diff --git a/doc/installation/checkInstallation.html b/doc/installation/checkInstallation.html index d9e06d5d..1fbfd73a 100644 --- a/doc/installation/checkInstallation.html +++ b/doc/installation/checkInstallation.html @@ -57,7 +57,7 @@

CROSS-REFERENCE INFORMATION ^ <h2><a name=SUBFUNCTIONS ^

+
  • function res = interpretResults(results)
  • function str = myStr(InputStr,len)
  • function status = makeBinaryExecutable(ravenDir)
  • function printOrange(stringToPrint)

    • SOURCE CODE ^

    0001 function currVer = checkInstallation(developMode)
@@ -91,328 +91,327 @@ 
    SOURCE CODE ^%Get the RAVEN path
 0030 [ST, I]=dbstack('-completenames');
 0031 [ravenDir,~,~]=fileparts(fileparts(ST(I).file));
-0032     status = makeBinaryExecutable();
-0033 
-0034 % Do not print first few lines if only version should be reported
-0035 if ~versionOnly
-0036     fprintf('\n*** THE RAVEN TOOLBOX ***\n\n');
-0037     %Print the RAVEN version if it is not the development version
-0038     fprintf([myStr(' > Installing from location',40) '%f']);
-0039     fprintf('%s\n',ravenDir)
-0040     fprintf([myStr(' > Checking RAVEN release',40) '%f']);
-0041 end
-0042 if exist(fullfile(ravenDir,'version.txt'), 'file') == 2
-0043     currVer = fgetl(fopen(fullfile(ravenDir,'version.txt')));
-0044     fclose('all');
-0045     if ~versionOnly
-0046         fprintf([currVer '\n']);
-0047         try
-0048             newVer=strtrim(webread('https://raw.githubusercontent.com/SysBioChalmers/RAVEN/main/version.txt'));
-0049             newVerNum=str2double(strsplit(newVer,'.'));
-0050             currVerNum=str2double(strsplit(currVer,'.'));
-0051             for i=1:3
-0052                 if currVerNum(i)<newVerNum(i)
-0053                     fprintf([myStr('   > Latest RAVEN release available',40) '%f'])
-0054                     printOrange([newVer,'\n'])
-0055                     hasGit=isfolder(fullfile(ravenDir,'.git'));
-0056                     if hasGit
-0057                         printOrange('     Run git pull in your favourite git client\n')
-0058                         printOrange('     to get the latest RAVEN release\n');
-0059                     else
-0060                         printOrange([myStr('     Instructions on how to upgrade',40) '%f'])
-0061                         fprintf('<a href="https://github.com/SysBioChalmers/RAVEN/wiki/Installation#upgrade-to-latest-raven-release">here</a>\n');
-0062                     end
-0063                     break
-0064                 elseif i==3
-0065                     fprintf('   > You are running the latest RAVEN release\n');
-0066                 end
-0067             end
-0068         catch
-0069             fprintf([myStr('   > Checking for latest RAVEN release',40) '%f'])
-0070             printOrange('Fail\n');
-0071             printOrange('     Cannot reach GitHub for release info\n');
-0072         end
-0073     end
-0074 else
-0075     currVer = 'develop';
-0076     if ~versionOnly; fprintf('DEVELOPMENT\n'); end
-0077 end
-0078 if strcmp(developMode,'versionOnly')
-0079     return;
-0080 end
-0081 
-0082 fprintf([myStr(' > Checking MATLAB release',40) '%f'])
-0083 fprintf([version('-release') '\n'])
-0084 fprintf([myStr(' > Checking system architecture',40) '%f'])
-0085 fprintf([computer('arch'),'\n'])
-0086 
-0087 fprintf([myStr(' > Set RAVEN in MATLAB path',40) '%f'])
-0088 subpath=regexp(genpath(ravenDir),pathsep,'split'); %List all subdirectories
-0089 pathsToKeep=cellfun(@(x) ~contains(x,'.git'),subpath) & cellfun(@(x) ~contains(x,'doc'),subpath);
-0090 try
-0091     addpath(strjoin(subpath(pathsToKeep),pathsep));
-0092     fprintf('Pass\n');
-0093     fprintf([myStr(' > Save MATLAB path',40) '%f'])
-0094     try
-0095         savepath
-0096         fprintf('Pass\n')   
-0097     catch
-0098         printOrange('Fail\n')
-0099         fprintf(['   You might have to rerun checkInstallation again\n'...
