commit: 1c4f022505e83357adc3fbab929ea55396aee27d Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Sun Jul 18 10:47:25 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Sun Jul 18 10:47:25 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1c4f0225
sci-biology/fsl: add version 6.0.4 Closes: https://github.com/gentoo/sci/pull/1074 Co-authored-by: Paul Polak <paul.polak <AT> med-image.info> Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> .../fsl/files/fsl-6.0.4-cuda_buildsettings.patch | 12 + sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch | 21 ++ sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch | 14 + sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch | 11 + .../fsl/files/fsl-6.0.4-fsldir_redux-p1.patch | 240 ++++++++++++++ .../fsl/files/fsl-6.0.4-fsldir_redux-p2.patch | 254 +++++++++++++++ .../fsl/files/fsl-6.0.4-gcc10_include.patch | 11 + sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch | 11 + .../fsl-6.0.4-remove_fslpy_collisions-p1.patch | 303 ++++++++++++++++++ .../fsl-6.0.4-remove_fslpy_collisions-p2.patch | 348 +++++++++++++++++++++ sci-biology/fsl/files/fsl-6.0.4-setup.patch | 174 +++++++++++ sci-biology/fsl/fsl-6.0.2-r1.ebuild | 4 +- sci-biology/fsl/fsl-6.0.2.ebuild | 6 +- .../fsl/{fsl-6.0.2-r1.ebuild => fsl-6.0.4.ebuild} | 36 ++- 14 files changed, 1429 insertions(+), 16 deletions(-) diff --git a/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch new file mode 100644 index 000000000..749e80623 --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch @@ -0,0 +1,12 @@ +diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk +--- fsl.orig/config/buildSettings.mk 2020-12-02 16:22:57.999912865 -0500 ++++ fsl/config/buildSettings.mk 2020-12-02 16:24:15.332915270 -0500 +@@ -144,7 +144,7 @@ + # CUDA development environment + CUDAVER := $(or $(CUDAVER),9.1) + #$(info $$CUDAVER is [${CUDAVER}]) +-CUDA_INSTALLATION = /opt/cuda-${CUDAVER} ++CUDA_INSTALLATION = /opt/cuda + ifdef SINGULARITY_NAME + CUDA_INSTALLATION = /usr/local/cuda-${CUDAVER} + endif diff --git a/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch new file mode 100644 index 000000000..ad118c39a --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch @@ -0,0 +1,21 @@ +diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile +--- fsl.orig/src/eddy/Makefile 2020-12-02 16:07:47.327884548 -0500 ++++ fsl/src/eddy/Makefile 2020-12-02 16:11:21.149891196 -0500 +@@ -29,6 +29,8 @@ + TMPCXXFLAGS_2= + TMPNAME_1= + TMPNAME_2= ++cuda=1 ++cpu=1 + TOPUP_DIR=../topup + + ifndef cuda +@@ -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-6.0.4-fdt_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch new file mode 100644 index 000000000..7f322027b --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch @@ -0,0 +1,14 @@ +diff -Naur fsl.orig/src/fdt/Makefile fsl/src/fdt/Makefile +--- fsl.orig/src/fdt/Makefile 2020-12-02 19:06:55.826218772 -0500 ++++ fsl/src/fdt/Makefile 2020-12-02 19:08:02.883220858 -0500 +@@ -6,7 +6,9 @@ + $(eval $($(PROJNAME)_MASTERBUILD)) + endif + +-ifeq ($(COMPILE_GPU), 1) ++# disable CUDA support for fdt ++#ifeq ($(COMPILE_GPU), 1) ++ifeq (0, 1) + COMPILE_WITH_GPU=libbedpostx_cuda.so merge_parts_gpu xfibres_gpu CUDA/split_parts_gpu + SCRIPTS_GPU=CUDA/bedpostx_gpu CUDA/bedpostx_postproc_gpu.sh + endif diff --git a/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch new file mode 100644 index 000000000..a991f1ed3 --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch @@ -0,0 +1,11 @@ +diff -Naur fsl.orig/src/flameo/Makefile fsl/src/flameo/Makefile +--- fsl.orig/src/flameo/Makefile 2021-01-06 14:04:35.728274475 -0500 ++++ fsl/src/flameo/Makefile 2021-01-06 14:08:18.204269285 -0500 +@@ -4,6 +4,7 @@ + + 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 + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} ++USRCXXFLAGS = -std=c++11 + + UNAME := $(shell uname) + ifeq (${UNAME},Darwin) diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch new file mode 100644 index 000000000..ca3945442 --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch @@ -0,0 +1,240 @@ +From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001 +From: François Bissey <[email protected]> +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::volume<fl + 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 @@ string csfPriorName, grayPriorName, whitePriorName; + 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<<reg<<endl; + system(reg); +- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str()); ++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str()); + if(verbose.value()) + cout<<reg<<endl; + system(reg); +- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str()); ++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str()); + if(verbose.value()) + cout << reg << endl; + system(reg); +diff --git a/src/feat5/feat_model.cc b/src/feat5/feat_model.cc +index 399a13e..e15e43c 100644 +--- a/src/feat5/feat_model.cc ++++ b/src/feat5/feat_model.cc +@@ -744,7 +744,7 @@ int main(int argc, char **argv) + vector<int> G; + vector<string> 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<double> 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<float> 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<float> acs; + cerr << "Can't open output report file " << outputName << endl; + exit(1); + } +- outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText; ++ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText; + if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n"; + else outputFile << "\n</BODY></HTML>\n\n"; + outputFile.close(); +@@ -768,7 +767,7 @@ volume4D<float> acs; + cerr << "Can't open output report file " << outputName << endl; + exit(1); + } +- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl; ++ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << 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<float> 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<float> maskvol(refim); + maskvol=0.0f; + volume4D<float> 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<float>* immni = new volume<float>(); + +- 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<float>* immni = new volume<float>(); + +- 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 "<<endl; +- char* fsldir = getenv("FSLDIR"); +- if (fsldir == NULL) +- { +- cerr<<"FSLDIR has not been set. "<<endl; +- exit(EXIT_FAILURE); +- } + //file.bvars,mni_template.nii.gz + // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm"; + reconSurface_from_bvars( surf, string(argv[i_arg+1])); +@@ -612,12 +606,6 @@ int main (int argc, char * argv[]) + + }else if (command == "-reconAllFromBvarsAndSave"){ + cout<<"do recon+save "<<argc<<" "<<i_arg<<endl; +- char* fsldir = getenv("FSLDIR"); +- if (fsldir == NULL) +- { +- cerr<<"FSLDIR has not been set. "<<endl; +- exit(EXIT_FAILURE); +- } + //file.bvars,mni_template.nii.gz + // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm"; + cout<<"recon "<< string(argv[i_arg+1])<<endl; diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch new file mode 100644 index 000000000..af498b400 --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch @@ -0,0 +1,254 @@ +diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h +index a2f3855..5f440f2 100644 +--- a/src/libvis/miscpic.h ++++ b/src/libvis/miscpic.h +@@ -90,12 +90,7 @@ namespace MISCPIC{ + markRight=false; + trans= -10; + edgethresh = 0.0; +- if(getenv("FSLDIR")!