.0.8-setup.patch b/sci-biology/fsl/files/fsl-5.0.8-setup.patch
deleted file mode 100644
index 0cbda5d5c..000000000
--- a/sci-biology/fsl/files/fsl-5.0.8-setup.patch
+++ /dev/null
@@ -1,113 +0,0 @@
-diff -Naur fsl.orig/build fsl/build
---- fsl.orig/build 2015-03-29 00:10:39.845936000 +1300
-+++ fsl/build 2015-03-29 00:12:37.160487000 +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 $PROJECTS
-+echo "Finished build"
-
-diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
---- fsl.orig/config/common/buildproj 2015-03-29 00:11:47.130998000 +1300
-+++ fsl/config/common/buildproj 2015-03-29 00:12:37.164319000 +1300
-@@ -11,10 +11,10 @@
- fi
- PROJECTS="$@" ; 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 ;
-@@ -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 -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk
---- fsl.orig/config/common/vars.mk 2015-03-29 00:11:47.183520000 +1300
-+++ fsl/config/common/vars.mk 2015-03-29 00:18:53.151222000 +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} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-- ${AccumulatedIncFlags}
-+ ${AccumulatedIncFlags} ${USERCFLAGS}
-
- CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-- ${AccumulatedIncFlags}
-+ ${AccumulatedIncFlags} ${USERCXXFLAGS}
-
- HFILES = *.h
- AFILES = *.a
-diff -Naur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk
---- fsl.orig/config/generic/systemvars.mk 2015-03-29 00:11:47.534246000 +1300
-+++ fsl/config/generic/systemvars.mk 2015-03-29 00:12:37.162129000 +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
-diff -Naur fsl.orig/extras/build fsl/extras/build
---- fsl.orig/extras/build 2015-03-29 00:11:15.080236000 +1300
-+++ fsl/extras/build 2015-03-29 00:15:53.170496000 +1300
-@@ -60,7 +60,7 @@
- if [ ${BUILDICONV} -eq 1 ]; then
- PROJECTS="${PROJECTS} libiconv"
- fi
--PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
-+PROJECTS="libgdc libprob libcprob newmat cprob newran"
- for projname in $PROJECTS; do
-
- if [ -d $FSLESRCDIR/$projname ] ; then
diff --git a/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch
deleted file mode 100644
index c28fabe42..000000000
--- a/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch
+++ /dev/null
@@ -1,456 +0,0 @@
-# Adapt hard-coded paths to the directory structure of Gentoo (including Prefix)
-# From: Francois Bissey <frp.bissey@gmail.com>
-# Signed-off-by: Horea Christian <horea.christ@gmail.com>
-
-diff -Naur fsl.orig/src/fast4/fast_two.cc fsl/src/fast4/fast_two.cc
---- fsl.orig/src/fast4/fast_two.cc 2015-03-30 11:54:10.522550233 +1300
-+++ fsl/src/fast4/fast_two.cc 2015-03-30 11:54:18.412569892 +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<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout << reg << endl;
- system(reg);
-diff -Naur fsl.orig/src/feat5/feat_model.cc fsl/src/feat5/feat_model.cc
---- fsl.orig/src/feat5/feat_model.cc 2015-03-30 11:54:10.502550183 +1300
-+++ fsl/src/feat5/feat_model.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -741,7 +741,7 @@
- vector<int> G;
- vector<string> titles;
- float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
-- char fl[10000], *FSLDIR;
-+ char fl[10000];
- string fn, filename;
- FONT_DATA *font_data = new FONT_DATA[1];
-
-@@ -760,8 +760,6 @@
- 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));
-@@ -1491,7 +1489,7 @@
- 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);
-@@ -2134,6 +2132,6 @@
-
- fclose(outputfile);
-
-- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename;
-+ filename="wpng -q -overwrite " + filename;
- system(filename.c_str());
- }
-diff -Naur fsl.orig/src/feat5/tsplot.cc fsl/src/feat5/tsplot.cc
---- fsl.orig/src/feat5/tsplot.cc 2015-03-30 11:54:10.502550183 +1300
-+++ fsl/src/feat5/tsplot.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -293,7 +293,7 @@
- ofstream outputFile;