-0100                  '   next time you start up MATLAB\n'])        
-0101     end
-0102 catch
-0103     printOrange('Fail\n')
-0104 end
-0105 
-0106 if isunix
-0107     fprintf([myStr('   > Make binaries executable',40) '%f'])
-0108     status = makeBinaryExecutable();
-0109     if status == 0
-0110         fprintf('Pass\n')
-0111     else
-0112         printOrange('Fail\n')
-0113     end
-0114 end
-0115 
-0116 %Check if it is possible to parse an Excel file
-0117 fprintf('\n=== Model import and export ===\n');
-0118 fprintf([myStr(' > Add Java paths for Excel format',40) '%f'])
-0119 try
-0120     %Add the required classes to the static Java path if not already added
-0121     addJavaPaths();
-0122     fprintf('Pass\n')
-0123 catch
-0124     printOrange('Fail\n')
-0125 end
-0126 fprintf([myStr(' > Checking libSBML version',40) '%f'])
-0127 try
-0128     evalc('importModel(fullfile(ravenDir,''tutorial'',''empty.xml''))');
-0129     try
-0130         libSBMLver=OutputSBML; % Only works in libSBML 5.17.0+
-0131         fprintf([libSBMLver.libSBML_version_string '\n']);
-0132     catch
-0133         printOrange('Fail\n')
-0134         fprintf('   An older libSBML version was found, update to version 5.17.0 or higher for a significant improvement of model import\n');
-0135     end
-0136 catch
-0137     printOrange('Fail\n')
-0138     fprintf('   Download libSBML from http://sbml.org/Software/libSBML/Downloading_libSBML and add to MATLAB path\n');
-0139 end
-0140 fprintf(' > Checking model import and export\n')
-0141 [~,res]=evalc("runtests('importExportTests.m');");
-0142 
-0143 fprintf([myStr('   > Import Excel format',40) '%f'])
-0144 if res(1).Passed == 1
-0145     fprintf('Pass\n')
-0146 else
-0147     printOrange('Fail\n')
-0148     addList = matlab.addons.installedAddons;
-0149     if any(strcmpi(addList.Name,'Text Analytics Toolbox'))
-0150         fprintf(['   Excel import/export is incompatible with MATLAB Text Analytics Toolbox.\n' ...
-0151                  '   Further instructions => https://github.com/SysBioChalmers/RAVEN/issues/55#issuecomment-1514369299\n'])
-0152     end
-0153 end
-0154 
-0155 fprintf([myStr('   > Export Excel format',40) '%f'])
-0156 if res(3).Passed == 1
-0157     fprintf('Pass\n')
-0158 else
-0159     printOrange('Fail\n')
-0160 end
-0161 
-0162 fprintf([myStr('   > Import SBML format',40) '%f'])
-0163 if res(2).Passed == 1
-0164     fprintf('Pass\n')
-0165 else
-0166     printOrange('Fail\n')
-0167 end
-0168 
-0169 fprintf([myStr('   > Export SBML format',40) '%f'])
-0170 if res(4).Passed == 1
-0171     fprintf('Pass\n')
-0172 else
-0173     printOrange('Fail\n')
-0174 end
-0175 
-0176 if res(1).Passed~=1 && res(3).Passed~=1 && exist('vaderSentimentScores.m','file')==2
-0177     fprintf(['   > MATLAB Text Analytics Toolbox found. This should be\n'...
-0178              '     uninstalled if you want to read/write Excel files.\n'...
