From e70a178d1f25d4a537db84f43c78e03ca855ed21 Mon Sep 17 00:00:00 2001 From: Michael Mair-Keimberger Date: Sat, 30 Dec 2023 18:52:36 +0100 Subject: sci-biology/fsl: remove unused patches Signed-off-by: Michael Mair-Keimberger Signed-off-by: Andrew Ammerlaan --- .../fsl/files/fsl-6.0.2-cuda_buildsettings.patch | 12 -- sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch | 21 --- .../fsl/files/fsl-6.0.2-gcc10_include.patch | 10 -- sci-biology/fsl/files/fsl-6.0.2-setup.patch | 198 --------------------- 4 files changed, 241 deletions(-) delete mode 100644 sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch delete mode 100644 sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch delete mode 100644 sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch delete mode 100644 sci-biology/fsl/files/fsl-6.0.2-setup.patch (limited to 'sci-biology') diff --git a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch deleted file mode 100644 index a3872acf0..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk ---- fsl.orig/config/buildSettings.mk 2020-07-23 15:43:42.277064365 -0400 -+++ fsl/config/buildSettings.mk 2020-07-23 15:45:17.705069496 -0400 -@@ -141,7 +141,7 @@ - # CUDA development environment - CUDAVER := $(or $(CUDAVER),9.1) - #$(info $$CUDAVER is [${CUDAVER}]) --CUDA_INSTALLATION = /opt/cuda-${CUDAVER} -+CUDA_INSTALLATION = /opt/cuda - GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION}) - LIB_CUDA = ${CUDA_INSTALLATION}/lib64 - INC_CUDA = ${CUDA_INSTALLATION}/include diff --git a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch deleted file mode 100644 index 40409ec08..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile ---- fsl.orig/src/eddy/Makefile 2020-07-30 14:30:06.414884410 -0400 -+++ fsl/src/eddy/Makefile 2020-07-30 14:33:03.400889914 -0400 -@@ -29,6 +29,8 @@ - TMPCXXFLAGS_2= - TMPNAME_1= - TMPNAME_2= -+cuda=1 -+cpu=1 - - ifndef cuda - ifndef cpu #Default single cpu, no threading -@@ -74,7 +75,7 @@ - ifdef NVCC11 - NVCC=${NVCC11} - endif --NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 -+NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@ - ifeq ($(CLOBBER_CLANG),1) - NVCCFLAGS+= -DCLOBBER_CLANG - endif diff --git a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch deleted file mode 100644 index 9ddb11a2b..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/src/newimage/newimageio.h 2020-06-18 06:05:51.287864975 -0400 -+++ b/src/newimage/newimageio.h 2020-06-18 06:06:27.535129711 -0400 -@@ -75,6 +75,7 @@ - #include - #include - #include -+#include - #include "NewNifti/NewNifti.h" - #include "newmatio.h" - #include "newimage.h" diff --git a/sci-biology/fsl/files/fsl-6.0.2-setup.patch b/sci-biology/fsl/files/fsl-6.0.2-setup.patch deleted file mode 100644 index 39737fd85..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-setup.patch +++ /dev/null @@ -1,198 +0,0 @@ -From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001 -From: François Bissey -Date: Mon, 20 Jan 2020 11:54:37 +1300 -Subject: [PATCH] Adjust the build system so it doesnt build packages - externally provided by portage. Make the compilation flags more generic and - easily adjustable. Make the build system stop at the first fault. - ---- - build | 6 +++--- - config/buildSettings.mk | 20 ++++++++++---------- - config/common/buildproj | 8 +++++--- - config/common/vars.mk | 10 +++++----- - extras/build | 8 ++++---- - src/mist-clean/Makefile | 2 +- - 6 files changed, 28 insertions(+), 26 deletions(-) - -diff --git a/build b/build -index 05dac06c..d90e407b 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 dpm topup \ - asl_mfree \ -@@ -80,8 +80,8 @@ xtract"; - 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/buildSettings.mk b/config/buildSettings.mk -index b2e1f150..04532fc2 100644 ---- a/config/buildSettings.mk -+++ b/config/buildSettings.mk -@@ -18,7 +18,7 @@ MV = /bin/mv - CHMOD = /bin/chmod - MKDIR = /bin/mkdir - INSTALL = install -p --TCLSH = ${FSLDIR}/bin/fsltclsh -+TCLSH = tclsh - DEPENDFLAGS = -MM - MACHDBGFLAGS = -g - ##################################################################### -@@ -124,19 +124,19 @@ endif # if Darwin - ##################################################################### - ifeq ($(SYSTYPE), Linux) - ############### System Vars ##################################### --CC = gcc --CXX = c++ --CXX11 = c++ -+CC = @@GENTOO_CC@@ -+CXX = @@GENTOO_CXX@@ -+CXX11 = @@GENTOO_CXX@@ - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static --ARCHFLAGS = -m64 --ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib' -+ARCHFLAGS = -+ARCHLDFLAGS = - PARALLELFLAGS = -fopenmp --OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS = - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long - SGI_ANSI_FLAGS = -ansi -fullwarn - ANSI_FLAGS = ${GNU_ANSI_FLAGS} --RANLIB = echo -+RANLIB = @@GENTOO_RANLIB@@ - FSLML = ${FSLDIR}/bin/fslml - # CUDA development environment - CUDAVER := $(or $(CUDAVER),9.1) -@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include - NVCC = ${CUDA_INSTALLATION}/bin/nvcc - ############### External Libs ##################################### - # ZLIB library --LIB_ZLIB = /lib64 --INC_ZLIB = /usr/include -+#LIB_ZLIB = /lib64 -+#INC_ZLIB = /usr/include - # QT library - QTDIR = /usr/lib/qt3 - LIB_QT = ${QTDIR}/lib -diff --git a/config/common/buildproj b/config/common/buildproj -index 2f0f2b8f..48624a1f 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` - FSLMASTERBUILD=1 - export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD - -@@ -67,7 +67,7 @@ for projname in $PROJECTS; do - if [ -x ./fslconfig ] ; then - . ./fslconfig ; - fi -- if ${MAKE} -k ${MAKEOPTIONS} ; then -+ if ${MAKE} ${MAKEOPTIONS} ; then - if ${MAKE} ${MAKEOPTIONS} install ; then - installok=true; - # Clean up after ourselves -@@ -82,6 +82,7 @@ for projname in $PROJECTS; do - if [ $installok = false ] ; then - echo " " - echo "ERROR::Could not install $projname successfully" ; -+ exit 1 - fi - else - echo " " -@@ -90,6 +91,7 @@ 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 b027b010..aeeae67c 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} ${USERCXXFLAGS} - - HFILES = *.h - AFILES = *.a -diff --git a/extras/build b/extras/build -index 59e7a2ed..0d68232e 100755 ---- a/extras/build -+++ b/extras/build -@@ -96,16 +96,16 @@ if [ X"${OS}" = "XDarwin" ]; then - BUILDICONV=1 - fi - fi --PROJECTS="tcl tk" -+#PROJECTS="tcl tk" - if [ ${BUILDZLIB} -eq 1 ]; then - PROJECTS="${PROJECTS} zlib" - fi --PROJECTS="${PROJECTS} libpng" -+#PROJECTS="${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 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat" -+PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran" -+PROJECTS="${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 20402cca..6918bee4 100755 ---- a/src/mist-clean/Makefile -+++ b/src/mist-clean/Makefile -@@ -52,6 +52,6 @@ installpython: - cp -r python/* ${DESTDIR}/python/mist - - clean: -- rm -f ${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 --- -2.24.1 - -- cgit v1.2.3-65-gdbad