- int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600);
- vector<double> 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 << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
-+ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
- if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
- else outputFile << "\n</BODY></HTML>\n\n";
- outputFile.close();
-@@ -740,7 +739,7 @@
- cerr << "Can't open output report file " << outputName << endl;
- exit(1);
- }
-- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
-+ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
- outputFile.close();
-
- /* now output same thing without start and end, for inclusion in feat report */
-diff -Naur fsl.orig/src/first/first_utils.cc fsl/src/first/first_utils.cc
---- fsl.orig/src/first/first_utils.cc 2015-03-30 11:54:10.482550135 +1300
-+++ fsl/src/first/first_utils.cc 2015-03-30 11:54:18.412569892 +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<float> 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<float> maskvol(refim);
- maskvol=0.0f;
- volume4D<float> volnormals;
-diff -Naur fsl.orig/src/fnirt/fnirtfns.cpp fsl/src/fnirt/fnirtfns.cpp
---- fsl.orig/src/fnirt/fnirtfns.cpp 2015-03-30 11:54:10.522550233 +1300
-+++ fsl/src/fnirt/fnirtfns.cpp 2015-03-30 11:54:18.412569892 +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");
-diff -Naur fsl.orig/src/fslsurface/fslsurface_first.cc fsl/src/fslsurface/fslsurface_first.cc
---- fsl.orig/src/fslsurface/fslsurface_first.cc 2015-03-30 11:54:10.522550233 +1300
-+++ fsl/src/fslsurface/fslsurface_first.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -500,8 +500,7 @@
-
- volume<float>* immni = new volume<float>();
-
-- 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<float>* immni = new volume<float>();
-
-- 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);
-
-diff -Naur fsl.orig/src/fslsurface/fslsurfacemaths.cpp fsl/src/fslsurface/fslsurfacemaths.cpp
---- fsl.orig/src/fslsurface/fslsurfacemaths.cpp 2015-03-30 11:54:10.522550233 +1300
-+++ fsl/src/fslsurface/fslsurfacemaths.cpp 2015-03-30 11:54:18.412569892 +1300
-@@ -598,12 +598,6 @@
-
- }else if (command == "-reconFromBvars"){
- cout<<"do recon "<<endl;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- reconSurface_from_bvars( surf, string(argv[i_arg+1]));
-@@ -612,12 +606,6 @@
-
- }else if (command == "-reconAllFromBvarsAndSave"){
- cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- cout<<"recon "<< string(argv[i_arg+1])<<endl;
-diff -Naur fsl.orig/src/libvis/miscpic.h fsl/src/libvis/miscpic.h
---- fsl.orig/src/libvis/miscpic.h 2015-03-30 11:54:10.482550135 +1300
-+++ fsl/src/libvis/miscpic.h 2015-03-30 11:54:18.412569892 +1300
-@@ -89,12 +89,7 @@
- LR_label_flag = true;
- trans= -10;
- edgethresh = 0.0;
-- if(getenv("FSLDIR")!=0){
-- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
-- }
-- else{
-- lutbase = string("/");
-- }
-+ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
- title = string("");
- cbartype = string("");
- cbarptr = NULL;
-diff -Naur fsl.orig/src/melodic/meldata.cc fsl/src/melodic/meldata.cc
---- fsl.orig/src/melodic/meldata.cc 2015-03-30 11:54:10.502550183 +1300
-+++ fsl/src/melodic/meldata.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -971,7 +971,7 @@
- void MelodicData::est_smoothness()
- {
- if(Resels == 0){
-- string SM_path = opts.binpath + "smoothest";
-+ string SM_path = "smoothest";
- string Mask_fname = logger.appendDir("mask");
-
- if(opts.segment.value().length()>0){
-@@ -1136,7 +1136,7 @@
- // set up all strings
- string BET_outputfname = string(Mean_fname)+"_brain";
-
-- string BET_path = opts.binpath + "bet";
-+ string BET_path = "bet";
- string BET_optarg = "-m -f 0.4"; // see man bet
- string Mask_fname = BET_outputfname+"_mask";
-
-diff -Naur fsl.orig/src/melodic/meloptions.cc fsl/src/melodic/meloptions.cc