-0179              '     See RAVEN GitHub Issues page for instructions.\n'])
-0180 end
-0181 
-0182 %Check if it is possible to import an YAML model
-0183 % fprintf(' > Checking import of model in YAML format:\t\t\t');
-0184 % try
-0185 %     readYaml(ymlFile,true);
-0186 %     fprintf('Pass\n');
-0187 % catch
-0188 %     printOrange('Fail\n');
-0189 % end
-0190 
-0191 fprintf('\n=== Model solvers ===\n');
-0192 
-0193 %Get current solver. Set it to 'none', if it is not set
-0194 fprintf(' > Checking for LP solvers\n')
-0195 [~,res]=evalc("runtests('solverTests.m');");
-0196 
-0197 fprintf([myStr('   > glpk',40) '%f'])
-0198 if res(1).Passed == 1
-0199     fprintf('Pass\n')
-0200 else
-0201     printOrange('Fail\n')
-0202 end
-0203 
-0204 fprintf([myStr('   > gurobi',40) '%f'])
-0205 if res(2).Passed == 1
-0206     fprintf('Pass\n')
-0207 else
-0208     printOrange('Fail\n')
-0209 end
-0210 
-0211 fprintf([myStr('   > scip',40) '%f'])
-0212 if res(3).Passed == 1
-0213     fprintf('Pass\n')
-0214 else
-0215     printOrange('Fail\n')
-0216 end
-0217 
-0218 fprintf([myStr('   > cobra',40) '%f'])
-0219 if res(4).Passed == 1
-0220     fprintf('Pass\n')
-0221 else
-0222     printOrange('Fail\n')
-0223 end
-0224 fprintf([myStr(' > Set RAVEN solver',40) '%f'])
-0225 try
-0226     oldSolver=getpref('RAVEN','solver');
-0227     solverIdx=find(strcmp(oldSolver,{'glpk','gurobi','scip','cobra'}));
-0228 catch
-0229     solverIdx=0;
-0230 end
-0231 % Do not change old solver if functional
-0232 if solverIdx~=0 && res(solverIdx).Passed == 1
-0233     fprintf([oldSolver '\n'])
-0234 % Order of preference: gurobi > glpk > soplex > cobra
-0235 elseif res(2).Passed == 1
-0236     fprintf('gurobi\n')
-0237     setRavenSolver('gurobi');
-0238 elseif res(1).Passed == 1
-0239     fprintf('glpk\n')
-0240     setRavenSolver('glpk');
-0241 elseif res(3).Passed == 1
-0242     fprintf('soplex\n')
-0243     setRavenSolver('soplex');    
-0244 elseif res(4).Passed == 1
-0245     fprintf('cobra\n')
-0246     setRavenSolver('cobra');
-0247 else
-0248     fprintf('None, no functional solvers\n')
-0249     fprintf('    The glpk should always be working, check your RAVEN installation to make sure all files are present\n')
-0250 end
-0251 
-0252 fprintf('\n=== Essential binary executables ===\n');
-0253 fprintf([myStr(' > Checking BLAST+',40) '%f'])
-0254 [~,res]=evalc("runtests('blastPlusTests.m');");
-0255 res=interpretResults(res);
-0256 if res==false
-0257     fprintf('   This is essential to run getBlast()\n')
-0258 end
-0259 
-0260 fprintf([myStr(' > Checking DIAMOND',40) '%f'])
-0261 [~,res]=evalc("runtests('diamondTests.m');");
-0262 res=interpretResults(res);
-0263 if res==false
-0264     fprintf('   This is essential to run the getDiamond()\n')
-0265 end
-0266 
-0267 fprintf([myStr(' > Checking HMMER',40) '%f'])
-0268 [~,res]=evalc("runtests('hmmerTests.m')");
-0269 res=interpretResults(res);
-0270 if res==false
-0271     fprintf(['   This is essential to run getKEGGModelFromHomology()\n'...