=0){ +- lutbase = string(getenv("FSLDIR")) + "/etc/luts/"; +- } +- else{ +- lutbase = string("/"); +- } ++ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/"; + title = string(""); + cbartype = string(""); + cbarptr = NULL; +diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc +index 1749a45..c4ad234 100644 +--- a/src/melodic/meldata.cc ++++ b/src/melodic/meldata.cc +@@ -992,7 +992,7 @@ namespace Melodic{ + void MelodicData::est_smoothness() + { + if(Resels == 0){ +- string SM_path = opts.binpath + "smoothest"; ++ string SM_path = "smoothest"; + string Mask_fname = logger.appendDir("mask"); + + if(opts.segment.value().length()>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 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + +- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl ++ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl + << "<style type=\"text/css\">OBJECT { width: 100% }</style>" + << "<TITLE>FSL</TITLE></HEAD>" << endl + << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50 +@@ -486,8 +486,8 @@ namespace Melodic{ + + {//start IC2 page + IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html"); +- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + +- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl ++ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl + << "<style type=\"text/css\">OBJECT { width: 100% }</style>" + << "<TITLE>FSL</TITLE></HEAD>" << endl + << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50 +@@ -665,8 +665,8 @@ namespace Melodic{ + IChtml << "<HTML> " << endl + << "<TITLE>MELODIC Component " << num2str(cnum) + << "</TITLE>" << endl +- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") +- << "/doc/images/fsl-bg.jpg\">" << endl ++ << "<BODY BACKGROUND=\"file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl + << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum) + << "</H1>"<< endl; + +diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h +index 574fc4c..e444681 100644 +--- a/src/melodic/melreport.h ++++ b/src/melodic/melreport.h +@@ -104,21 +104,21 @@ namespace Melodic{ + const time_t tmptime = time(NULL); + system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str()); + report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out); +- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + +- (string) getenv("FSLDIR") +"/doc/fsl.css>" ++ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" + << "<TITLE>MELODIC report</TITLE></HEAD><BODY>" + << endl <<endl; + loghtml.setDir(report.getDir(),"log.html"); +- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + +- (string) getenv("FSLDIR") +"/doc/fsl.css>" ++ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" + << "<TITLE>MELODIC report</TITLE></HEAD><BODY>" + << endl <<endl; + navigator.setDir(report.getDir(),"nav.html"); + head.setDir(report.getDir(),"head.html"); +- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+ +- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl; +- head << "<link REL=stylesheet TYPE=text/css href=file:"+ +- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl; ++ navigator << "<link REL=stylesheet TYPE=text/css href=file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl; ++ head << "<link REL=stylesheet TYPE=text/css href=file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl; + head <<"<TABLE BORDER=0><TR>" << endl + <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl + <<"<TABLE BORDER=0>"<< endl +@@ -130,8 +130,8 @@ namespace Melodic{ + << "</tr></table>" << endl + << "<TD ALIGN=RIGHT>" << endl + << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl +- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR") +- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl ++ << "<IMG BORDER=0 SRC=file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl + << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl; + if(opts.guireport.value()==""){ + report <<"<OBJECT data=head.html></OBJECT>" << endl; +diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc +index b8e6167..5f00693 100644 +--- a/src/mm/mixture_model.cc ++++ b/src/mm/mixture_model.cc +@@ -2224,8 +2224,8 @@ namespace Mm { + + htmllog << "<HTML> " << endl + << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl +- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") +- << "/doc/images/fsl-bg.jpg\">" << endl ++ << "<BODY BACKGROUND=\"file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl + << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl; + + htmllog << "<hr><p>" << endl; +diff -Naur fsl.orig/src/siena/siena_diff.cc fsl/src/siena/siena_diff.cc +--- fsl.orig/src/siena/siena_diff.cc 2020-12-02 15:52:50.359856656 -0500 ++++ fsl/src/siena/siena_diff.cc 2020-12-02 16:03:25.699876412 -0500 +@@ -107,7 +107,7 @@ + { + // {{{ vars + +-char thestring[10000], segoptions[10000], fsldir[10000]; ++char thestring[10000], segoptions[10000]; + int x_size, y_size, z_size, size, x, y, z, i, count, + seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0, + ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0; +@@ -124,8 +124,6 @@ + + string argv1(argv[1]), argv2(argv[2]); + +-sprintf(fsldir,"%s",getenv("FSLDIR")); +- + for (i = 3; i < argc; i++) + { + if (!strcmp(argv[i], "-i")) +@@ -206,26 +204,26 @@ + // }}} + // {{{ transform images and masks + +-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", +- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); ++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", ++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); + printf("%s\n",thestring); system(thestring); + +-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", +- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); ++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", ++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); + printf("%s\n",thestring); system(thestring); + +-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", +- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); ++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", ++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); + printf("%s\n",thestring); system(thestring); + +-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", +- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); ++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", ++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); + printf("%s\n",thestring); system(thestring); + + if (edge_masking) + { +- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s", +- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); ++ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s", ++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); + printf("%s\n",thestring); system(thestring); + } + +@@ -284,8 +282,8 @@ + cout << "saving image 1 to disk prior to segmentation" << endl; + save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain"); + in1.destroy(); +- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1", +- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]); ++ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1", ++ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]); + cout << thestring << endl; + system(thestring); + } +diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp +index 6873758..9e8b956 100644 +--- a/src/topup/topupfns.cpp ++++ b/src/topup/topupfns.cpp +@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname) + if (TOPUP::check_exist(ecfname)) return(ecfname); + } + if (!TOPUP::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 (TOPUP::check_exist(ecfname)) return(ecfname); + else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given + ecfname += string(".cnf"); +-- +2.24.1 + diff --git a/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch new file mode 100644 index 000000000..ae836c065 --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch @@ -0,0 +1,11 @@ +diff -Naur fsl.orig/src/newimage/newimageio.h fsl/src/newimage/newimageio.h +--- fsl.orig/src/newimage/newimageio.h 2020-12-02 15:15:27.012786899 -0500 ++++ fsl/src/newimage/newimageio.h 2020-12-02 15:19:51.046795110 -0500 +@@ -75,6 +75,7 @@ + #include <iostream> + #include <fstream> + #include <sstream> ++#include <stdexcept> + #include "NewNifti/NewNifti.h" + #include "newmatio.h" + #include "newimage.h" diff --git a/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch new file mode 100644 index 000000000..83b5b9932 --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch @@ -0,0 +1,11 @@ +diff -Naur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile +--- fsl.orig/src/melodic/Makefile 2021-01-06 14:04:35.743274475 -0500 ++++ fsl/src/melodic/Makefile 2021-01-06 14:11:27.924264859 -0500 +@@ -9,6 +9,7 @@ + + 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 + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB} ++USRCXXFLAGS = -std=c++11 + + UNAME := $(shell uname) + ifeq (${UNAME},Darwin) diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch new file mode 100644 index 000000000..434dc9cf6 --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch @@ -0,0 +1,303 @@ +diff -Naur fsl.orig/src/fslio/imln fsl/src/fslio/imln +--- fsl.orig/src/fslio/imln 2021-02-01 15:29:34.842752994 -0500 ++++ fsl/src/fslio/imln 1969-12-31 19:00:00.000000000 -0500 +@@ -1,90 +0,0 @@ +-#!/bin/sh +- +-# imln - make symbolic link(s) to image file(s) +-# +-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group +-# +-# Copyright (C) 1999-2004 University of Oxford +-# +-# Part of FSL - FMRIB's Software Library +-# http://www.fmrib.ox.ac.uk/fsl +-# [email protected] +-# +-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +-# Imaging of the Brain), Department of Clinical Neurology, Oxford +-# University, Oxford, UK +-# +-# +-# LICENCE +-# +-# FMRIB Software Library, Release 6.0 (c) 2018, The University of +-# Oxford (the "Software") +-# +-# The Software remains the property of the Oxford University Innovation +-# ("the University"). +-# +-# The Software is distributed "AS IS" under this Licence solely for +-# non-commercial use in the hope that it will be useful, but in order +-# that the University as a charitable foundation protects its assets for +-# the benefit of its educational and research purposes, the University +-# makes clear that no condition is made or to be implied, nor is any +-# warranty given or to be implied, as to the accuracy of the Software, +-# or that it will be suitable for any particular purpose or for use +-# under any specific conditions. Furthermore, the University disclaims +-# all responsibility for the use which is made of the Software. It +-# further disclaims any liability for the outcomes arising from using +-# the Software. +-# +-# The Licensee agrees to indemnify the University and hold the +-# University harmless from and against any and all claims, damages and +-# liabilities asserted by third parties (including claims for +-# negligence) which arise directly or indirectly from the use of the +-# Software or the sale of any products based on the Software. +-# +-# No part of the Software may be reproduced, modified, transmitted or +-# transferred in any form or by any means, electronic or mechanical, +-# without the express permission of the University. The permission of +-# the University is not required if the said reproduction, modification, +-# transmission or transference is done without financial return, the +-# conditions of this Licence are imposed upon the receiver of the +-# product, and all original and amended source code is included in any +-# transmitted product. You may be held legally responsible for any +-# copyright infringement that is caused or encouraged by your failure to +-# abide by these terms and conditions. +-# +-# You are not permitted under this Licence to use this Software +-# commercially. Use for which any financial return is received shall be +-# defined as commercial use, and includes (1) integration of all or part +-# of the source code or the Software into a product for sale or license +-# by or on behalf of Licensee to third parties or (2) use of the +-# Software or any derivative of it for research with the final aim of +-# developing software products for sale or license to a third party or +-# (3) use of the Software or any derivative of it for research with the +-# final aim of developing non-software products for sale or license to a +-# third party, or (4) use of the Software to provide any service to an +-# external organisation for which payment is received. If you are +-# interested in using the Software commercially, please contact Oxford +-# University Innovation ("OUI"), the technology transfer company of the +-# University, to negotiate a licence. Contact details are: +-# [email protected] quoting Reference Project 9564, FSL. +-export LC_ALL=C +- +-if [ $# -lt 2 ] ; then +- echo "Usage: $0 <file1> <file2>" +- echo " Makes a link (called file2) to file1" +- echo " NB: filenames can be basenames or include an extension" +- exit 1; +-fi +- +-f1=`${FSLDIR}/bin/remove_ext $1`; +-f2=`${FSLDIR}/bin/remove_ext $2`; +- +-if [ -f ${f1}.hdr ] ; then ln -fs ${f1}.hdr ${f2}.hdr ; fi +-if [ -f ${f1}.hdr.gz ] ; then ln -fs ${f1}.hdr.gz ${f2}.hdr.gz ; fi +-if [ -f ${f1}.img ] ; then ln -fs ${f1}.img ${f2}.img ; fi +-if [ -f ${f1}.img.gz ] ; then ln -fs ${f1}.img.gz ${f2}.img.gz ; fi +-if [ -f ${f1}.nii ] ; then ln -fs ${f1}.nii ${f2}.nii ; fi +-if [ -f ${f1}.nii.gz ] ; then ln -fs ${f1}.nii.gz ${f2}.nii.gz ; fi +-if [ -f ${f1}.mnc ] ; then ln -fs ${f1}.mnc ${f2}.mnc ; fi +-if [ -f ${f1}.mnc.gz ] ; then ln -fs ${f1}.mnc.gz ${f2}.mnc.gz ; fi +- +diff -Naur fsl.orig/src/fslio/imrm fsl/src/fslio/imrm +--- fsl.orig/src/fslio/imrm 2021-02-01 15:29:34.842752994 -0500 ++++ fsl/src/fslio/imrm 1969-12-31 19:00:00.000000000 -0500 +@@ -1,83 +0,0 @@ +-#!