commit: 0d75b7b6bc3b549e4d3fbe95c65ebce4ef1d92cc Author: Horea Christian <horea.christ <AT> yandex <DOT> com> AuthorDate: Tue Aug 8 13:37:56 2017 +0000 Commit: Benda XU <heroxbd <AT> gentoo <DOT> org> CommitDate: Thu Sep 21 02:39:21 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0d75b7b6
sci-biology/fsl: version bump. made env.dfile prefix-compatible Closes: https://github.com/gentoo/sci/pull/804 Package-Manager: Portage-2.3.8, Repoman-2.3.3 sci-biology/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-5.0.8.ebuild | 4 +- .../fsl/{fsl-5.0.8.ebuild => fsl-5.0.9.ebuild} | 68 ++- 5 files changed, 621 insertions(+), 37 deletions(-) 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 new file mode 100644 index 000000000..c28fabe42 --- /dev/null +++ b/sci-biology/fsl/files/fsl-5.0.9-fsldir_redux.patch @@ -0,0 +1,456 @@ +# Adapt hard-coded paths to the directory structure of Gentoo (including Prefix) +# From: Francois Bissey <[email protected]> +# Signed-off-by: Horea Christian <[email protected]> + +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<<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 -Naur fsl.orig/src/feat5/feat_model.cc fsl/src/feat5/feat_model.cc +--- fsl.orig/src/feat5/feat_model.cc 2015-03-30 11:54:10.502550183 +1300 ++++ fsl/src/feat5/feat_model.cc 2015-03-30 11:54:18.412569892 +1300 +@@ -741,7 +741,7 @@ + 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]; + +@@ -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<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 @@ + 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 << "<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(); +@@ -740,7 +739,7 @@ + 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 -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<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 -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<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 @@ + + 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 -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 "<<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 @@ + + }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 -Naur fsl.orig/src/libvis/miscpic.h fsl/src/libvis/miscpic.h +--- fsl.orig/src/libvis/miscpic.h 2015-03-30 11:54:10.482550135 +1300 ++++ fsl/src/libvis/miscpic.h 2015-03-30 11:54:18.412569892 +1300 +@@ -89,12 +89,7 @@ + LR_label_flag = true; + 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 -Naur fsl.orig/src/melodic/meldata.cc fsl/src/melodic/meldata.cc +--- fsl.orig/src/melodic/meldata.cc 2015-03-30 11:54:10.502550183 +1300 ++++ fsl/src/melodic/meldata.cc 2015-03-30 11:54:18.412569892 +1300 +@@ -971,7 +971,7 @@ + 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){ +@@ -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 << "<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 +@@ -487,8 +487,8 @@ + + {//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 +@@ -666,8 +666,8 @@ + 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 -Naur fsl.orig/src/melodic/melreport.h fsl/src/melodic/melreport.h +--- fsl.orig/src/melodic/melreport.h 2015-03-30 11:54:10.502550183 +1300 ++++ fsl/src/melodic/melreport.h 2015-03-30 12:11:17.995116883 +1300 +@@ -104,21 +104,21 @@ + 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 @@ + << "</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 -Naur fsl.orig/src/mm/mixture_model.cc fsl/src/mm/mixture_model.cc +--- fsl.orig/src/mm/mixture_model.cc 2015-03-30 11:54:10.522550233 +1300 ++++ fsl/src/mm/mixture_model.cc 2015-03-30 11:54:18.412569892 +1300 +@@ -2224,8 +2224,8 @@ + + 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 2015-03-30 11:54:10.482550135 +1300 ++++ fsl/src/siena/siena_diff.cc 2015-03-30 11:54:18.412569892 +1300 +@@ -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")) + ignore_z=1; +@@ -209,26 +207,26 @@ + // }}} + // {{{ 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); + } + +@@ -287,8 +285,8 @@ + 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 -Naur fsl.orig/src/topup/topupfns.cpp fsl/src/topup/topupfns.cpp +--- fsl.orig/src/topup/topupfns.cpp 2015-03-30 11:54:10.522550233 +1300 ++++ fsl/src/topup/topupfns.cpp 2015-03-30 11:54:18.412569892 +1300 +@@ -463,8 +463,7 @@ + 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"); + diff --git a/sci-biology/fsl/files/fsl-5.0.9-headers.patch b/sci-biology/fsl/files/fsl-5.0.9-headers.patch new file mode 100644 index 000000000..663dc565c --- /dev/null +++ b/sci-biology/fsl/files/fsl-5.0.9-headers.patch @@ -0,0 +1,15 @@ +# Include zlib header directly. +# From: Francois Bissey <[email protected]> +# Signed-off-by: Horea Christian <[email protected]> +# 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 <stdlib.h> /* 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-5.0.9-setup.patch b/sci-biology/fsl/files/fsl-5.0.9-setup.patch new file mode 100644 index 000000000..c688cd6e8 --- /dev/null +++ b/sci-biology/fsl/files/fsl-5.0.9-setup.patch @@ -0,0 +1,115 @@ +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 +@@ -11,9 +11,8 @@ + ifit load_varian load_dicom misc_scripts fdt first possum sgeutils \ + flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp verbena"; + fi + +-echo "Building projects - see build.log file for progress..." +-./config/common/buildproj $PROJECTS > ./build.log 2>&1 +-echo "Finished build : end of log file shows ..." +-tail -10 build.log ++echo "Building projects" ++./config/common/buildproj $PROJECTS ++echo "Finished build" + +diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj +--- fsl.orig/config/common/buildproj 2015-03-29 00:11:47.130998000 +1300 ++++ fsl/config/common/buildproj 2015-03-29 00:12:37.164319000 +1300 +@@ -11,10 +11,10 @@ + fi + PROJECTS="$@" ; 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} 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 = ${USRINCFLAGS} -I. -I${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} ++ ${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 +@@ -104,8 +104,8 @@ + if [ ${BUILDICONV} -eq 1 ]; then + PROJECTS="${PROJECTS} libiconv" + fi +-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw" ++PROJECTS="libgdc libprob libcprob newmat cprob newran" + PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxml++-2.34.0" + for projname in $PROJECTS; do + + if [ -d $FSLESRCDIR/$projname ] ; then diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild index 467255c5f..7916c0811 100644 --- a/sci-biology/fsl/fsl-5.0.8.ebuild +++ b/sci-biology/fsl/fsl-5.0.8.ebuild @@ -133,7 +133,9 @@ src_install() { dosym /etc /usr/share/fsl/etc dosym /usr/share/doc/${P} /usr/share/fsl/doc - doenvd "${FILESDIR}"/99fsl + cp "${FILESDIR}"/99fsl "${TMPDIR}"/99fsl || die + eprefixify "${TMPDIR}"/99fsl + doenvd "${TMPDIR}"/99fsl mv "${ED}"/usr/bin/{,fsl_}cluster || die } diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.9.ebuild similarity index 64% copy from sci-biology/fsl/fsl-5.0.8.ebuild copy to sci-biology/fsl/fsl-5.0.9.ebuild index 467255c5f..bc96cec06 100644 --- a/sci-biology/fsl/fsl-5.0.8.ebuild +++ b/sci-biology/fsl/fsl-5.0.9.ebuild @@ -3,7 +3,7 @@ EAPI=6 -inherit eutils toolchain-funcs prefix +inherit toolchain-funcs prefix DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data" HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"; @@ -29,13 +29,16 @@ RDEPEND="${COMMON_DEPEND} " S=${WORKDIR}/${PN} +UPSTREAM_FSLDIR="/usr/share/fsl" -src_prepare(){ - epatch \ - "${FILESDIR}/${PN}"-5.0.8-setup.patch \ - "${FILESDIR}/${PN}"-5.0.8-headers.patch \ - "${FILESDIR}/${PN}"-5.0.8-fsldir_redux.patch +PATCHES=( + "${FILESDIR}/${PN}"-5.0.9-setup.patch + "${FILESDIR}/${PN}"-5.0.9-headers.patch + "${FILESDIR}/${PN}"-5.0.9-fsldir_redux.patch +) +src_prepare(){ + default sed -i \ -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \ -e "s:@@GENTOO_CC@@:$(tc-getCC):" \ @@ -57,36 +60,28 @@ src_prepare(){ -e "s:-L\${LIB_ZLIB}::" \ ${makefilelist} || die - sed -i "s:\${FSLDIR}/bin/::g" \ - $(grep -rl "\${FSLDIR}/bin" src/*) \ - $(grep -rl "\${FSLDIR}/bin" etc/matlab/*) - sed -i "s:\$FSLDIR/bin/::g" \ - $(grep -rl "\$FSLDIR/bin" src/*) \ - $(grep -rl "\$FSLDIR/bin" etc/matlab/*) - - sed -i "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \ - $(grep -rl "\$FSLDIR/data" src/*) + sed -e "s:\${FSLDIR}/bin/::g" \ + -e "s:\$FSLDIR/bin/::g" \ + -i $(grep -rl "\${FSLDIR}/bin" src/*) \ + $(grep -rl "\${FSLDIR}/bin" etc/matlab/*) || die - sed -i "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \ - $(grep -rl "\${FSLDIR}/data" src/*) + sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \ + -e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \ + -i $(grep -rl "\$FSLDIR/data" src/*) \ + $(grep -rl "\${FSLDIR}/data" src/*) || die - sed -i "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \ - $(grep -rl "\$FSLDIR/etc" src/*) + sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \ + -e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \ + -i $(grep -rl "\$FSLDIR/doc" src/*) \ + $(grep -rl "\${FSLDIR}/doc" src/*) || die - sed -i "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \ - $(grep -rl "\${FSLDIR}/etc" src/*) + sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \ + $(grep -rl "/usr/share/fsl/doc" src/*) || die - sed -i "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \ - $(grep -rl "\$FSLDIR/doc" src/*) - - sed -i "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \ - $(grep -rl "\${FSLDIR}/doc" src/*) - - sed -i "s:\'\${FSLDIR}\'/doc:${EPREFIX}/usr/share/fsl/doc:g" \ - $(grep -rl "\'\${FSLDIR}\'/doc" src/*) - - sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *` - default + sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \ + -e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \ + -i $(grep -rlI "\$FSLDIR/etc" *) \ + -i $(grep -rlI "\${FSLDIR}/etc" *) || die } src_compile() { @@ -128,12 +123,13 @@ src_install() { #fi #the following is needed for FSL and depending programs to be able - #to find its files, since FSL uses an uncommon: + #to find its files, since FSL uses an uncommon installation path: #https://github.com/gentoo-science/sci/pull/612#r60289295 - dosym /etc /usr/share/fsl/etc - dosym /usr/share/doc/${P} /usr/share/fsl/doc + dosym /etc ${UPSTREAM_FSLDIR}/etc + dosym /usr/share/doc/${PF} ${UPSTREAM_FSLDIR}/doc + dosym /usr/bin ${UPSTREAM_FSLDIR}/bin - doenvd "${FILESDIR}"/99fsl + doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)" mv "${ED}"/usr/bin/{,fsl_}cluster || die }