-0272              '   when using a FASTA file as input\n'])
-0273 end
-0274 
-0275 if developMode
-0276     fprintf('\n=== Development binary executables ===\n');
-0277     fprintf('NOTE: These binaries are only required when using KEGG FTP dump files in getKEGGModelForOrganism\n');
-0278 
-0279     fprintf([myStr(' > Checking CD-HIT',40) '%f'])
-0280     [~,res]=evalc("runtests('cdhitTests.m');");
-0281     interpretResults(res);
-0282 
-0283     fprintf([myStr(' > Checking MAFFT',40) '%f'])
-0284     [~,res]=evalc("runtests('mafftTests.m');");
-0285     interpretResults(res);
-0286 end
-0287 
-0288 fprintf('\n=== Compatibility ===\n');
-0289 fprintf([myStr(' > Checking function uniqueness',40) '%f'])
-0290 checkFunctionUniqueness();
-0291 
-0292 fprintf('\n*** checkInstallation complete ***\n\n');
-0293 end
-0294 
-0295 function res = interpretResults(results)
-0296 if results.Failed==0 && results.Incomplete==0
-0297     fprintf('Pass\n');
-0298     res=true;
-0299 else
-0300     printOrange('Fail\n')
-0301     fprintf('   Download/compile the binary and rerun checkInstallation\n');
-0302     res=false;
+0032 
+0033 % Do not print first few lines if only version should be reported
+0034 if ~versionOnly
+0035     fprintf('\n*** THE RAVEN TOOLBOX ***\n\n');
+0036     %Print the RAVEN version if it is not the development version
+0037     fprintf([myStr(' > Installing from location',40) '%f']);
+0038     fprintf('%s\n',ravenDir)
+0039     fprintf([myStr(' > Checking RAVEN release',40) '%f']);
+0040 end
+0041 if exist(fullfile(ravenDir,'version.txt'), 'file') == 2
+0042     currVer = fgetl(fopen(fullfile(ravenDir,'version.txt')));
+0043     fclose('all');
+0044     if ~versionOnly
+0045         fprintf([currVer '\n']);
+0046         try
+0047             newVer=strtrim(webread('https://raw.githubusercontent.com/SysBioChalmers/RAVEN/main/version.txt'));
+0048             newVerNum=str2double(strsplit(newVer,'.'));
+0049             currVerNum=str2double(strsplit(currVer,'.'));
+0050             for i=1:3
+0051                 if currVerNum(i)<newVerNum(i)
+0052                     fprintf([myStr('   > Latest RAVEN release available',40) '%f'])
+0053                     printOrange([newVer,'\n'])
+0054                     hasGit=isfolder(fullfile(ravenDir,'.git'));
+0055                     if hasGit
+0056                         printOrange('     Run git pull in your favourite git client\n')
+0057                         printOrange('     to get the latest RAVEN release\n');
+0058                     else
+0059                         printOrange([myStr('     Instructions on how to upgrade',40) '%f'])
+0060                         fprintf('<a href="https://github.com/SysBioChalmers/RAVEN/wiki/Installation#upgrade-to-latest-raven-release">here</a>\n');
+0061                     end
+0062                     break
+0063                 elseif i==3
+0064                     fprintf('   > You are running the latest RAVEN release\n');
+0065                 end
+0066             end
+0067         catch
+0068             fprintf([myStr('   > Checking for latest RAVEN release',40) '%f'])
+0069             printOrange('Fail\n');
+0070             printOrange('     Cannot reach GitHub for release info\n');
+0071         end
+0072     end
+0073 else
+0074     currVer = 'develop';
+0075     if ~versionOnly; fprintf('DEVELOPMENT\n'); end
+0076 end
+0077 if strcmp(developMode,'versionOnly')
+0078     return;
+0079 end
+0080 
+0081 fprintf([myStr(' > Checking MATLAB release',40) '%f'])
+0082 fprintf([version('-release') '\n'])
+0083 fprintf([myStr(' > Checking system architecture',40) '%f'])
+0084 fprintf([computer('arch'),'\n'])
+0085 
+0086 fprintf([myStr(' > Set RAVEN in MATLAB path',40) '%f'])
+0087 subpath=regexp(genpath(ravenDir),pathsep,'split'); %List all subdirectories
+0088 pathsToKeep=cellfun(@(x) ~contains(x,'.git'),subpath) & cellfun(@(x) ~contains(x,'doc'),subpath);
+0089 try
+0090     addpath(strjoin(subpath(pathsToKeep),pathsep));
+0091     fprintf('Pass\n');
+0092     fprintf([myStr(' > Save MATLAB path',40) '%f'])
+0093     try
+0094         savepath
+0095         fprintf('Pass\n')   
+0096     catch
+0097         printOrange('Fail\n')
+0098         fprintf(['   You might have to rerun checkInstallation again\n'...