/bin/sh +- +-# imrm - remove image files +-# +-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group +-# +-# Copyright (C) 1999-2004 University of Oxford +-# +-# Part of FSL - FMRIB's Software Library +-# http://www.fmrib.ox.ac.uk/fsl +-# [email protected] +-# +-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +-# Imaging of the Brain), Department of Clinical Neurology, Oxford +-# University, Oxford, UK +-# +-# +-# LICENCE +-# +-# FMRIB Software Library, Release 6.0 (c) 2018, The University of +-# Oxford (the "Software") +-# +-# The Software remains the property of the Oxford University Innovation +-# ("the University"). +-# +-# The Software is distributed "AS IS" under this Licence solely for +-# non-commercial use in the hope that it will be useful, but in order +-# that the University as a charitable foundation protects its assets for +-# the benefit of its educational and research purposes, the University +-# makes clear that no condition is made or to be implied, nor is any +-# warranty given or to be implied, as to the accuracy of the Software, +-# or that it will be suitable for any particular purpose or for use +-# under any specific conditions. Furthermore, the University disclaims +-# all responsibility for the use which is made of the Software. It +-# further disclaims any liability for the outcomes arising from using +-# the Software. +-# +-# The Licensee agrees to indemnify the University and hold the +-# University harmless from and against any and all claims, damages and +-# liabilities asserted by third parties (including claims for +-# negligence) which arise directly or indirectly from the use of the +-# Software or the sale of any products based on the Software. +-# +-# No part of the Software may be reproduced, modified, transmitted or +-# transferred in any form or by any means, electronic or mechanical, +-# without the express permission of the University. The permission of +-# the University is not required if the said reproduction, modification, +-# transmission or transference is done without financial return, the +-# conditions of this Licence are imposed upon the receiver of the +-# product, and all original and amended source code is included in any +-# transmitted product. You may be held legally responsible for any +-# copyright infringement that is caused or encouraged by your failure to +-# abide by these terms and conditions. +-# +-# You are not permitted under this Licence to use this Software +-# commercially. Use for which any financial return is received shall be +-# defined as commercial use, and includes (1) integration of all or part +-# of the source code or the Software into a product for sale or license +-# by or on behalf of Licensee to third parties or (2) use of the +-# Software or any derivative of it for research with the final aim of +-# developing software products for sale or license to a third party or +-# (3) use of the Software or any derivative of it for research with the +-# final aim of developing non-software products for sale or license to a +-# third party, or (4) use of the Software to provide any service to an +-# external organisation for which payment is received. If you are +-# interested in using the Software commercially, please contact Oxford +-# University Innovation ("OUI"), the technology transfer company of the +-# University, to negotiate a licence. Contact details are: +-# [email protected] quoting Reference Project 9564, FSL. +-export LC_ALL=C +- +-if [ $# -lt 1 ] ; then +- echo "Usage: $0 <list of image names to remove>" +- echo "NB: filenames can be basenames or not" +- exit 1; +-fi +- +-for f in $@ ; do +- fn=`${FSLDIR}/bin/remove_ext $f`; +- # do the rm silently +- /bin/rm -f ${fn}.img ${fn}.hdr ${fn}.hdr.gz ${fn}.img.gz ${fn}.nii ${fn}.nii.gz ${fn}.mnc ${fn}.mnc.gz +-done +- +diff -Naur fsl.orig/src/fslio/imtest fsl/src/fslio/imtest +--- fsl.orig/src/fslio/imtest 2021-02-01 15:29:34.842752994 -0500 ++++ fsl/src/fslio/imtest 1969-12-31 19:00:00.000000000 -0500 +@@ -1,118 +0,0 @@ +-#!/bin/sh +- +-# imtest - test to see if a valid image file exists with this name (root) +-# +-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group +-# +-# Copyright (C) 1999-2004 University of Oxford +-# +-# Part of FSL - FMRIB's Software Library +-# http://www.fmrib.ox.ac.uk/fsl +-# [email protected] +-# +-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +-# Imaging of the Brain), Department of Clinical Neurology, Oxford +-# University, Oxford, UK +-# +-# +-# LICENCE +-# +-# FMRIB Software Library, Release 6.0 (c) 2018, The University of +-# Oxford (the "Software") +-# +-# The Software remains the property of the Oxford University Innovation +-# ("the University"). +-# +-# The Software is distributed "AS IS" under this Licence solely for +-# non-commercial use in the hope that it will be useful, but in order +-# that the University as a charitable foundation protects its assets for +-# the benefit of its educational and research purposes, the University +-# makes clear that no condition is made or to be implied, nor is any +-# warranty given or to be implied, as to the accuracy of the Software, +-# or that it will be suitable for any particular purpose or for use +-# under any specific conditions. Furthermore, the University disclaims +-# all responsibility for the use which is made of the Software. It +-# further disclaims any liability for the outcomes arising from using +-# the Software. +-# +-# The Licensee agrees to indemnify the University and hold the +-# University harmless from and against any and all claims, damages and +-# liabilities asserted by third parties (including claims for +-# negligence) which arise directly or indirectly from the use of the +-# Software or the sale of any products based on the Software. +-# +-# No part of the Software may be reproduced, modified, transmitted or +-# transferred in any form or by any means, electronic or mechanical, +-# without the express permission of the University. The permission of +-# the University is not required if the said reproduction, modification, +-# transmission or transference is done without financial return, the +-# conditions of this Licence are imposed upon the receiver of the +-# product, and all