---- fsl.orig/src/melodic/meloptions.cc 2015-03-30 11:54:10.502550183 +1300
-+++ fsl/src/melodic/meloptions.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -93,14 +93,6 @@
- explicitnums = false;
- logfname = string("log.txt");
-
-- // work out the path to the $FSLDIR/bin directory
-- if(getenv("FSLDIR")!=0){
-- binpath = (string) getenv("FSLDIR") + "/bin/";
-- } else{
-- binpath = argv[0];
-- binpath = binpath.substr(0,binpath.length()-7);
-- }
--
- // parse once to establish log directory name
- for(int a = options.parse_command_line(argc, argv); a < argc; a++);
-
-diff -Naur fsl.orig/src/melodic/meloptions.h fsl/src/melodic/meloptions.h
---- fsl.orig/src/melodic/meloptions.h 2015-03-30 11:54:10.502550183 +1300
-+++ fsl/src/melodic/meloptions.h 2015-03-30 11:54:18.412569892 +1300
-@@ -93,7 +93,6 @@
- ~MelodicOptions() { delete gopt; }
-
- string version;
-- string binpath;
- string logfname;
- bool filtermode;
- bool explicitnums;
-diff -Naur fsl.orig/src/melodic/melreport.cc fsl/src/melodic/melreport.cc
---- fsl.orig/src/melodic/melreport.cc 2015-03-30 11:54:10.502550183 +1300
-+++ fsl/src/melodic/melreport.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -84,8 +84,8 @@
- IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
-
- {//start IC page
-- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
-@@ -487,8 +487,8 @@
-
- {//start IC2 page
- IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
-- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
-@@ -666,8 +666,8 @@
- IChtml << "<HTML> " << endl
- << "<TITLE>MELODIC Component " << num2str(cnum)
- << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
- << "</H1>"<< endl;
-
-diff -Naur fsl.orig/src/melodic/melreport.h fsl/src/melodic/melreport.h
---- fsl.orig/src/melodic/melreport.h 2015-03-30 11:54:10.502550183 +1300
-+++ fsl/src/melodic/melreport.h 2015-03-30 12:11:17.995116883 +1300
-@@ -104,21 +104,21 @@
- const time_t tmptime = time(NULL);
- system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
- report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
-- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- loghtml.setDir(report.getDir(),"log.html");
-- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- navigator.setDir(report.getDir(),"nav.html");
- head.setDir(report.getDir(),"head.html");
-- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-- head << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-+ navigator << "<link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
-+ head << "<link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
- head <<"<TABLE BORDER=0><TR>" << endl
- <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
- <<"<TABLE BORDER=0>"<< endl
-@@ -130,8 +130,8 @@
- << "</tr></table>" << endl
- << "<TD ALIGN=RIGHT>" << endl
- << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
-- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
-- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
-+ << "<IMG BORDER=0 SRC=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
- << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
- if(opts.guireport.value()==""){
- report <<"<OBJECT data=head.html></OBJECT>" << endl;
-diff -Naur fsl.orig/src/mm/mixture_model.cc fsl/src/mm/mixture_model.cc
---- fsl.orig/src/mm/mixture_model.cc 2015-03-30 11:54:10.522550233 +1300
-+++ fsl/src/mm/mixture_model.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -2224,8 +2224,8 @@
-
- htmllog << "<HTML> " << endl
- << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
-
- htmllog << "<hr><p>" << endl;
-diff -Naur fsl.orig/src/siena/siena_diff.cc fsl/src/siena/siena_diff.cc
---- fsl.orig/src/siena/siena_diff.cc 2015-03-30 11:54:10.482550135 +1300
-+++ fsl/src/siena/siena_diff.cc 2015-03-30 11:54:18.412569892 +1300
-@@ -107,7 +107,7 @@
- {
- // {{{ vars
-
--char thestring[10000], segoptions[10000], fsldir[10000];