+0099                  '   next time you start up MATLAB\n'])        
+0100     end
+0101 catch
+0102     printOrange('Fail\n')
+0103 end
+0104 
+0105 if isunix
+0106     fprintf([myStr('   > Make binaries executable',40) '%f'])
+0107     status = makeBinaryExecutable(ravenDir);
+0108     if status == 0
+0109         fprintf('Pass\n')
+0110     else
+0111         printOrange('Fail\n')
+0112     end
+0113 end
+0114 
+0115 %Check if it is possible to parse an Excel file
+0116 fprintf('\n=== Model import and export ===\n');
+0117 fprintf([myStr(' > Add Java paths for Excel format',40) '%f'])
+0118 try
+0119     %Add the required classes to the static Java path if not already added
+0120     addJavaPaths();
+0121     fprintf('Pass\n')
+0122 catch
+0123     printOrange('Fail\n')
+0124 end
+0125 fprintf([myStr(' > Checking libSBML version',40) '%f'])
+0126 try
+0127     evalc('importModel(fullfile(ravenDir,''tutorial'',''empty.xml''))');
+0128     try
+0129         libSBMLver=OutputSBML; % Only works in libSBML 5.17.0+
+0130         fprintf([libSBMLver.libSBML_version_string '\n']);
+0131     catch
+0132         printOrange('Fail\n')
+0133         fprintf('   An older libSBML version was found, update to version 5.17.0 or higher for a significant improvement of model import\n');
+0134     end
+0135 catch
+0136     printOrange('Fail\n')
+0137     fprintf('   Download libSBML from http://sbml.org/Software/libSBML/Downloading_libSBML and add to MATLAB path\n');
+0138 end
+0139 fprintf(' > Checking model import and export\n')
+0140 [~,res]=evalc("runtests('importExportTests.m');");
+0141 
+0142 fprintf([myStr('   > Import Excel format',40) '%f'])
+0143 if res(1).Passed == 1
+0144     fprintf('Pass\n')
+0145 else
+0146     printOrange('Fail\n')
+0147     addList = matlab.addons.installedAddons;
+0148     if any(strcmpi(addList.Name,'Text Analytics Toolbox'))
+0149         fprintf(['   Excel import/export is incompatible with MATLAB Text Analytics Toolbox.\n' ...
+0150                  '   Further instructions => https://github.com/SysBioChalmers/RAVEN/issues/55#issuecomment-1514369299\n'])
+0151     end
+0152 end
+0153 
+0154 fprintf([myStr('   > Export Excel format',40) '%f'])
+0155 if res(3).Passed == 1
+0156     fprintf('Pass\n')
+0157 else
+0158     printOrange('Fail\n')
+0159 end
+0160 
+0161 fprintf([myStr('   > Import SBML format',40) '%f'])
+0162 if res(2).Passed == 1
+0163     fprintf('Pass\n')
+0164 else
+0165     printOrange('Fail\n')
+0166 end
+0167 
+0168 fprintf([myStr('   > Export SBML format',40) '%f'])
+0169 if res(4).Passed == 1
+0170     fprintf('Pass\n')
+0171 else
+0172     printOrange('Fail\n')
+0173 end
+0174 
+0175 if res(1).Passed~=1 && res(3).Passed~=1 && exist('vaderSentimentScores.m','file')==2
+0176     fprintf(['   > MATLAB Text Analytics Toolbox found. This should be\n'...
+0177              '     uninstalled if you want to read/write Excel files.\n'...