original and amended source code is included in any +-# transmitted product. You may be held legally responsible for any +-# copyright infringement that is caused or encouraged by your failure to +-# abide by these terms and conditions. +-# +-# You are not permitted under this Licence to use this Software +-# commercially. Use for which any financial return is received shall be +-# defined as commercial use, and includes (1) integration of all or part +-# of the source code or the Software into a product for sale or license +-# by or on behalf of Licensee to third parties or (2) use of the +-# Software or any derivative of it for research with the final aim of +-# developing software products for sale or license to a third party or +-# (3) use of the Software or any derivative of it for research with the +-# final aim of developing non-software products for sale or license to a +-# third party, or (4) use of the Software to provide any service to an +-# external organisation for which payment is received. If you are +-# interested in using the Software commercially, please contact Oxford +-# University Innovation ("OUI"), the technology transfer company of the +-# University, to negotiate a licence. Contact details are: +-# [email protected] quoting Reference Project 9564, FSL. +-export LC_ALL=C +- +-# return 0 if no image exists or 1 if the image exists +- +-if [ $# -lt 1 ] ; then +- echo "0"; +- exit; +-fi +- +-inputfile=$1 +- +- +- +-for i in 1 2 3 4 5 6 7 8 9 10 11 12 +-do +-if [ -h $inputfile ] ; then +-inputfile=`readlink $inputfile`; +-fi +-done +- +-filename=`${FSLDIR}/bin/remove_ext $inputfile`; +- +-if [ -r ${filename}.nii ] || [ -r ${filename}.nii.gz ] ; then +- echo "1"; +- exit; +-fi +- +-if [ -r ${filename}.mnc ] || [ -r ${filename}.mnc.gz ] ; then +- echo "1"; +- exit; +-fi +- +-if [ ! -r ${filename}.hdr ] && [ ! -r ${filename}.hdr.gz ] ; then +- # return 0 here as no header exists and no single image means no image! +- echo "0"; +- exit; +-fi +- +-if [ ! -r ${filename}.img ] && [ ! -r ${filename}.img.gz ] ; then +- # return 0 here as no img file exists and no single image means no image! +- echo "0"; +- exit; +-fi +- +-# only gets to here if there was a hdr and an img file +- +-echo "1"; +-exit; +- diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch new file mode 100644 index 000000000..ddb7cfb67 --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch @@ -0,0 +1,348 @@ +diff -Naur fsl.orig/src/fslio/Makefile fsl/src/fslio/Makefile +--- fsl.orig/src/fslio/Makefile 2021-02-01 15:29:34.842752994 -0500 ++++ fsl/src/fslio/Makefile 2021-02-01 15:32:19.723761859 -0500 +@@ -6,7 +6,7 @@ + + OBJS=fslio.o + +-SCRIPTS = remove_ext fsloutputtype imtest imglob imcp imln imrm immv ++SCRIPTS = fsloutputtype imglob imcp immv + + all: + +diff -Naur fsl.orig/src/fslio/remove_ext fsl/src/fslio/remove_ext +--- fsl.orig/src/fslio/remove_ext 2021-02-01 15:29:34.842752994 -0500 ++++ fsl/src/fslio/remove_ext 1969-12-31 19:00:00.000000000 -0500 +@@ -1,87 +0,0 @@ +-#!/bin/sh +- +-# remove_ext - remove extension from image filename +-# +-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group +-# +-# Copyright (C) 1999-2004 University of Oxford +-# +-# Part of FSL - FMRIB's Software Library +-# http://www.fmrib.ox.ac.uk/fsl +-# [email protected] +-# +-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +-# Imaging of the Brain), Department of Clinical Neurology, Oxford +-# University, Oxford, UK +-# +-# +-# LICENCE +-# +-# FMRIB Software Library, Release 6.0 (c) 2018, The University of +-# Oxford (the "Software") +-# +-# The Software remains the property of the Oxford University Innovation +-# ("the University"). +-# +-# The Software is distributed "AS IS" under this Licence solely for +-# non-commercial use in the hope that it will be useful, but in order +-# that the University as a charitable foundation protects its assets for +-# the benefit of its educational and research purposes, the University +-# makes clear that no condition is made or to be implied, nor is any +-# warranty given or to be implied, as to the accuracy of the Software, +-# or that it will be suitable for any particular purpose or for use +-# under any specific conditions. Furthermore, the University disclaims +-# all responsibility for the use which is made of the Software. It +-# further disclaims any liability for the outcomes arising from using +-# the Software. +-# +-# The Licensee agrees to indemnify the University and hold the +-# University harmless from and against any and all claims, damages and +-# liabilities asserted by third parties (including claims for +-# negligence) which arise directly or indirectly from the use of the +-# Software or the sale of any products based on the Software. +-# +-# No part of the Software may be reproduced, modified, transmitted or +-# transferred in any form or by any means, electronic or mechanical, +-# without the express permission of the University. The permission of +-# the University is not required if the said reproduction, modification, +-# transmission or transference is done without financial return, the +-# conditions of this Licence are imposed upon the receiver of the +-# product, and all original and amended source code is included in any +-# transmitted product. You may be held legally responsible for any +-# copyright infringement that is caused or encouraged by your failure to +-# abide by these terms and conditions. +-# +-# You are not permitted under this Licence to use this Software +-# commercially. Use for which any financial return is received shall be +-# defined as commercial use, and includes (1) integration of all or part +-# of the source code or the Software into a product for sale or license +-# by or on behalf of Licensee to third parties or (2) use of the +-# Software or any derivative of it for research with the final aim of +-# developing software products for sale or license to a third party or +-# (3) use of the Software or any derivative of it for research with the +-# final aim of developing non-software products for sale or license to a +-# third party, or (4) use of the Software to provide any service to an +-# external organisation for which payment is received. If you are +-# interested in using the Software commercially, please contact Oxford +-# University Innovation ("OUI"), the technology transfer company of the +-# University, to negotiate a licence. Contact details are: +-# [email protected] quoting Reference Project 9564, FSL. +-export LC_ALL=C +- +- +-if [ $# -lt 1 ] ; then +- exit 1 +-fi +- +-lst=""; +-for fn in $@ ; do +- # for the ones at the end of the line +- f=`echo "$fn" | sed 's/\.hdr\.gz$//' | sed 's/\.img\.gz$//' | sed 's/\.hdr$//' | sed 's/\.img$//' | sed 's/\.nii.gz$//' | sed 's/\.nii$//' | sed 's/\.mnc.gz$//' | sed 's/\.mnc$//' | sed 's/\.