-+char thestring[10000], segoptions[10000];
- int x_size, y_size, z_size, size, x, y, z, i, count,
- seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
- ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
-@@ -124,8 +124,6 @@
-
- string argv1(argv[1]), argv2(argv[2]);
-
--sprintf(fsldir,"%s",getenv("FSLDIR"));
--
- for (i = 3; i < argc; i++) {
- if (!strcmp(argv[i], "-i"))
- ignore_z=1;
-@@ -209,26 +207,26 @@
- // }}}
- // {{{ transform images and masks
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
- if (edge_masking)
- {
-- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
- }
-
-@@ -287,8 +285,8 @@
- cout << "saving image 1 to disk prior to segmentation" << endl;
- save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
- in1.destroy();
-- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
-+ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-+ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
- cout << thestring << endl;
- system(thestring);
- }
-diff -Naur fsl.orig/src/topup/topupfns.cpp fsl/src/topup/topupfns.cpp
---- fsl.orig/src/topup/topupfns.cpp 2015-03-30 11:54:10.522550233 +1300
-+++ fsl/src/topup/topupfns.cpp 2015-03-30 11:54:18.412569892 +1300
-@@ -463,8 +463,7 @@
- if (TOPUP::check_exist(ecfname)) return(ecfname);
- }
- if (!TOPUP::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 (TOPUP::check_exist(ecfname)) return(ecfname);
- else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
- ecfname += string(".cnf");
-
diff --git a/sci-biology/fsl/files/fsl-5.0.9-setup.patch b/sci-biology/fsl/files/fsl-5.0.9-setup.patch
deleted file mode 100644
index c688cd6e8..000000000
--- a/sci-biology/fsl/files/fsl-5.0.9-setup.patch
+++ /dev/null
@@ -1,115 +0,0 @@
-diff -Naur fsl.orig/build fsl/build
---- fsl.orig/build 2015-03-29 00:10:39.845936000 +1300
-+++ fsl/build 2015-03-29 00:12:37.160487000 +1300
-@@ -11,9 +11,8 @@
- ifit load_varian load_dicom misc_scripts fdt first possum sgeutils \
- flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp verbena";
- 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 $PROJECTS
-+echo "Finished build"
-
-diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
---- fsl.orig/config/common/buildproj 2015-03-29 00:11:47.130998000 +1300
-+++ fsl/config/common/buildproj 2015-03-29 00:12:37.164319000 +1300
-@@ -11,10 +11,10 @@
- fi
- PROJECTS="$@" ; 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 ;
-@@ -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 -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk
---- fsl.orig/config/common/vars.mk 2015-03-29 00:11:47.183520000 +1300
-+++ fsl/config/common/vars.mk 2015-03-29 00:18:53.151222000 +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} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-- ${AccumulatedIncFlags}
-+ ${AccumulatedIncFlags} ${USERCFLAGS}
-
- CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
-- ${AccumulatedIncFlags}
-+ ${AccumulatedIncFlags} ${USERCXXFLAGS}
-
- HFILES = *.h
- AFILES = *.a
-diff -Naur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk
---- fsl.orig/config/generic/systemvars.mk 2015-03-29 00:11:47.534246000 +1300
-+++ fsl/config/generic/systemvars.mk 2015-03-29 00:12:37.162129000 +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
-diff -Naur fsl.orig/extras/build fsl/extras/build
---- fsl.orig/extras/build 2015-03-29 00:11:15.080236000 +1300
-+++ fsl/extras/build 2015-03-29 00:15:53.170496000 +1300
-@@ -104,8 +104,8 @@
- if [ ${BUILDICONV} -eq 1 ]; then
- PROJECTS="${PROJECTS} libiconv"
- fi
--PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
-+PROJECTS="libgdc libprob libcprob newmat cprob newran"
- PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxml++-2.34.0"
- for projname in $PROJECTS; do
-
- if [ -d $FSLESRCDIR/$projname ] ; then
diff --git a/sci-biology/fsl/fsl-5.0.11.ebuild b/sci-biology/fsl/fsl-5.0.11.ebuild
