Version bump

4 files changed, 60 insertions, 37 deletions

diff --git a/.SRCINFO b/.SRCINFO
index c651090baaef..91089d7c0033 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = fsl
 	pkgdesc = A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data
-	pkgver = 6.0.0
+	pkgver = 6.0.1
 	pkgrel = 1
 	url = http://www.fmrib.ox.ac.uk/fsl/
 	arch = x86_64
@@ -26,20 +26,24 @@ pkgbase = fsl
 	depends = fslpy
 	depends = bc
 	optdepends = cuda
-	source = http://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.0-sources.tar.gz
-	source = http://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.0-feeds.tar.gz
+	source = http://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.1-sources.tar.gz
+	source = http://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.1-feeds.tar.gz
+	source = externallibs.mk
+	source = systemvars.mk
 	source = imcp
 	source = imglob
 	source = immv
 	source = 001-use_distribution_environment.patch
 	source = 002-fix_meldata_usage_of_ifstream.patch
 	source = 003-fix_fsl_exec_empty_errorCode.patch
-	sha256sums = 94853ddd1c16d03050a0ef58b8801fd094a7b3636cc3cf35b36c576091143276
-	sha256sums = 0d41376add12a6dbf67da19c1875f18bb6fa05e24e8a43d97eff160c70881ad2
+	sha256sums = ccab9709239340299b0ca034cb00d6ce0170b9e0d075b3adb55c556feacfb2da
+	sha256sums = 91aa756d5a052702cc68e41bcc9a64ba7c7f8853feb215d5a44eeb710c4a0fd0
+	sha256sums = e3345af9d3a1bca157c3a5700c63c4d0e01da3cec525f8ffb8f1a04b048aeff1
+	sha256sums = 326c73cf0fb07ef9436ec31dda00f1e77488949152aa908b50aa4059701b2984
 	sha256sums = c61f185fbe7e297c4518e96377aa5ff4852f90eda0dbb9ae8edc5e24735e14ad
 	sha256sums = 7a1039cdc38b4d728f14efce3b0fda0cadc7bfcd3432556c3f3113985bf2720a
 	sha256sums = b6f61a6d5672b6684f19150f6e21ded1bd04ec6415dcf07a32291e4002bfa5d8
-	sha256sums = d1dada74e7625ce3a9031af851ff1f3aed9a3f5600dc49a5db13f829cb8c41cb
+	sha256sums = b59921d9b76c07da6c775d63d5fe99ca5069a15827aa7a3d44c2e5eb6f3638d6
 	sha256sums = 13d4cf35343e7a73bc2534c94b1b0d4db41c338d374e6982091e4cf7a421d420
 	sha256sums = 64b4ccefa63a3cf920b185dd52e94b918c24f2cedaebcec8efb767bd80a6418a
 
diff --git a/PKGBUILD b/PKGBUILD
index dcc5383a058c..fbaa3af33a87 100755
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -2,7 +2,7 @@
 # Contributor: fishburn <frankthefishburn@gmail.com>
 
 pkgname=fsl
-pkgver=6.0.0
+pkgver=6.0.1
 pkgrel=1
 pkgdesc="A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data"
 arch=("x86_64")
@@ -13,21 +13,25 @@ makedepends=(boost fftw)
 optdepends=(cuda)
 source=("http://www.fmrib.ox.ac.uk/fsldownloads/fsl-${pkgver}-sources.tar.gz"
         "http://www.fmrib.ox.ac.uk/fsldownloads/fsl-${pkgver}-feeds.tar.gz"
-	"imcp"
-	"imglob"
-	"immv"
-	"001-use_distribution_environment.patch"
-	"002-fix_meldata_usage_of_ifstream.patch"
-	"003-fix_fsl_exec_empty_errorCode.patch")
+        "externallibs.mk"
+	    "systemvars.mk"
+        "imcp"
+	    "imglob"
+	    "immv"
+	    "001-use_distribution_environment.patch"
+	    "002-fix_meldata_usage_of_ifstream.patch"
+	    "003-fix_fsl_exec_empty_errorCode.patch")
 