$//'`; +- # for the ones in the middle of the line +- f=`echo "$f" | sed 's/\.hdr\.gz[ ]/ /g' | sed 's/\.img\.gz[ ]/ /g' | sed 's/\.hdr[ ]/ /g' | sed 's/\.img[ ]/ /g' | sed 's/\.nii\.gz[ ]/ /g' | sed 's/\.nii[ ]/ /g' | sed 's/\.mnc\.gz[ ]/ /g' | sed 's/\.mnc[ ]/ /g' |sed 's/\.[ ]/ /g'`; +- lst="$lst $f"; +-done +-echo $lst; +- +- +diff -Naur fsl.orig/src/misc_scripts/fsl_abspath fsl/src/misc_scripts/fsl_abspath +--- fsl.orig/src/misc_scripts/fsl_abspath 2021-02-01 15:29:34.828752994 -0500 ++++ fsl/src/misc_scripts/fsl_abspath 1969-12-31 19:00:00.000000000 -0500 +@@ -1,71 +0,0 @@ +-#!/usr/bin/env fslpython +-# fsl_abspath - return true file path +-# Matthew Webster FMRIB Image Analysis Group +-# Copyright (C) 2009 University of Oxford +-# Part of FSL - FMRIB's Software Library +-# http://www.fmrib.ox.ac.uk/fsl +-# [email protected] +-# +-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +-# Imaging of the Brain), Department of Clinical Neurology, Oxford +-# University, Oxford, UK +-# +-# +-# LICENCE +-# +-# FMRIB Software Library, Release 6.0 (c) 2018, The University of +-# Oxford (the "Software") +-# +-# The Software remains the property of the Oxford University Innovation +-# ("the University"). +-# +-# The Software is distributed "AS IS" under this Licence solely for +-# non-commercial use in the hope that it will be useful, but in order +-# that the University as a charitable foundation protects its assets for +-# the benefit of its educational and research purposes, the University +-# makes clear that no condition is made or to be implied, nor is any +-# warranty given or to be implied, as to the accuracy of the Software, +-# or that it will be suitable for any particular purpose or for use +-# under any specific conditions. Furthermore, the University disclaims +-# all responsibility for the use which is made of the Software. It +-# further disclaims any liability for the outcomes arising from using +-# the Software. +-# +-# The Licensee agrees to indemnify the University and hold the +-# University harmless from and against any and all claims, damages and +-# liabilities asserted by third parties (including claims for +-# negligence) which arise directly or indirectly from the use of the +-# Software or the sale of any products based on the Software. +-# +-# No part of the Software may be reproduced, modified, transmitted or +-# transferred in any form or by any means, electronic or mechanical, +-# without the express permission of the University. The permission of +-# the University is not required if the said reproduction, modification, +-# transmission or transference is done without financial return, the +-# conditions of this Licence are imposed upon the receiver of the +-# product, and all original and amended source code is included in any +-# transmitted product. You may be held legally responsible for any +-# copyright infringement that is caused or encouraged by your failure to +-# abide by these terms and conditions. +-# +-# You are not permitted under this Licence to use this Software +-# commercially. Use for which any financial return is received shall be +-# defined as commercial use, and includes (1) integration of all or part +-# of the source code or the Software into a product for sale or license +-# by or on behalf of Licensee to third parties or (2) use of the +-# Software or any derivative of it for research with the final aim of +-# developing software products for sale or license to a third party or +-# (3) use of the Software or any derivative of it for research with the +-# final aim of developing non-software products for sale or license to a +-# third party, or (4) use of the Software to provide any service to an +-# external organisation for which payment is received. If you are +-# interested in using the Software commercially, please contact Oxford +-# University Innovation ("OUI"), the technology transfer company of the +-# University, to negotiate a licence. Contact details are: +-# [email protected] quoting Reference Project 9564, FSL. +-from __future__ import print_function +-import sys +-import os +- +-print (os.path.realpath(sys.argv[1])) +-sys.exit(0) +diff -Naur fsl.orig/src/misc_scripts/Makefile fsl/src/misc_scripts/Makefile +--- fsl.orig/src/misc_scripts/Makefile 2021-02-01 15:29:34.828752994 -0500 ++++ fsl/src/misc_scripts/Makefile 2021-02-01 15:32:56.027763811 -0500 +@@ -2,6 +2,6 @@ + + PROJNAME = misc_scripts + +-SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct Text2Vest Vest2Text AnatomicalAverage fsl_abspath fsl_anat fslFixText ++SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct AnatomicalAverage fsl_anat fslFixText + + all: +diff -Naur fsl.orig/src/misc_scripts/Text2Vest fsl/src/misc_scripts/Text2Vest +--- fsl.orig/src/misc_scripts/Text2Vest 2021-02-01 15:29:34.828752994 -0500 ++++ fsl/src/misc_scripts/Text2Vest 1969-12-31 19:00:00.000000000 -0500 +@@ -1,80 +0,0 @@ +-#!/bin/sh +-# Copyright (C) 2012 University of Oxford +-# +-# Part of FSL - FMRIB's Software Library +-# http://www.fmrib.ox.ac.uk/fsl +-# [email protected] +-# +-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +-# Imaging of the Brain), Department of Clinical Neurology, Oxford +-# University, Oxford, UK +-# +-# +-# LICENCE +-# +-# FMRIB Software Library, Release 6.0 (c) 2018, The University of +-# Oxford (the "Software") +-# +-# The Software remains the property of the Oxford University Innovation +-# ("the University"). +-# +-# The Software is distributed "AS IS" under this Licence solely for +-# non-commercial use in the hope that it will be useful, but in order +-# that the University as a charitable foundation protects its assets for +-# the benefit of its educational and research purposes, the University +-# makes clear that no condition is made or to be implied, nor is any +-# warranty given or to be implied, as to the accuracy of the Software, +-# or that it will be suitable for any particular purpose or for use +-# under any specific conditions. Furthermore, the University disclaims +-# all responsibility for the use which is made of the Software. It +-# further disclaims any liability for the outcomes arising from using +-# the Software. +-# +-# The Licensee agrees to indemnify the University and hold the +-# University harmless from and against any and all claims, damages and +-# liabilities asserted by third parties (including claims for +-# negligence) which arise directly or indirectly from the use of the +-# Software or the sale of any products based on the Software. +-# +-# No part of the Software may be reproduced, modified, transmitted or +-# transferred in any form or by any means, electronic or mechanical, +-# without the express permission of the University. The permission of +-# the University is not required if the said reproduction, modification, +-# transmission or transference is done without