deleted file mode 100644
index d3985072d..000000000
--- a/sci-biology/fsl/fsl-5.0.11.ebuild
+++ /dev/null
@@ -1,157 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-COMMON_DEPEND="
- dev-libs/boost
- media-gfx/graphviz
- media-libs/gd
- media-libs/glu
- media-libs/libpng:0=
- sci-libs/ciftilib
- sci-libs/nlopt
- sys-libs/zlib
- "
-DEPEND="${COMMON_DEPEND}"
-RDEPEND="${COMMON_DEPEND}
- dev-lang/tcl:0=
- dev-lang/tk:0=
- "
-
-S=${WORKDIR}/${PN}
-UPSTREAM_FSLDIR="/usr/share/fsl"
-
-PATCHES=(
- "${FILESDIR}/${PN}"-5.0.11-setup.patch
- "${FILESDIR}/${PN}"-5.0.11-no_xmlpp.patch
- "${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
- "${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
- "${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
- "${FILESDIR}/${PN}"-5.0.11-qstring_compat.patch
- "${FILESDIR}/${PN}"-5.0.9-headers.patch
- "${FILESDIR}/${PN}"-5.0.9-fsldir_redux.patch
-)
-
-src_prepare(){
- default
-
- sed -i \
- -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
- -e "s:@@GENTOO_CC@@:$(tc-getCC):" \
- -e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
- config/generic/systemvars.mk || die
-
- eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
- etc/js/label-div.html
-
- makefilelist=$(find src/ -name Makefile)
-
- sed -i \
- -e "s:-I\${INC_BOOST}::" \
- -e "s:-I\${INC_ZLIB}::" \
- -e "s:-I\${INC_GD}::" \
- -e "s:-I\${INC_PNG}::" \
- -e "s:-L\${LIB_GD}::" \
- -e "s:-L\${LIB_PNG}::" \
- -e "s:-L\${LIB_ZLIB}::" \
- ${makefilelist} || die
-
- sed -e "s:\${FSLDIR}/bin/::g" \
- -e "s:\$FSLDIR/bin/::g" \
- -i $(grep -rl "\${FSLDIR}/bin" src/*) \
- $(grep -rl "\${FSLDIR}/bin" etc/matlab/*) || die
-
- sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
- -e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
- -i $(grep -rl "\$FSLDIR/data" src/*) \
- $(grep -rl "\${FSLDIR}/data" src/*) || die
-
- sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- -e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- -i $(grep -rl "\$FSLDIR/doc" src/*) \
- $(grep -rl "\${FSLDIR}/doc" src/*) || die
-
- sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- -i $(grep -rl "/usr/share/fsl/doc" src/*) || die
-
- sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
- -e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
- -i $(grep -rlI "\$FSLDIR/etc" *) \
- -i $(grep -rlI "\${FSLDIR}/etc" *) || die
-
- # script wanting to have access to flsversion at buildtime
- sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
- -i ${makefilelist} || die
-}
-
-src_compile() {
- export FSLDIR=${WORKDIR}/${PN}
- export FSLCONDIR=${WORKDIR}/${PN}/config
- export FSLMACHTYPE=generic
-
- export USERLDFLAGS="${LDFLAGS}"
- export USERCFLAGS="${CFLAGS}"
- export USERCXXFLAGS="${CXXFLAGS}"
-
- export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
- export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
-
- ./build || die
-}
-
-src_install() {
- sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
- $(grep -lI "\${FSLDIR}/tcl" bin/*) \
- $(grep -l "\${FSLDIR}/tcl" tcl/*) || die
- sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
- $(grep -l "\$FSLDIR/tcl" tcl/*) || die
-
- dobin bin/*
-
- insinto /usr/share/${PN}
- doins -r data
- dodoc -r doc/. refdoc
-
- insinto /usr/libexec/fsl
- doins -r tcl/*
-
- insinto /etc/fslconf
- doins etc/fslconf/fsl.sh
-
- insinto /etc
- doins etc/fslversion
- doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
- #if use matlab; then
- # doins etc/matlab
- #fi
-
- #the following is needed for FSL and depending programs to be able
- #to find its files, since FSL uses an uncommon installation path:
- #https://github.com/gentoo-science/sci/pull/612#r60289295
- dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
- dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
- dosym ../../bin ${UPSTREAM_FSLDIR}/bin