-sha256sums=('94853ddd1c16d03050a0ef58b8801fd094a7b3636cc3cf35b36c576091143276'
-	    '0d41376add12a6dbf67da19c1875f18bb6fa05e24e8a43d97eff160c70881ad2'
-	    'c61f185fbe7e297c4518e96377aa5ff4852f90eda0dbb9ae8edc5e24735e14ad'
-	    '7a1039cdc38b4d728f14efce3b0fda0cadc7bfcd3432556c3f3113985bf2720a'
-	    'b6f61a6d5672b6684f19150f6e21ded1bd04ec6415dcf07a32291e4002bfa5d8'
-	    'd1dada74e7625ce3a9031af851ff1f3aed9a3f5600dc49a5db13f829cb8c41cb'
-	    '13d4cf35343e7a73bc2534c94b1b0d4db41c338d374e6982091e4cf7a421d420'
-	    '64b4ccefa63a3cf920b185dd52e94b918c24f2cedaebcec8efb767bd80a6418a')
+sha256sums=('ccab9709239340299b0ca034cb00d6ce0170b9e0d075b3adb55c556feacfb2da'
+	        '91aa756d5a052702cc68e41bcc9a64ba7c7f8853feb215d5a44eeb710c4a0fd0'
+	        'e3345af9d3a1bca157c3a5700c63c4d0e01da3cec525f8ffb8f1a04b048aeff1'
+            '326c73cf0fb07ef9436ec31dda00f1e77488949152aa908b50aa4059701b2984'
+            'c61f185fbe7e297c4518e96377aa5ff4852f90eda0dbb9ae8edc5e24735e14ad'
+	        '7a1039cdc38b4d728f14efce3b0fda0cadc7bfcd3432556c3f3113985bf2720a'
+	        'b6f61a6d5672b6684f19150f6e21ded1bd04ec6415dcf07a32291e4002bfa5d8'
+	        'b59921d9b76c07da6c775d63d5fe99ca5069a15827aa7a3d44c2e5eb6f3638d6'
+	        '13d4cf35343e7a73bc2534c94b1b0d4db41c338d374e6982091e4cf7a421d420'
+	        '64b4ccefa63a3cf920b185dd52e94b918c24f2cedaebcec8efb767bd80a6418a')
 
 prepare() {
 	cd "${srcdir}"
@@ -36,8 +40,7 @@ prepare() {
 	export FSLMACHTYPE=$(${FSLDIR}/etc/fslconf/fslmachtype.sh)
 	mkdir "${FSLDIR}/config/${FSLMACHTYPE}"
 	# Use config linux_64-gcc4.8 as template
-	cp "${FSLDIR}"/config/linux_64-gcc4.8/{externallibs.mk,systemvars.mk} "${FSLDIR}/config/${FSLMACHTYPE}"
-	sed -i "s/_FSLMACHTYPE/${FSLMACHTYPE}/g" "${srcdir}/001-use_distribution_environment.patch"
+	cp "${srcdir}"/{externallibs.mk,systemvars.mk} "${FSLDIR}/config/${FSLMACHTYPE}"
 
 	# Apply patches
 	patch -Np1 -i "${srcdir}/001-use_distribution_environment.patch"
diff --git a/externallibs.mk b/externallibs.mk
index 3d980adb2101..e1c5e44798c7 100755
--- a/externallibs.mk
+++ b/externallibs.mk
@@ -1,4 +1,4 @@
-# $Id: externallibs.mk,v 1.1 2017/02/18 12:20:05 mwebster Exp $
+# $Id: externallibs.mk,v 1.3 2018/10/10 11:12:48 mwebster Exp $
 
 # External Library and Include Paths
 
@@ -7,8 +7,8 @@ FSLEXTINC=${FSLDIR}/extras/include
 FSLEXTBIN=${FSLDIR}/extras/bin
 
