Merge pull request #139 from DannyArends/minGW_R

Added support to build GEMMA using the Rtool chain in Windows (x64).

19 files changed, 119 insertions, 24 deletions

diff --git a/Makefile b/Makefile
index f8bacbf..bdb58b2 100644
--- a/Makefile
+++ b/Makefile
@@ -41,7 +41,19 @@
 GEMMA_VERSION = $(shell cat ./VERSION)
 
 # Set this variable to either LNX or MAC
-SYS                    = LNX # LNX|MAC (Linux is the default)
+ifeq ($(OS),Windows_NT)
+  SYS = WIN
+  VGEN = scripts/gen_version_info.cmd
+else
+  UNAME_S := $(shell uname -s)
+  ifeq ($(UNAME_S),Darwin)
+    SYS = MAC
+  else
+    SYS = LNX # default to linux
+  endif
+  VGEN = scripts/gen_version_info.sh
+endif
+
 # Leave blank after "=" to disable; put "= 1" to enable
 DIST_NAME              = gemma-$(GEMMA_VERSION)
 DEBUG                  = 1                # DEBUG mode, set DEBUG=0 for a release
@@ -53,8 +65,20 @@ OPENBLAS_LEGACY        =                  # Using older OpenBlas
 FORCE_STATIC           =                  # Static linking of libraries
 GCC_FLAGS              = -Wall -O3 -std=gnu++11 # extra flags -Wl,--allow-multiple-definition
 TRAVIS_CI              =                  # used by TRAVIS for testing
-EIGEN_INCLUDE_PATH     = /usr/include/eigen3
-OPENBLAS_INCLUDE_PATH  = /usr/local/opt/openblas/include
+
+GSL_INCLUDE_PATH =
+ifeq ($(SYS), WIN)
+  GSL_INCLUDE_PATH = -isystemc:/MinGW/include -LC:/MinGW/lib
+  EIGEN_INCLUDE_PATH = ../eigen-git-mirror
+  OPENBLAS_INCLUDE_PATH = ../OpenBLAS-v0.2.19-Win64-int32/include -L../OpenBLAS-v0.2.19-Win64-int32/lib
+else
+  OPENBLAS_INCLUDE_PATH = /usr/local/opt/openblas/include
+  ifeq ($(SYS), MAC)
+  EIGEN_INCLUDE_PATH = /usr/local/include/eigen3
+  else
+  EIGEN_INCLUDE_PATH = /usr/include/eigen3
+  endif
+endif
 
 # --------------------------------------------------------------------
 # Edit below this line with caution
@@ -73,13 +97,13 @@ endif
 
 ifeq ($(CPP), clang++)
   # macOS Homebrew settings (as used on Travis-CI)
-  GCC_FLAGS=-O3 -std=c++11 -stdlib=libc++ -isystem/$(OPENBLAS_INCLUDE_PATH) -isystem//usr/local/include/eigen3 -Wl,-L/usr/local/opt/openblas/lib
+  GCC_FLAGS=-O3 -std=c++11 -stdlib=libc++ -isystem$(OPENBLAS_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Wl,-L/usr/local/opt/openblas/lib
 endif
 
 ifdef WITH_OPENBLAS
   OPENBLAS=1
   # WITH_LAPACK =  # OPENBLAS usually includes LAPACK
-  CPPFLAGS += -DOPENBLAS -isystem/$(OPENBLAS_INCLUDE_PATH)
+  CPPFLAGS += -DOPENBLAS -isystem$(OPENBLAS_INCLUDE_PATH)
   ifdef OPENBLAS_LEGACY
     # Legacy version (mostly for Travis-CI)
     CPPFLAGS += -DOPENBLAS_LEGACY
@@ -87,10 +111,14 @@ ifdef WITH_OPENBLAS
 endif
 
 ifdef DEBUG
-  CPPFLAGS += -g $(GCC_FLAGS) -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+  CPPFLAGS += -g $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
 else
   # release mode
-  CPPFLAGS += -DNDEBUG $(GCC_FLAGS) -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+  CPPFLAGS += -DNDEBUG $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+endif
+
+ifeq ($(SYS), WIN)
+  CPPFLAGS += -Duint="unsigned int" -D__CRT__NO_INLINE -D__STRING="__STRINGIFY" -DWINDOWS -DWITH_GSLCBLAS=1
 endif
 
 ifdef SHOW_COMPILER_WARNINGS
@@ -149,7 +177,7 @@ OBJS = $(SOURCES:.cpp=.o)
 all: $(OUTPUT)
 