-
- doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
- mv "${ED}"/usr/bin/{,fsl_}cluster || die
-}
-
-pkg_postinst() {
- echo
- einfo "Please run the following commands if you"
- einfo "intend to use fsl from an existing shell:"
- einfo "env-update && source /etc/profile"
- echo
-}
diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
deleted file mode 100644
index d420bbacc..000000000
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ /dev/null
@@ -1,148 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}-sources.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-COMMON_DEPEND="
- dev-libs/boost
- media-gfx/graphviz
- media-libs/gd
- media-libs/glu
- media-libs/libpng:0=
- sys-libs/zlib
- "
-DEPEND="${COMMON_DEPEND}"
-RDEPEND="${COMMON_DEPEND}
- dev-lang/tcl:0=
- dev-lang/tk:0=
- "
-
-S=${WORKDIR}/${PN}
-
-src_prepare(){
- epatch \
- "${FILESDIR}/${PN}"-5.0.8-setup.patch \
- "${FILESDIR}/${PN}"-5.0.8-headers.patch \
- "${FILESDIR}/${PN}"-5.0.8-fsldir_redux.patch
-
- sed -i \
- -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
- -e "s:@@GENTOO_CC@@:$(tc-getCC):" \
- -e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
- config/generic/systemvars.mk || die
-
- eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
- etc/js/label-div.html
-
- makefilelist=$(find src/ -name Makefile)
-
- sed -i \
- -e "s:-I\${INC_BOOST}::" \
- -e "s:-I\${INC_ZLIB}::" \
- -e "s:-I\${INC_GD}::" \
- -e "s:-I\${INC_PNG}::" \
- -e "s:-L\${LIB_GD}::" \
- -e "s:-L\${LIB_PNG}::" \
- -e "s:-L\${LIB_ZLIB}::" \
- ${makefilelist} || die
-
- sed -i "s:\${FSLDIR}/bin/::g" \
- $(grep -rl "\${FSLDIR}/bin" src/*) \
- $(grep -rl "\${FSLDIR}/bin" etc/matlab/*)
- sed -i "s:\$FSLDIR/bin/::g" \
- $(grep -rl "\$FSLDIR/bin" src/*) \
- $(grep -rl "\$FSLDIR/bin" etc/matlab/*)
-
- sed -i "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
- $(grep -rl "\$FSLDIR/data" src/*)
-
- sed -i "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
- $(grep -rl "\${FSLDIR}/data" src/*)
-
- sed -i "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
- $(grep -rl "\$FSLDIR/etc" src/*)
-
- sed -i "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
- $(grep -rl "\${FSLDIR}/etc" src/*)
-
- sed -i "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- $(grep -rl "\$FSLDIR/doc" src/*)
-
- sed -i "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- $(grep -rl "\${FSLDIR}/doc" src/*)
-
- sed -i "s:\'\${FSLDIR}\'/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- $(grep -rl "\'\${FSLDIR}\'/doc" src/*)
-
- sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *`
- default
-}
-
-src_compile() {
- export FSLDIR=${WORKDIR}/${PN}
- export FSLCONDIR=${WORKDIR}/${PN}/config
- export FSLMACHTYPE=generic
-
- export USERLDFLAGS="${LDFLAGS}"
- export USERCFLAGS="${CFLAGS}"
- export USERCXXFLAGS="${CXXFLAGS}"
-
- ./build || die
-}
-
-src_install() {
- sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
- $(grep -lI "\${FSLDIR}/tcl" bin/*) \
- $(grep -l "\${FSLDIR}/tcl" tcl/*) || die
- sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
- $(grep -l "\$FSLDIR/tcl" tcl/*) || die
-
- dobin bin/*
-
- insinto /usr/share/${PN}
- doins -r data
- dodoc -r doc/. refdoc
-
- insinto /usr/libexec/fsl
- doins -r tcl/*
-
- insinto /etc/fslconf
- doins etc/fslconf/fsl.sh
-
- insinto /etc
- doins etc/fslversion
- doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
- #if use matlab; then
- # doins etc/matlab
- #fi
-
- #the following is needed for FSL and depending programs to be able
- #to find its files, since FSL uses an uncommon:
- #https://github.com/gentoo-science/sci/pull/612#r60289295
- dosym ../../../etc /usr/share/fsl/etc
- dosym ../doc/${P} /usr/share/fsl/doc
-
- cp "${FILESDIR}"/99fsl "${TMPDIR}"/99fsl || die
- eprefixify "${TMPDIR}"/99fsl
- doenvd "${TMPDIR}"/99fsl
- mv "${ED}"/usr/bin/{,fsl_}cluster || die
-}
