From 0bde5926d1890ea27b45e3c19b9dca07c9422462 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sun, 21 Oct 2018 16:40:21 +0200 Subject: [PATCH] Merged https://gitweb.gentoo.org/proj/sci.git/commit/?id=c7f45b539af87c6ba4fe535181d5d4afa25baa66 --- sci-biology/fsl/Manifest | 1 - sci-biology/fsl/files/99fsl | 5 - sci-biology/fsl/files/fsl-5.0.10-setup.patch | 121 ----- .../fsl/files/fsl-5.0.9-fsldir_redux.patch | 456 ------------------ sci-biology/fsl/files/fsl-5.0.9-headers.patch | 15 - sci-biology/fsl/files/fsl-5.0.9-setup.patch | 115 ----- sci-biology/fsl/fsl-5.0.11.ebuild | 147 ------ sci-biology/fsl/metadata.xml | 11 - 8 files changed, 871 deletions(-) delete mode 100644 sci-biology/fsl/Manifest delete mode 100644 sci-biology/fsl/files/99fsl delete mode 100644 sci-biology/fsl/files/fsl-5.0.10-setup.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.9-headers.patch delete mode 100644 sci-biology/fsl/files/fsl-5.0.9-setup.patch delete mode 100644 sci-biology/fsl/fsl-5.0.11.ebuild delete mode 100644 sci-biology/fsl/metadata.xml diff --git a/sci-biology/fsl/Manifest b/sci-biology/fsl/Manifest deleted file mode 100644 index 4590c99..0000000 --- a/sci-biology/fsl/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST fsl-5.0.11.tar.gz 1507525689 SHA256 8a76d36ff280ab3bfa79c46838a1baf7ea8ffe21d0b84bc7546cb8a1cef46c57 SHA512 6f859723f8e4bd7e381761983f6423364180f5d3300cb165a3e57f3535d5301624ecb30c1796dae9579da5dd16e80a8a62d9994fec1caebf0835c2f6795ca055 WHIRLPOOL 00075ce453db0e65fd513d66cea8519193f5aee3bc0c971df0e4c637a453e3dfead464fcf615d15b743110633a05d0216a2867092ad68ef90593d32dadd0d247 diff --git a/sci-biology/fsl/files/99fsl b/sci-biology/fsl/files/99fsl deleted file mode 100644 index 41db5c5..0000000 --- a/sci-biology/fsl/files/99fsl +++ /dev/null @@ -1,5 +0,0 @@ -FSLOUTPUTTYPE=NIFTI_GZ -FSLMULTIFILEQUIT=TRUE -FSLTCLSH=tclsh -FSLWISH=wish -FSLDIR=/usr/share/fsl diff --git a/sci-biology/fsl/files/fsl-5.0.10-setup.patch b/sci-biology/fsl/files/fsl-5.0.10-setup.patch deleted file mode 100644 index e19203e..0000000 --- a/sci-biology/fsl/files/fsl-5.0.10-setup.patch +++ /dev/null @@ -1,121 +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 -@@ -26,5 +26,5 @@ - fi - --echo "Building projects - see build.log file for progress..." --./config/common/buildproj $PROJECTS > ./build.log 2>&1 -+echo "Building projects" -+./config/common/buildproj $PROJECTS - finalStatus=$? -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} ${MAKEOPTIONS} 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} ${USERLDFLAGS} - --AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} -+AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${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 -@@ -104,7 +104,7 @@ - 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} boost libsqlite libnlopt ../include/armawrap/dummy_newmat" - for projname in $PROJECTS; do - if [ -d $FSLESRCDIR/$projname ] ; then -diff -Naur fsl.orig/src/mist-clean/Makefile fsl/src/mist-clean/Makefile ---- fsl.orig/src/mist-clean/Makefile 2006-03-27 10:48:16.000000000 +0200 -+++ fsl/src/mist-clean/Makefile 2018-10-08 16:16:01.180310611 +0200 -@@ -52,6 +52,6 @@ - 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-5.0.9-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch deleted file mode 100644 index c28fabe..0000000 --- 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 -# Signed-off-by: Horea Christian - -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< G; - vector 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 normalisedContrasts, model, triggers; -- string fmriFileName, fslPath, featdir, vType, indexText; -+ string fmriFileName, featdir, vType, indexText; - ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4); - bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false); - bool zWeightClusters(true); -@@ -307,7 +307,6 @@ - if (argc<2) usage(""); - featdir=string(argv[1]); - fmriFileName=featdir+"/filtered_func_data"; -- fslPath=string(getenv("FSLDIR")); - - string outputName(featdir); - -@@ -725,7 +724,7 @@ - cerr << "Can't open output report file " << outputName << endl; - exit(1); - } -- outputFile << "\n"<< statType << num2str(i) <<"\n\n
\n

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

\n
\n
Full plots

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

\n

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

\n
\n
Full plots

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

Peristimulus plots

\n"<< peristimulusText <<"\n

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

FEAT Time Series Report

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

FEAT Time Series Report

\n
\n
" << indexText << "
" << endl << endl; - outputFile.close(); - - /* now output same thing without start and end, for inclusion in feat report */ -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 refim; -- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } -- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } -+ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } -+ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } - volume maskvol(refim); - maskvol=0.0f; - volume4D volnormals; -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* immni = new volume(); - -- char* fsldir = getenv("FSLDIR"); -- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm"); -+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); - - //read_volume_hdr_only(*immni, template_name); - -@@ -699,8 +698,7 @@ - - volume* immni = new volume(); - -- char* fsldir = getenv("FSLDIR"); -- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm"); -+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); - - //read_volume_hdr_only(*immni, template_name); - -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 "<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 << "" << endl -+ IChtml << "" << endl - << "" - << "FSL" << endl - << "