From b756f9a6d77cdb3c1ec847d81b200f0cec461b4e Mon Sep 17 00:00:00 2001
From: mca-sh <melodiehadzic@protonmail.com>
Date: Tue, 23 Mar 2021 09:58:15 +0100
Subject: [PATCH] create readme file for solving  mex compilation issues at
 MASH startup on Linux

---
 .../divers/mex-compilation/checkMASHmex.m     | 126 ++++++++++++++++++
 .../source/divers/mex-compilation/readme.txt  |  26 ++++
 2 files changed, 152 insertions(+)
 create mode 100644 MASH-FRET/source/divers/mex-compilation/checkMASHmex.m
 create mode 100644 MASH-FRET/source/divers/mex-compilation/readme.txt

diff --git a/MASH-FRET/source/divers/mex-compilation/checkMASHmex.m b/MASH-FRET/source/divers/mex-compilation/checkMASHmex.m
new file mode 100644
index 00000000..d0d4b9d1
--- /dev/null
+++ b/MASH-FRET/source/divers/mex-compilation/checkMASHmex.m
@@ -0,0 +1,126 @@
+function checkMASHmex()
+
+% compile molecule localization method Schmied2012
+if exist('forloop','file')~=3
+    cd(fileparts(which('forloop.c')));
+    try
+        mex('forloop.c');
+    catch err
+        dispMatlabErr(err);
+    end
+end
+
+% compile image filters
+% if exist('FilterArray','file')~=3
+%     pname = fileparts(which('FilterArray.c'));
+%     % set runtime library path for LINUX
+%     if strcmp(computer,'GLNXA86') || strcmp(computer,'GLNXA64')
+%         system(['LD_LIBRARY_PATH=$LD_LIBRARY_PATH:',matlabroot,filesep,...
+%             'glnxa64:',matlabroot,filesep,'sys',filesep,'os',filesep,...
+%             'glnxa64']);
+%     end
+%     if strcmp(computer,'PCWIN') || strcmp(computer,'GLNX86') % 32bit OS
+%         runtimefolder = 'runtime32';
+%         libflag = '-lITASL32';
+% 
+%     elseif strcmp(computer,'PCWIN64') || strcmp(computer,'GLNX64') % 64bit OS
+%         runtimefolder = 'runtime64';
+%         libflag = '-lITASL64';
+%     end
+%     cd([pname,filesep,'..',filesep,runtimefolder]);
+%     try
+%         mex('-R2018a',[pname,filesep,'FilterArray.c'],...
+%             ['-L',pname,filesep,'lib'],libflag);
+%     catch err
+%         dispMatlabErr(err);
+%     end
+% end
+
+% compile SIF file import
+if exist('SIFImport','file')~=3
+    
+    % libraries unavailable for LINUX
+    if strcmp(computer,'GLNXA86') || strcmp(computer,'GLNXA64') || ...
+            strcmp(computer,'MACI86') || strcmp(computer,'MACI64')
+        disp(['import of old versions of SIF files is not supported ',...
+            'on MacOS and Linux systems']);
+    else
+        pname = fileparts(which('SIFImport.c'));
+
+        if strcmp(computer,'PCWIN') || strcmp(computer,'MACI86') % 32bit OS
+            runtimefolder = 'runtime32';
+            libflag = '-lITASL32';
+
+        elseif strcmp(computer,'PCWIN64') || strcmp(computer,'MACI64') % 64bit OS
+            runtimefolder = 'runtime64';
+            libflag = '-lITASL64';
+        end
+        cd([pname,filesep,'..',filesep,runtimefolder]);
+        try
+            mex('-R2018a',[pname,filesep,'SIFImport.c'],...
+                ['-L',pname,filesep,'lib'],libflag);
+        catch err
+            dispMatlabErr(err);
+        end
+    end
+end
+
+% compile SPE file import
+if exist('SPEImport','file')~=3
+    
+    % libraries unavailable for LINUX
+    if strcmp(computer,'GLNXA86') || strcmp(computer,'GLNXA64') || ...
+            strcmp(computer,'MACI86') || strcmp(computer,'MACI64')
+        disp(['import of SPE files is not supported on MacOS and Linux ',...
+            'systems']);
+    else
+        pname = fileparts(which('SPEImport.c'));
+
+        if strcmp(computer,'PCWIN') % 32bit OS
+            runtimefolder = 'runtime32';
+            libflag = '-lITASL32';
+
+        elseif strcmp(computer,'PCWIN64') % 64bit OS
+            runtimefolder = 'runtime64';
+            libflag = '-lITASL64';
+        end
+        cd([pname,filesep,'..',filesep,runtimefolder]);
+        try
+            mex('-R2018a',[pname,filesep,'SPEImport.c'],...
+                ['-L',pname,filesep,'lib'],libflag);
+        catch err
+            dispMatlabErr(err);
+        end
+    end
+end
+
+% compile DPH training algorithm
+if exist('trainPH','file')~=3
+    cd(fileparts(which('trainPH.c')));
+    try
+        mex -R2018a -O trainPH.c vectop.c
+    catch err
+        dispMatlabErr(err);
+    end
+end
+
+% compile Baum-Welch algorithm
+if exist('baumwelch','file')~=3
+    cd(fileparts(which('baumwelch.c')));
+    try
+        mex -R2018a -O baumwelch.c vectop.c fwdbwd.c
+    catch err
+        dispMatlabErr(err);
+    end
+end
+
+% compile model error calculation
+if exist('calcmdlconfiv','file')~=3
+    cd(fileparts(which('calcmdlconfiv.c')));
+    try
+        mex -R2018a -O calcmdlconfiv.c vectop.c fwdbwd.c
+    catch err
+        dispMatlabErr(err);
+    end
+end
+    
\ No newline at end of file
diff --git a/MASH-FRET/source/divers/mex-compilation/readme.txt b/MASH-FRET/source/divers/mex-compilation/readme.txt
new file mode 100644
index 00000000..203c2bc0
--- /dev/null
+++ b/MASH-FRET/source/divers/mex-compilation/readme.txt
@@ -0,0 +1,26 @@
+To solve MEX file compilation issues happening at MASH-FRET startup on Linux, please read the following instructions.
+
+ERROR MESSAGE 1:
+	An error occurred:
+	Supported compiler not found. For options, visit https://www.mathworks.com/support/compilers.
+	function: checkMASHmex, line: 7
+	function: MASH, line: 13
+
+SOLUTION 1:
+	MATLAB supports GCC compiler up to version 9.x
+	Install gcc-9 package with the shell command:
+		sudo apt install gcc-9
+	Create a soft link "gcc" pointing to gcc-9 with the shell comand:
+		sudo ln -s /usr/bin/gcc-9 /usr/bin/gcc
+
+ERROR MESSAGE 2:
+	An error occurred:
+	/usr/bin/ld : ne peut trouver -lstdc++
+	collect2: error: ld returned 1 exit status
+	function: checkMASHmex, line: 7
+	function: MASH, line: 13
+	
+SOLUTION 2:
+	MATLAB looks for a file named libstdc++.so which is named "libstdc++.so.6" on your computer
+	Create a soft link "libstdc++.so" pointing to libstdc++.so.6 with the shell comand:
+		sudo ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/lib/x86_64-linux-gnu/libstdc++.so