diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog deleted file mode 100644 index 06dd698..0000000 --- a/sci-biology/fsl/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -*fsl-6.0.2 (08 Aug 2020) - - 08 Aug 2020; +files/99fsl, - +files/fsl-5.0.11-fslsurface_parallel_make.patch, - +files/fsl-5.0.11-ifstream_use.patch, +files/fsl-5.0.11-niftiio_var_fix.patch, - +files/fsl-5.0.9-headers.patch, +files/fsl-6.0.2-fsldir_redux.patch, - +files/fsl-6.0.2-gcc10_include.patch, +files/fsl-6.0.2-no_xmlpp.patch, - +files/fsl-6.0.2-qstring_compat.patch, +files/fsl-6.0.2-setup.patch, - +files/fsl-6.0.2-template.patch, +fsl-6.0.2.ebuild, +metadata.xml: - sci-biology/fsl: patching to allow compilation with modern toolchains - https://github.com/gentoo/sci/issues/963 diff --git a/sci-biology/fsl/Manifest b/sci-biology/fsl/Manifest deleted file mode 100644 index 6fb2c02..0000000 --- a/sci-biology/fsl/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST fsl-6.0.2.tar.gz 2505331864 SHA256 c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd SHA512 fe308393076c51c50b086f9bf7ff5ddebcf8b1284128e734b9d9e501019917ceba7c0ee5cd5aa1ed44452bcd042ad72653c1a8693f94eab9b83a80fe508a56ca WHIRLPOOL ecb62e9d09cc34ac926353e4a9a131be875428b729bcf2d6f1433d9ea1a7e2b9382d1a1b305651705449a48eb3c576899f09f82ae4254b149a6219096eb45d3d 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-5.0.11-fslsurface_parallel_make.patch b/sci-biology/fsl/files/fsl-5.0.11-fslsurface_parallel_make.patch deleted file mode 100644 index 026543d..0000000 --- a/sci-biology/fsl/files/fsl-5.0.11-fslsurface_parallel_make.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff --git a/src/fslsurface/Makefile b/src/fslsurface/Makefile -index 37f459c..008f443 100644 ---- a/src/fslsurface/Makefile -+++ b/src/fslsurface/Makefile -@@ -57,7 +57,7 @@ fslsurfacegl.a: fslsurfacegl.o fslsurface.a - ${AR} -r libfslsurfacegl.a fslsurfacegl.o - fslsurface_backcompat.a: fslsurface_first.o fslsurface_dataconv.o fslsurface.a - ${AR} -r libfslsurface_backcompat.a fslsurface_first.o fslsurface_dataconv.o --fslsurfacemaths: fslsurface.a fslsurfacemaths.o -+fslsurfacemaths: fslsurface.a fslsurfacemaths.o fslsurfaceio.o fslsurfacefns.o fslsurface_first.o fslsurface.o - ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ fslsurfacemaths.o fslsurfaceio.o fslsurfacefns.o fslsurface_first.o fslsurface.o ${LIBS} ${FMLIBS} --marching_cubes: fslsurface.a marching_cubes.o -+marching_cubes: fslsurface.a marching_cubes.o fslsurfaceio.o fslsurfacefns.o - ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ marching_cubes.o fslsurfaceio.o fslsurfacefns.o ${LIBS} ${FMLIBS} diff --git a/sci-biology/fsl/files/fsl-5.0.11-ifstream_use.patch b/sci-biology/fsl/files/fsl-5.0.11-ifstream_use.patch deleted file mode 100644 index c4ba003..0000000 --- a/sci-biology/fsl/files/fsl-5.0.11-ifstream_use.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc -index f310dc7..03fe8bb 100644 ---- a/src/melodic/meldata.cc -+++ b/src/melodic/meldata.cc -@@ -1015,7 +1015,7 @@ namespace Melodic{ - Resels = 1.0; - - in.open(logger.appendDir("smoothest").c_str(), ios::in); -- if(in>0){ -+ if(in.is_open()){ - for(int ctr=1; ctr<7; ctr++) - in >> str; - in.close(); diff --git a/sci-biology/fsl/files/fsl-5.0.11-niftiio_var_fix.patch b/sci-biology/fsl/files/fsl-5.0.11-niftiio_var_fix.patch deleted file mode 100644 index f1a833b..0000000 --- a/sci-biology/fsl/files/fsl-5.0.11-niftiio_var_fix.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff --git a/src/fslio/dbh.h b/src/fslio/dbh.h -index eff0a50a..fbce1770 100644 ---- a/src/fslio/dbh.h -+++ b/src/fslio/dbh.h -@@ -79,19 +79,6 @@ struct dsr /* dsr */ - struct data_history hist; /* 148 + 200 */ - }; /* total=348 */ - --/* Acceptable values for hdr.dime.datatype */ -- --#define DT_NONE 0 --#define DT_UNKNOWN 0 --#define DT_BINARY 1 --#define DT_UNSIGNED_CHAR 2 --#define DT_SIGNED_SHORT 4 --#define DT_SIGNED_INT 8 --#define DT_FLOAT 16 --#define DT_COMPLEX 32 --#define DT_DOUBLE 64 --#define DT_RGB 128 --#define DT_ALL 255 - - typedef struct - { diff --git a/sci-biology/fsl/files/fsl-5.0.9-headers.patch b/sci-biology/fsl/files/fsl-5.0.9-headers.patch deleted file mode 100644 index 663dc56..0000000 --- a/sci-biology/fsl/files/fsl-5.0.9-headers.patch +++ /dev/null @@ -1,15 +0,0 @@ -# Include zlib header directly. -# From: Francois Bissey -# Signed-off-by: Horea Christian -# Submitted upstream: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1709&L=FSL&F=&S=&X=95C10F0B7D62EAAE7A&P=169254 - ---- fsl/src/miscvis/writepng.c.orig 2013-10-19 00:18:32.415203592 +1300 -+++ fsl/src/miscvis/writepng.c 2013-10-19 00:19:05.414255132 +1300 -@@ -32,6 +32,7 @@ - - #include /* 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 */ - diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch deleted file mode 100644 index dc1babd..0000000 --- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux.patch +++ /dev/null @@ -1,495 +0,0 @@ -From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001 -From: François Bissey -Date: Mon, 20 Jan 2020 11:40:53 +1300 -Subject: [PATCH] Making sure fsl code and executable can find other executable - and data in standard location. - ---- - src/fast4/fast_two.cc | 8 ++++---- - src/feat5/feat_model.cc | 8 +++----- - src/feat5/tsplot.cc | 7 +++---- - src/first/first_utils.cc | 4 ++-- - src/fnirt/fnirtfns.cpp | 11 ++++------- - src/fslsurface/fslsurface_first.cc | 6 ++---- - src/fslsurface/fslsurfacemaths.cpp | 12 ------------ - src/libvis/miscpic.h | 7 +------ - src/melodic/meldata.cc | 4 ++-- - src/melodic/meloptions.cc | 8 -------- - src/melodic/meloptions.h | 1 - - src/melodic/melreport.cc | 12 ++++++------ - src/melodic/melreport.h | 20 ++++++++++---------- - src/mm/mixture_model.cc | 4 ++-- - src/siena/siena_diff.cc | 28 +++++++++++++--------------- - src/topup/topupfns.cpp | 3 +-- - 16 files changed, 53 insertions(+), 90 deletions(-) - -diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc -index 592b5df..b525444 100644 ---- a/src/fast4/fast_two.cc -+++ b/src/fast4/fast_two.cc -@@ -166,7 +166,7 @@ int prior_registration(string inname, string main_prior_vol, NEWIMAGE::volume0) - { - 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]; - -@@ -763,8 +763,6 @@ int main(int argc, char **argv) - 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)); -@@ -1510,7 +1508,7 @@ int main(int argc, char **argv) - 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); -@@ -2161,6 +2159,6 @@ char the_string[10000]; - - fclose(outputfile); - -- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename; -+ filename="wpng -q -overwrite " + filename; - system(filename.c_str()); - } -diff --git a/src/feat5/tsplot.cc b/src/feat5/tsplot.cc -index ae191fd..3a02b55 100644 ---- a/src/feat5/tsplot.cc -+++ b/src/feat5/tsplot.cc -@@ -293,7 +293,7 @@ int main(int argc, char **argv) - 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 @@ volume immask; - if (argc<2) usage(""); - featdir=string(argv[1]); - fmriFileName=featdir+"/filtered_func_data"; -- fslPath=string(getenv("FSLDIR")); - - string outputName(featdir); - -@@ -753,7 +752,7 @@ volume4D acs; - 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(); -@@ -768,7 +767,7 @@ volume4D acs; - 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 --git a/src/first/first_utils.cc b/src/first/first_utils.cc -index 68be44b..85960f4 100644 ---- a/src/first/first_utils.cc -+++ b/src/first/first_utils.cc -@@ -1954,8 +1954,8 @@ void do_work_bvars(){ - 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 --git a/src/fnirt/fnirtfns.cpp b/src/fnirt/fnirtfns.cpp -index 24e26fd..77899e7 100644 ---- a/src/fnirt/fnirtfns.cpp -+++ b/src/fnirt/fnirtfns.cpp -@@ -1203,8 +1203,7 @@ string existing_ref_fname(const string& ref_fname) - 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::FslFileExists(eref_fname)) return(eref_fname); - else return(string("")); - } -@@ -1230,9 +1229,8 @@ string existing_ref_fname(const string& ref_fname) - 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 @@ string existing_conf_file(const string& cfname) - 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 --git a/src/fslsurface/fslsurface_first.cc b/src/fslsurface/fslsurface_first.cc -index faec642..b2ef794 100644 ---- a/src/fslsurface/fslsurface_first.cc -+++ b/src/fslsurface/fslsurface_first.cc -@@ -500,8 +500,7 @@ namespace fslsurface_name { - - 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 @@ namespace fslsurface_name { - - 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 --git a/src/fslsurface/fslsurfacemaths.cpp b/src/fslsurface/fslsurfacemaths.cpp -index eaf55eb..3dc184d 100644 ---- a/src/fslsurface/fslsurfacemaths.cpp -+++ b/src/fslsurface/fslsurfacemaths.cpp -@@ -598,12 +598,6 @@ int main (int argc, char * argv[]) - - }else if (command == "-reconFromBvars"){ - cout<<"do recon "<0){ -@@ -1157,7 +1157,7 @@ namespace Melodic{ - // 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 --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc -index 08170c7..252e72b 100644 ---- a/src/melodic/meloptions.cc -+++ b/src/melodic/meloptions.cc -@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL; - 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 --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h -index f546125..b964b7d 100644 ---- a/src/melodic/meloptions.h -+++ b/src/melodic/meloptions.h -@@ -93,7 +93,6 @@ class MelodicOptions { - ~MelodicOptions() { delete gopt; } - - string version; -- string binpath; - string logfname; - bool filtermode; - bool explicitnums; -diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc -index 141b6c2..2625059 100644 ---- a/src/melodic/melreport.cc -+++ b/src/melodic/melreport.cc -@@ -84,8 +84,8 @@ namespace Melodic{ - IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html"); - - {//start IC page -- IChtml << "" << endl -+ IChtml << "" << endl - << "" - << "FSL" << endl - << "