 # GD library
-INC_GD = /usr/include
 LIB_GD = /usr/lib
+INC_GD = /usr/include
 
 # GDC library
 LIB_GDC = ${FSLEXTLIB}
@@ -20,13 +20,14 @@ INC_XML2 = /usr/include/libxml2
 # LIBXML++ library
 INC_XML++ = /usr/include/libxml++-2.6
 INC_XML++CONF = /usr/lib/libxml++-2.6/include
+
 # GSL library
 LIB_GSL = /usr/lib
 INC_GSL = /usr/include/gsl
 
 # PNG library
 LIB_PNG = /usr/lib
-INC_PNG = /usr/include/libpng16
+INC_PNG = /usr/include/libpng1.6
 
 # PROB library
 LIB_PROB = ${FSLEXTLIB}
@@ -37,8 +38,11 @@ LIB_CPROB = ${FSLEXTLIB}
 INC_CPROB = ${FSLEXTINC}/libcprob
 
 # NEWMAT library
-LIB_NEWMAT = /usr/lib
-INC_NEWMAT = /usr/include/newmat
+#LIB_NEWMAT = ${FSLEXTLIB} -llapack -lblas or just -lopenblas
+#LIB_NEWMAT = /usr/lib/newmat
+#INC_NEWMAT = /usr/include/newmat
+LIB_NEWMAT = ${FSLEXTLIB} -llapack -lblas
+INC_NEWMAT = ${FSLEXTINC}/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD
 
 # NEWRAN library
 LIB_NEWRAN = ${FSLEXTLIB}
@@ -49,14 +53,25 @@ LIB_ZLIB = /usr/lib
 INC_ZLIB = /usr/include
 
 # BOOST library
-INC_BOOST = /usr/include/boost
+#BOOSTDIR = ${FSLEXTINC}/boost
 LIB_BOOST = /usr/lib
+INC_BOOST = /usr/include/boost
+
+# QT library
+#QTDIR = /usr/lib/qt5
+LIB_QT = /usr/lib
+INC_QT = ${QTDIR}/include/qt
+
+# QWT library
+#QWTDIR = /usr/local/qwt
+LIB_QWT = /usr/lib
+INC_QWT = /usr/include/qwt
 
 # FFTW3 library
-INC_FFTW3 = /usr/include
 LIB_FFTW3 = /usr/lib
+INC_FFTW3 = /usr/include
 
-# VTK library 
-VTKDIR_INC = /opt/vtk6/include/vtk
-VTKDIR_LIB = /opt/vtk6/lib
-VTKSUFFIX = 
+# VTK library
+VTKDIR_INC = /usr/include/vtk
+VTKDIR_LIB = /usr/lib
+VTKSUFFIX =
diff --git a/systemvars.mk b/systemvars.mk
index 41661c37da58..33d1cc67c8b8 100755
--- a/systemvars.mk
+++ b/systemvars.mk
@@ -1,4 +1,4 @@
-# $Id: systemvars.mk,v 1.1 2017/02/18 12:20:05 mwebster Exp $
+# $Id: systemvars.mk,v 1.6 2019/02/14 13:29:45 mwebster Exp $
 
 # System dependent paths
 
@@ -25,12 +25,13 @@ CSTATICFLAGS = -static
 CXXSTATICFLAGS = -static
 
 ARCHFLAGS = -m64 
+ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
 
 PARALLELFLAGS = -fopenmp
 
 DEPENDFLAGS = -MM
 
-OPTFLAGS = -march=native -O3 -fexpensive-optimizations ${ARCHFLAGS}
+OPTFLAGS = -march=native -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
 MACHDBGFLAGS = -g
 GNU_ANSI_FLAGS = -Wall -ansi -pedantic -std=c++11 -Wno-long-long
 SGI_ANSI_FLAGS = -ansi -fullwarn
@@ -42,4 +43,4 @@ GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INST
 LIB_CUDA = ${CUDA_INSTALLATION}/lib64
 INC_CUDA = ${CUDA_INSTALLATION}/include
 NVCC = ${CUDA_INSTALLATION}/bin/nvcc
-NVCC11=${CUDA_INSTALLATION}/bin/nvcc
+NVCC11= ${CUDA_INSTALLATION}/bin/nvcc