+0178              '     See RAVEN GitHub Issues page for instructions.\n'])
+0179 end
+0180 
+0181 %Check if it is possible to import an YAML model
+0182 % fprintf(' > Checking import of model in YAML format:\t\t\t');
+0183 % try
+0184 %     readYaml(ymlFile,true);
+0185 %     fprintf('Pass\n');
+0186 % catch
+0187 %     printOrange('Fail\n');
+0188 % end
+0189 
+0190 fprintf('\n=== Model solvers ===\n');
+0191 
+0192 %Get current solver. Set it to 'none', if it is not set
+0193 fprintf(' > Checking for LP solvers\n')
+0194 [~,res]=evalc("runtests('solverTests.m');");
+0195 
+0196 fprintf([myStr('   > glpk',40) '%f'])
+0197 if res(1).Passed == 1
+0198     fprintf('Pass\n')
+0199 else
+0200     printOrange('Fail\n')
+0201 end
+0202 
+0203 fprintf([myStr('   > gurobi',40) '%f'])
+0204 if res(2).Passed == 1
+0205     fprintf('Pass\n')
+0206 else
+0207     printOrange('Fail\n')
+0208 end
+0209 
+0210 fprintf([myStr('   > scip',40) '%f'])
+0211 if res(3).Passed == 1
+0212     fprintf('Pass\n')
+0213 else
+0214     printOrange('Fail\n')
+0215 end
+0216 
+0217 fprintf([myStr('   > cobra',40) '%f'])
+0218 if res(4).Passed == 1
+0219     fprintf('Pass\n')
+0220 else
+0221     printOrange('Fail\n')
+0222 end
+0223 fprintf([myStr(' > Set RAVEN solver',40) '%f'])
+0224 try
+0225     oldSolver=getpref('RAVEN','solver');
+0226     solverIdx=find(strcmp(oldSolver,{'glpk','gurobi','scip','cobra'}));
+0227 catch
+0228     solverIdx=0;
+0229 end
+0230 % Do not change old solver if functional
+0231 if solverIdx~=0 && res(solverIdx).Passed == 1
+0232     fprintf([oldSolver '\n'])
+0233 % Order of preference: gurobi > glpk > soplex > cobra
+0234 elseif res(2).Passed == 1
+0235     fprintf('gurobi\n')
+0236     setRavenSolver('gurobi');
+0237 elseif res(1).Passed == 1
+0238     fprintf('glpk\n')
+0239     setRavenSolver('glpk');
+0240 elseif res(3).Passed == 1
+0241     fprintf('soplex\n')
+0242     setRavenSolver('soplex');    
+0243 elseif res(4).Passed == 1
+0244     fprintf('cobra\n')
+0245     setRavenSolver('cobra');
+0246 else
+0247     fprintf('None, no functional solvers\n')
+0248     fprintf('    The glpk should always be working, check your RAVEN installation to make sure all files are present\n')
+0249 end
+0250 
+0251 fprintf('\n=== Essential binary executables ===\n');
+0252 fprintf([myStr(' > Checking BLAST+',40) '%f'])
+0253 [~,res]=evalc("runtests('blastPlusTests.m');");
+0254 res=interpretResults(res);
+0255 if res==false
+0256     fprintf('   This is essential to run getBlast()\n')
+0257 end
+0258 
+0259 fprintf([myStr(' > Checking DIAMOND',40) '%f'])
+0260 [~,res]=evalc("runtests('diamondTests.m');");
+0261 res=interpretResults(res);
+0262 if res==false
+0263     fprintf('   This is essential to run the getDiamond()\n')
+0264 end
+0265 
+0266 fprintf([myStr(' > Checking HMMER',40) '%f'])
+0267 [~,res]=evalc("runtests('hmmerTests.m')");
+0268 res=interpretResults(res);
+0269 if res==false
+0270     fprintf(['   This is essential to run getKEGGModelFromHomology()\n'...