-
-pkg_postinst() {
- echo
- einfo "Please run the following commands if you"
- einfo "intend to use fsl from an existing shell:"
- einfo "env-update && source /etc/profile"
- echo
-}
diff --git a/sci-biology/fsl/fsl-5.0.9.ebuild b/sci-biology/fsl/fsl-5.0.9.ebuild
deleted file mode 100644
index 6e9ff6233..000000000
--- a/sci-biology/fsl/fsl-5.0.9.ebuild
+++ /dev/null
@@ -1,142 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}-sources.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-COMMON_DEPEND="
- dev-libs/boost
- media-gfx/graphviz
- media-libs/gd
- media-libs/glu
- media-libs/libpng:0=
- sys-libs/zlib
- "
-DEPEND="${COMMON_DEPEND}"
-RDEPEND="${COMMON_DEPEND}
- dev-lang/tcl:0=
- dev-lang/tk:0=
- "
-
-S=${WORKDIR}/${PN}
-UPSTREAM_FSLDIR="/usr/share/fsl"
-
-PATCHES=(
- "${FILESDIR}/${PN}"-5.0.9-setup.patch
- "${FILESDIR}/${PN}"-5.0.9-headers.patch
- "${FILESDIR}/${PN}"-5.0.9-fsldir_redux.patch
-)
-
-src_prepare(){
- default
- sed -i \
- -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
- -e "s:@@GENTOO_CC@@:$(tc-getCC):" \
- -e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
- config/generic/systemvars.mk || die
-
- eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
- etc/js/label-div.html
-
- makefilelist=$(find src/ -name Makefile)
-
- sed -i \
- -e "s:-I\${INC_BOOST}::" \
- -e "s:-I\${INC_ZLIB}::" \
- -e "s:-I\${INC_GD}::" \
- -e "s:-I\${INC_PNG}::" \
- -e "s:-L\${LIB_GD}::" \
- -e "s:-L\${LIB_PNG}::" \
- -e "s:-L\${LIB_ZLIB}::" \
- ${makefilelist} || die
-
- sed -e "s:\${FSLDIR}/bin/::g" \
- -e "s:\$FSLDIR/bin/::g" \
- -i $(grep -rl "\${FSLDIR}/bin" src/*) \
- $(grep -rl "\${FSLDIR}/bin" etc/matlab/*) || die
-
- sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
- -e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
- -i $(grep -rl "\$FSLDIR/data" src/*) \
- $(grep -rl "\${FSLDIR}/data" src/*) || die
-
- sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- -e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- -i $(grep -rl "\$FSLDIR/doc" src/*) \
- $(grep -rl "\${FSLDIR}/doc" src/*) || die
-
- sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
- $(grep -rl "/usr/share/fsl/doc" src/*) || die
-
- sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
- -e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
- -i $(grep -rlI "\$FSLDIR/etc" *) \
- -i $(grep -rlI "\${FSLDIR}/etc" *) || die
-}
-
-src_compile() {
- export FSLDIR=${WORKDIR}/${PN}
- export FSLCONDIR=${WORKDIR}/${PN}/config
- export FSLMACHTYPE=generic
-
- export USERLDFLAGS="${LDFLAGS}"
- export USERCFLAGS="${CFLAGS}"
- export USERCXXFLAGS="${CXXFLAGS}"
-
- ./build || die
-}
-
-src_install() {
- sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
- $(grep -lI "\${FSLDIR}/tcl" bin/*) \
- $(grep -l "\${FSLDIR}/tcl" tcl/*) || die
- sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
- $(grep -l "\$FSLDIR/tcl" tcl/*) || die
-
- dobin bin/*
-
- insinto /usr/share/${PN}
- doins -r data
- dodoc -r doc/. refdoc
-
- insinto /usr/libexec/fsl
- doins -r tcl/*
-
- insinto /etc/fslconf
- doins etc/fslconf/fsl.sh
-
- insinto /etc
- doins etc/fslversion
- doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
- #if use matlab; then
- # doins etc/matlab
- #fi
-
- #the following is needed for FSL and depending programs to be able
- #to find its files, since FSL uses an uncommon installation path:
- #https://github.com/gentoo-science/sci/pull/612#r60289295
- dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
- dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
- dosym ../../bin ${UPSTREAM_FSLDIR}/bin
-
- doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
- mv "${ED}"/usr/bin/{,fsl_}cluster || die
-}
-
-pkg_postinst() {
- echo
- einfo "Please run the following commands if you"
- einfo "intend to use fsl from an existing shell:"
- einfo "env-update && source /etc/profile"
- echo
-}