financial return, the +-# conditions of this Licence are imposed upon the receiver of the +-# product, and all original and amended source code is included in any +-# transmitted product. You may be held legally responsible for any +-# copyright infringement that is caused or encouraged by your failure to +-# abide by these terms and conditions. +-# +-# You are not permitted under this Licence to use this Software +-# commercially. Use for which any financial return is received shall be +-# defined as commercial use, and includes (1) integration of all or part +-# of the source code or the Software into a product for sale or license +-# by or on behalf of Licensee to third parties or (2) use of the +-# Software or any derivative of it for research with the final aim of +-# developing software products for sale or license to a third party or +-# (3) use of the Software or any derivative of it for research with the +-# final aim of developing non-software products for sale or license to a +-# third party, or (4) use of the Software to provide any service to an +-# external organisation for which payment is received. If you are +-# interested in using the Software commercially, please contact Oxford +-# University Innovation ("OUI"), the technology transfer company of the +-# University, to negotiate a licence. Contact details are: +-# [email protected] quoting Reference Project 9564, FSL. +-export LC_ALL=C +-if [ $# -lt 2 ] ; then +- echo "`basename $0` <text file> <vest file>" +- exit 0 +-fi +- +-NumPoints=`grep -cve '^\s*$' $1` +-NumWaves=`wc $1 | awk '{ print $2 }'` +-NumWaves=`expr $NumWaves / $NumPoints` +- +-echo /NumWaves $NumWaves > $2 +-echo /NumPoints $NumPoints >> $2 +-echo /Matrix >> $2 +- +-cat $1 >> $2 +- +diff -Naur fsl.orig/src/misc_scripts/Vest2Text fsl/src/misc_scripts/Vest2Text +--- fsl.orig/src/misc_scripts/Vest2Text 2021-02-01 15:29:34.828752994 -0500 ++++ fsl/src/misc_scripts/Vest2Text 1969-12-31 19:00:00.000000000 -0500 +@@ -1,71 +0,0 @@ +-#!/bin/sh +-# Copyright (C) 2012 University of Oxford +-# +-# Part of FSL - FMRIB's Software Library +-# http://www.fmrib.ox.ac.uk/fsl +-# [email protected] +-# +-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance +-# Imaging of the Brain), Department of Clinical Neurology, Oxford +-# University, Oxford, UK +-# +-# +-# LICENCE +-# +-# FMRIB Software Library, Release 6.0 (c) 2018, The University of +-# Oxford (the "Software") +-# +-# The Software remains the property of the Oxford University Innovation +-# ("the University"). +-# +-# The Software is distributed "AS IS" under this Licence solely for +-# non-commercial use in the hope that it will be useful, but in order +-# that the University as a charitable foundation protects its assets for +-# the benefit of its educational and research purposes, the University +-# makes clear that no condition is made or to be implied, nor is any +-# warranty given or to be implied, as to the accuracy of the Software, +-# or that it will be suitable for any particular purpose or for use +-# under any specific conditions. Furthermore, the University disclaims +-# all responsibility for the use which is made of the Software. It +-# further disclaims any liability for the outcomes arising from using +-# the Software. +-# +-# The Licensee agrees to indemnify the University and hold the +-# University harmless from and against any and all claims, damages and +-# liabilities asserted by third parties (including claims for +-# negligence) which arise directly or indirectly from the use of the +-# Software or the sale of any products based on the Software. +-# +-# No part of the Software may be reproduced, modified, transmitted or +-# transferred in any form or by any means, electronic or mechanical, +-# without the express permission of the University. The permission of +-# the University is not required if the said reproduction, modification, +-# transmission or transference is done without financial return, the +-# conditions of this Licence are imposed upon the receiver of the +-# product, and all original and amended source code is included in any +-# transmitted product. You may be held legally responsible for any +-# copyright infringement that is caused or encouraged by your failure to +-# abide by these terms and conditions. +-# +-# You are not permitted under this Licence to use this Software +-# commercially. Use for which any financial return is received shall be +-# defined as commercial use, and includes (1) integration of all or part +-# of the source code or the Software into a product for sale or license +-# by or on behalf of Licensee to third parties or (2) use of the +-# Software or any derivative of it for research with the final aim of +-# developing software products for sale or license to a third party or +-# (3) use of the Software or any derivative of it for research with the +-# final aim of developing non-software products for sale or license to a +-# third party, or (4) use of the Software to provide any service to an +-# external organisation for which payment is received. If you are +-# interested in using the Software commercially, please contact Oxford +-# University Innovation ("OUI"), the technology transfer company of the +-# University, to negotiate a licence. Contact details are: +-# [email protected] quoting Reference Project 9564, FSL. +-export LC_ALL=C +-if [ $# -lt 2 ] ; then +- echo "`basename $0` <vest file> <text file>" +- exit 0 +-fi +-sed -e "/\//d" $1 | sed '/^$/d' > $2 +- diff --git a/sci-biology/fsl/files/fsl-6.0.4-setup.patch b/sci-biology/fsl/files/fsl-6.0.4-setup.patch new file mode 100644 index 000000000..061e1a22a --- /dev/null +++ b/sci-biology/fsl/files/fsl-6.0.4-setup.patch @@ -0,0 +1,174 @@ +diff -Naur fsl.orig/build fsl/build +--- fsl.orig/build 2020-12-02 15:29:12.180812558 -0500 ++++ fsl/build 2020-12-02 15:34:03.854821628 -0500 +@@ -28,7 +28,6 @@ + # The build order for MASTERLIBS is very important, and should not be modified unless you know what + # you are doing. + MASTERLIBS=" +- CiftiLib-master \ + utils \ + znzlib \ + NewNifti \ +@@ -157,8 +156,8 @@ + done #project (MASTERPROJECTS) + fi #full build + +-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 -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk +--- fsl.orig/config/buildSettings.mk 2020-12-02 15:29:11.993812552 -0500 ++++ fsl/config/buildSettings.mk 2020-12-02 15:39:37.269831995 -0500 +@@ -18,7 +18,7 @@ + CHMOD = /bin/chmod + MKDIR = /bin/mkdir + INSTALL = install -p +-TCLSH = ${FSLDIR}/bin/fsltclsh ++TCLSH = tclsh + DEPENDFLAGS = -MM + MACHDBGFLAGS = -g + ##################################################################### +@@ -127,19 +127,19 @@ + ##################################################################### + 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) +@@ -158,8 +158,8 @@ + NVCC = ${CUDA_INSTALLATION}/bin/nvcc + ############### External Libs ##################################### + # ZLIB library +-LIB_ZLIB = ${FSLEXTLIB} +-INC_ZLIB = ${FSLEXTINC} ++#LIB_ZLIB = ${FSLEXTLIB} ++#INC_ZLIB = ${FSLEXTINC} + # QT library + QTDIR = /usr/lib/qt3 + LIB_QT = ${QTDIR}/lib +diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj +--- fsl.orig/config/common/buildproj 2020-12-02 15:29:11.993812552 -0500 ++++ fsl/config/common/buildproj 2020-12-02 15:41:25.579835363 -0500 +@@ -11,10 +11,10 @@ + fi + PROJECTS="$@" ; export PROJECTS ; + +-FSLDIR=`pwd` ++#FSLDIR=`pwd` + FSLDEVDIR=${FSLDIR} + FSLCONFDIR=${FSLDIR}/config +-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` ++#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` + FSLMASTERBUILD=1 + export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD + +@@ -67,7 +67,7 @@ + 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 @@ + if [ $installok = false ] ; then + echo " " + echo "ERROR::Could not install $projname successfully" ; ++ exit 1 + fi + else + echo " " +@@ -90,6 +91,7 @@ + echo " " + echo " " + errorprojs="$errorprojs $projname" ; export errorprojs ; ++ exit 1 + fi + fi + done +diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk +--- fsl.orig/config/common/vars.mk 2020-12-02 15:29:11.993812552 -0500 ++++ fsl/config/common/vars.mk 2020-12-02 15:43:00.602838318 -0500 +@@ -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 = ${USRINCFLAGS} -I. -I${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 -Naur fsl.orig/extras/build fsl/extras/build +--- fsl.orig/extras/build 2020-12-02 15:29:12.404812565 -0500 ++++ fsl/extras/build 2020-12-02 15:44:06.906840380 -0500 +@@ -96,16 +96,16 @@ + 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 -Naur fsl.orig/src/mist/Makefile fsl/src/mist/Makefile +--- fsl.orig/src/mist/Makefile 2020-12-02 15:29:12.875812580 -0500 ++++ fsl/src/mist/Makefile 2020-12-02 15:45:09.805842335 -0500 +@@ -52,6 +52,8 @@ + cp -r python/* ${DESTDIR}/python/mist + + clean: +- rm -f ${OBJS} mist/mist.o mist/mist ++ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion." ++ ++ + + .PHONY: all clean installdata diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild b/sci-biology/fsl/fsl-6.0.2-r1.ebuild index 71314a8f8..ae12098ec 100644 --- a/sci-biology/fsl/fsl-6.0.2-r1.ebuild +++ b/sci-biology/fsl/fsl-6.0.2-r1.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit cuda flag-o-matic toolchain-funcs prefix DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data" -HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"; +HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"; SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz" LICENSE="FSL BSD-2 newmat" @@ -16,7 +16,7 @@ IUSE="cuda" DEPEND=" dev-libs/boost - dev-python/fslpy + <dev-python/fslpy-3 media-gfx/graphviz media-libs/gd media-libs/glu diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild index 8a7e0eebb..f490b6e7c 100644 --- a/sci-biology/fsl/fsl-6.0.2.ebuild +++ b/sci-biology/fsl/fsl-6.0.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -6,7 +6,7 @@ EAPI=7 inherit flag-o-matic toolchain-funcs prefix DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data" -HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"; +HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"; SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz" LICENSE="FSL BSD-2 newmat" @@ -16,7 +16,7 @@ IUSE="" DEPEND=" dev-libs/boost - dev-python/fslpy + <dev-python/fslpy-3 media-gfx/graphviz media-libs/gd media-libs/glu diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild similarity index 83% copy from sci-biology/fsl/fsl-6.0.2-r1.ebuild copy to sci-biology/fsl/fsl-6.0.4.ebuild index 71314a8f8..e0feb82d9 100644 --- a/sci-biology/fsl/fsl-6.0.2-r1.ebuild +++ b/sci-biology/fsl/fsl-6.0.4.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit cuda flag-o-matic toolchain-funcs prefix DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data" -HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"; +HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"; SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz" LICENSE="FSL BSD-2 newmat" @@ -16,7 +16,7 @@ IUSE="cuda" DEPEND=" dev-libs/boost - dev-python/fslpy + >=dev-python/fslpy-3 media-gfx/graphviz media-libs/gd media-libs/glu @@ -42,8 +42,8 @@ S=${WORKDIR}/${PN} UPSTREAM_FSLDIR="/usr/share/fsl" PATCHES=( - "${FILESDIR}/${PN}"-6.0.2-gcc10_include.patch - "${FILESDIR}/${PN}"-6.0.2-setup.patch + "${FILESDIR}/${P}"-gcc10_include.patch + "${FILESDIR}/${P}"-setup.patch "${FILESDIR}/${PN}"-6.0.2-template.patch "${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch "${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch @@ -51,8 +51,13 @@ PATCHES=( "${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch "${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch "${FILESDIR}/${PN}"-5.0.9-headers.patch - "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p1.patch - "${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p2.patch + "${FILESDIR}/${P}"-fsldir_redux-p1.patch + "${FILESDIR}/${P}"-fsldir_redux-p2.patch + "${FILESDIR}/${P}"-flameo_std.patch + "${FILESDIR}/${P}"-melodic_std.patch + "${FILESDIR}/${P}"-remove_fslpy_collisions-p1.patch + "${FILESDIR}/${P}"-remove_fslpy_collisions-p2.patch + "${FILESDIR}/${P}"-fdt_cuda.patch ) src_prepare() { @@ -67,8 +72,11 @@ src_prepare() { eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \ etc/js/label-div.html - # Disable mist-clean the hard way for now. - rm -rf src/mist-clean + # Disable mist the hard way for now. + rm -r src/mist || die + + # Disable ptx2 for now + rm -r src/ptx2 || die makefilelist=$(find src/ -name Makefile) @@ -111,7 +119,7 @@ src_prepare() { sed -e "s:-lopenblas:-llapack -lblas:g" \ -i $(grep -rlI lopenblas *) || die - # script wanting to have access to flsversion at buildtime + # script wanting to have access to fslversion at buildtime sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \ -i ${makefilelist} || die @@ -129,8 +137,8 @@ src_prepare() { CUDA_INSTALLATION="/opt/cuda" CUDAVER=`cuda_toolkit_version` - eapply "${FILESDIR}/${PN}-6.0.2-eddy_cuda.patch" - eapply "${FILESDIR}/${PN}-6.0.2-cuda_buildsettings.patch" + eapply "${FILESDIR}/${P}-eddy_cuda.patch" + eapply "${FILESDIR}/${P}-cuda_buildsettings.patch" sed -i \ -e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \ @@ -145,8 +153,14 @@ src_compile() { export FSLCONDIR=${WORKDIR}/${PN}/config export FSLMACHTYPE=generic + # define the default build system to match upstream official standard + # -> individual projects may overwrite the '-std=' flag + export ANSI_CFLAGS="-std=c99" + export ANSI_CXXFLAGS="-std=c++98" + export USERLDFLAGS="${LDFLAGS}" export USERCFLAGS="${CFLAGS}" + export USERCPPFLAGS="${CPPFLAGS}" export USERCXXFLAGS="${CXXFLAGS}" export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