+0271              '   when using a FASTA file as input\n'])
+0272 end
+0273 
+0274 if developMode
+0275     fprintf('\n=== Development binary executables ===\n');
+0276     fprintf('NOTE: These binaries are only required when using KEGG FTP dump files in getKEGGModelForOrganism\n');
+0277 
+0278     fprintf([myStr(' > Checking CD-HIT',40) '%f'])
+0279     [~,res]=evalc("runtests('cdhitTests.m');");
+0280     interpretResults(res);
+0281 
+0282     fprintf([myStr(' > Checking MAFFT',40) '%f'])
+0283     [~,res]=evalc("runtests('mafftTests.m');");
+0284     interpretResults(res);
+0285 end
+0286 
+0287 fprintf('\n=== Compatibility ===\n');
+0288 fprintf([myStr(' > Checking function uniqueness',40) '%f'])
+0289 checkFunctionUniqueness();
+0290 
+0291 fprintf('\n*** checkInstallation complete ***\n\n');
+0292 end
+0293 
+0294 function res = interpretResults(results)
+0295 if results.Failed==0 && results.Incomplete==0
+0296     fprintf('Pass\n');
+0297     res=true;
+0298 else
+0299     printOrange('Fail\n')
+0300     fprintf('   Download/compile the binary and rerun checkInstallation\n');
+0301     res=false;
+0302 end
 0303 end
-0304 end
-0305 
-0306 function str = myStr(InputStr,len)
-0307 str=InputStr;
-0308 lenDiff = len - length(str);
-0309 if lenDiff < 0
-0310     warning('String too long');
-0311 else
-0312     str = [str blanks(lenDiff)];
+0304 
+0305 function str = myStr(InputStr,len)
+0306 str=InputStr;
+0307 lenDiff = len - length(str);
+0308 if lenDiff < 0
+0309     warning('String too long');
+0310 else
+0311     str = [str blanks(lenDiff)];
+0312 end
 0313 end
-0314 end
-0315 
-0316 function status = makeBinaryExecutable()
-0317 if ispc
-0318     status = 0; % No need to run on Windows
-0319     return;
-0320 end
-0321 binDir = fullfile(findRAVENroot(),'software');
-0322 
-0323 binList = {fullfile(binDir,'blast+','blastp');                  fullfile(binDir,'blast+','blastp.mac');
-0324            fullfile(binDir,'blast+','makeblastdb');             fullfile(binDir,'blast+','makeblastdb.mac');
-0325            fullfile(binDir,'cd-hit','cd-hit');                  fullfile(binDir,'cd-hit','cd-hit.mac');
-0326            fullfile(binDir,'diamond','diamond');                fullfile(binDir,'diamond','diamond.mac');
-0327            fullfile(binDir,'hmmer','hmmbuild');                 fullfile(binDir,'hmmer','hmmbuild.mac');
-0328            fullfile(binDir,'hmmer','hmmsearch');                fullfile(binDir,'hmmer','hmmsearch.mac');
-0329            fullfile(binDir,'GLPKmex','glpkcc.mexa64');          fullfile(binDir,'GLPKmex','glpkcc.mexglx');         fullfile(binDir,'GLPKmex','glpkcc.mexmaci64');
-0330            fullfile(binDir,'libSBML','TranslateSBML.mexa64');   fullfile(binDir,'libSBML','TranslateSBML.mexglx');  fullfile(binDir,'libSBML','TranslateSBML.mexmaci64');
-0331            fullfile(binDir,'libSBML','OutputSBML.mexa64');      fullfile(binDir,'libSBML','OutputSBML.mexglx');     fullfile(binDir,'libSBML','OutputSBML.mexmaci64');
-0332            fullfile(binDir,'mafft','mafft-linux64','mafft.bat');
-0333            fullfile(binDir,'mafft','mafft-mac','mafft.bat');};
-0334 
-0335 for i=1:numel(binList)
-0336     [status,cmdout] = system(['chmod +x "' binList{i} '"']);
-0337     if status ~= 0
-0338         warning('Failed to make %s executable: %s ',binList{i},strip(cmdout))
-0339     end
+0314 
+0315 function status = makeBinaryExecutable(ravenDir)
+0316 if ispc
+0317     status = 0; % No need to run on Windows
+0318     return;
+0319 end
+0320 binDir = fullfile(ravenDir,'software');
