From 6dfe74edc7e6327b614f0e1d15f95aa9d05c9637 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Bissey?= Date: Fri, 8 Nov 2019 10:20:38 +1300 Subject: [PATCH] sci-biology/fsl: patch porting to deal with cifti Package-Manager: Portage-2.3.76, Repoman-2.3.16 --- sci-biology/fsl/ChangeLog | 5 ++ .../fsl/files/fsl-6.0.2-no_xmlpp.patch | 44 +++++++++++++++++ .../fsl/files/fsl-6.0.2-qstring_compat.patch | 48 +++++++++++++++++++ sci-biology/fsl/fsl-6.0.2.ebuild | 4 +- 4 files changed, 99 insertions(+), 2 deletions(-) create mode 100644 sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch create mode 100644 sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog index 753a4c3..bea88ac 100644 --- a/sci-biology/fsl/ChangeLog +++ b/sci-biology/fsl/ChangeLog @@ -1,3 +1,8 @@ + 07 Nov 2019; François Bissey + +files/fsl-6.0.2-no_xmlpp.patch, +files/fsl-6.0.2-qstring_compat.patch, + fsl-6.0.2.ebuild: + sci-biology/fsl: patch porting to deal with cifti + 07 Nov 2019; François Bissey fsl-6.0.2.ebuild: sci-biology/fsl: tcl/tk is needed at build time diff --git a/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch b/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch new file mode 100644 index 0000000..47c9120 --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.2-no_xmlpp.patch @@ -0,0 +1,44 @@ +diff --git a/src/flameo/Makefile b/src/flameo/Makefile +index d22eb965..e967e682 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 -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lprob -lz ++LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti ${CIFTILIBS} -lboost_filesystem -lboost_system -lznz -lprob -lz + + XFILES = flameo + +diff --git a/src/melodic/Makefile b/src/melodic/Makefile +index 50666517..0c356a2d 100644 +--- a/src/melodic/Makefile ++++ b/src/melodic/Makefile +@@ -7,7 +7,7 @@ OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui + + PROJNAME = melodic + +-USRINCFLAGS = -I${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 -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm -lgdc -lgd -lpng -lz ++LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti ${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-6.0.2-qstring_compat.patch b/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch new file mode 100644 index 0000000..c0e238c --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.2-qstring_compat.patch @@ -0,0 +1,48 @@ +diff --git a/src/flameo/gsa.cc b/src/flameo/gsa.cc +index 70f8f385..16167abe 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(make_basename(filename)+".nii"); ++ inputCifti.openFile((make_basename(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(make_basename(filename)+extension+".nii");//sets up on-disk writing with default writing version ++ outputFile.setWritingFile((make_basename(filename)+extension+".nii").c_str());//sets up on-disk writing with default writing version + outputFile.setCiftiXML(ciftiExemplar,false); + vector scratchRow(data.Nrows());//read/write a row at a time + for (int64_t row=0;row& dims = inputCifti.getDimensions(); + tmpData.ReSize(dims[0],dims[1]); //swapped compared to cifti + vector scratchRow(dims[0]);//read/write a row at a time +diff --git a/src/melodic/meldata.h b/src/melodic/meldata.h +index 49774003..f5326bdd 100644 +--- a/src/melodic/meldata.h ++++ b/src/melodic/meldata.h +@@ -109,7 +109,7 @@ namespace Melodic{ + message(" " << logger.appendDir(fname) << endl); + } else { //Process CIFTI save ICs as float + cifti::CiftiFile outputFile; +- outputFile.setWritingFile(logger.appendDir(fname)+".nii");//sets up on-disk writing with default writing version ++ outputFile.setWritingFile((logger.appendDir(fname)+".nii").c_str());//sets up on-disk writing with default writing version + cifti::CiftiXML xml(inputCifti.getCiftiXML()); + cifti::CiftiScalarsMap scalarsMap; + std::vector foo = xml.writeXMLToVector(); diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild index 16f4ec9..b45fd8d 100644 --- a/sci-biology/fsl/fsl-6.0.2.ebuild +++ b/sci-biology/fsl/fsl-6.0.2.ebuild @@ -33,11 +33,11 @@ UPSTREAM_FSLDIR="/usr/share/fsl" PATCHES=( "${FILESDIR}/${PN}"-6.0.2-setup.patch - #"${FILESDIR}/${PN}"-5.0.11-no_xmlpp.patch + "${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch "${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}/${PN}"-6.0.2-qstring_compat.patch "${FILESDIR}/${PN}"-5.0.9-headers.patch #"${FILESDIR}/${PN}"-5.0.9-fsldir_redux.patch )