+0321 
+0322 binList = {fullfile(binDir,'blast+','blastp');                  fullfile(binDir,'blast+','blastp.mac');
+0323            fullfile(binDir,'blast+','makeblastdb');             fullfile(binDir,'blast+','makeblastdb.mac');
+0324            fullfile(binDir,'cd-hit','cd-hit');                  fullfile(binDir,'cd-hit','cd-hit.mac');
+0325            fullfile(binDir,'diamond','diamond');                fullfile(binDir,'diamond','diamond.mac');
+0326            fullfile(binDir,'hmmer','hmmbuild');                 fullfile(binDir,'hmmer','hmmbuild.mac');
+0327            fullfile(binDir,'hmmer','hmmsearch');                fullfile(binDir,'hmmer','hmmsearch.mac');
+0328            fullfile(binDir,'GLPKmex','glpkcc.mexa64');          fullfile(binDir,'GLPKmex','glpkcc.mexglx');         fullfile(binDir,'GLPKmex','glpkcc.mexmaci64');
+0329            fullfile(binDir,'libSBML','TranslateSBML.mexa64');   fullfile(binDir,'libSBML','TranslateSBML.mexglx');  fullfile(binDir,'libSBML','TranslateSBML.mexmaci64');
+0330            fullfile(binDir,'libSBML','OutputSBML.mexa64');      fullfile(binDir,'libSBML','OutputSBML.mexglx');     fullfile(binDir,'libSBML','OutputSBML.mexmaci64');
+0331            fullfile(binDir,'mafft','mafft-linux64','mafft.bat');
+0332            fullfile(binDir,'mafft','mafft-mac','mafft.bat');};
+0333 
+0334 for i=1:numel(binList)
+0335     [status,cmdout] = system(['chmod +x "' binList{i} '"']);
+0336     if status ~= 0
+0337         warning('Failed to make %s executable: %s ',binList{i},strip(cmdout))
+0338     end
+0339 end
 0340 end
-0341 end
-0342 
-0343 function printOrange(stringToPrint)
-0344 % printOrange
-0345 %   Duplicate of RAVEN/core/printOrange is also kept here, as this function
-0346 %   should be able to run before adding RAVEN to the MATLAB path.
-0347 try useDesktop = usejava('desktop'); catch, useDesktop = false; end
-0348 if useDesktop
-0349     fprintf(['[\b' stringToPrint,']\b'])
-0350 else
-0351     fprintf(stringToPrint)
-0352 end
-0353 end
    +0341 +0342 function printOrange(stringToPrint) +0343 % printOrange +0344 % Duplicate of RAVEN/core/printOrange is also kept here, as this function +0345 % should be able to run before adding RAVEN to the MATLAB path. +0346 try useDesktop = usejava('desktop'); catch, useDesktop = false; end +0347 if useDesktop +0348 fprintf(['[\b' stringToPrint,']\b']) +0349 else +0350 fprintf(stringToPrint) +0351 end +0352 end
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/installation/checkInstallation.m b/installation/checkInstallation.m index 79e4c326..ae0bf51f 100755 --- a/installation/checkInstallation.m +++ b/installation/checkInstallation.m @@ -29,7 +29,6 @@ %Get the RAVEN path [ST, I]=dbstack('-completenames'); [ravenDir,~,~]=fileparts(fileparts(ST(I).file)); - status = makeBinaryExecutable(); % Do not print first few lines if only version should be reported if ~versionOnly @@ -105,7 +104,7 @@ if isunix fprintf([myStr(' > Make binaries executable',40) '%f']) - status = makeBinaryExecutable(); + status = makeBinaryExecutable(ravenDir); if status == 0 fprintf('Pass\n') else @@ -313,12 +312,12 @@ end end -function status = makeBinaryExecutable() +function status = makeBinaryExecutable(ravenDir) if ispc status = 0; % No need to run on Windows return; end -binDir = fullfile(findRAVENroot(),'software'); +binDir = fullfile(ravenDir,'software'); binList = {fullfile(binDir,'blast+','blastp'); fullfile(binDir,'blast+','blastp.mac'); fullfile(binDir,'blast+','makeblastdb'); fullfile(binDir,'blast+','makeblastdb.mac');