 ./src/version.h:
-	./scripts/gen_version_info.sh > src/version.h
+	$(VGEN) > src/version.h
 
 $(OUTPUT): $(OBJS)
 	$(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT)
diff --git a/doc/compile_GEMMA_win64.txt b/doc/compile_GEMMA_win64.txt
new file mode 100644
index 0000000..84f16ec
--- /dev/null
+++ b/doc/compile_GEMMA_win64.txt
@@ -0,0 +1,48 @@
+// install R 3.4.3
+https://cran.r-project.org/bin/windows/base/
+
+// install Rtools 3.4
+https://cran.r-project.org/bin/windows/Rtools/
+
+// Download openblas (v0.2.19-Win64-int32)
+https://sourceforge.net/projects/openblas/files/v0.2.19/
+
+// Make a place to store the files
+mkdir Github
+cd Github/
+
+// Clone the required dependancies
+git clone https://github.com/eigenteam/eigen-git-mirror.git
+git clone https://github.com/genetics-statistics/GEMMA.git
+
+// Download and install gsl2.4, unzip/tar into Github
+http://gnu.askapache.com/gsl/
+
+// Download and install msys from http://downloads.sourceforge.net/mingw/MSYS-1.0.11.exe
+cd c:/msys/1.0
+// Run mysys
+msys.bat
+
+// Under msys, Compile GSL-2.4 inside the msys
+cd /c/
+cd Github/gsl-2.4
+./configure --prefix=C:/MinGW
+make -j 4
+make install
+
+// Building Gemma on the R tool chain under windows using CMD compile gemma
+cd gemma
+make -j 2
+
+// Get all the DLLs from:
+- MinGW DLLs: https://sourceforge.net/projects/openblas/files/v0.2.12/mingw64_dll.zip/download
+- DLLs from the compiled gsl-2.4
+- DLLs from openBLAS
+
+// Required DLLs:
++ libgcc_s_seh-1.dll
++ libgfortran-3.dll
++ libgsl-23.dll
++ libgslcblas-0.dll
++ libopenblas.dll
++ libquadmath-0.dll
diff --git a/scripts/gen_version_info.cmd b/scripts/gen_version_info.cmd
new file mode 100644
index 0000000..d824687
--- /dev/null
+++ b/scripts/gen_version_info.cmd
@@ -0,0 +1,16 @@
+@echo off
+rem https://stackoverflow.com/questions/3472631/how-do-i-get-the-day-month-and-year-from-a-windows-cmd-exe-script
+FOR /F "skip=1 tokens=1-6" %%A IN ('WMIC Path Win32_LocalTime Get Day^,Hour^,Minute^,Month^,Second^,Year /Format:table') DO (
+    if "%%B" NEQ "" (
+        SET /A FDATE=%%F*10000+%%D*100+%%A
+    )
+)
+set year=%FDATE:~0,4%
+set /p version=<VERSION
+
+echo // version.h generated by GEMMA
+rem https://stackoverflow.com/questions/7105433/windows-batch-echo-without-new-line
+echo|set /p="#define GEMMA_VERSION ""
+echo %version%"
+echo #define GEMMA_DATE "%FDATE:~0,8%"
+echo #define GEMMA_YEAR "%year%"
diff --git a/src/bslmmdap.cpp b/src/bslmmdap.cpp
index e9900e3..6220bb5 100644
--- a/src/bslmmdap.cpp
+++ b/src/bslmmdap.cpp
@@ -39,7 +39,7 @@
 #include "gsl/gsl_vector.h"
 
 #include "bslmmdap.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "lm.h"
 #include "lmm.h"
diff --git a/src/gemma.cpp b/src/gemma.cpp
index edd79d7..5f742bd 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -48,7 +48,7 @@ extern "C" {
 #include "bslmm.h"
 #include "bslmmdap.h"
 #include "gemma.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "ldr.h"
 #include "lm.h"
diff --git a/src/io.cpp b/src/gemma_io.cpp
index d20b473..1876a7b 100644
--- a/src/io.cpp
+++ b/src/gemma_io.cpp
@@ -45,7 +45,7 @@
 // #include "eigenlib.h"
 #include "fastblas.h"
 #include "gzstream.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "mathfunc.h"
 
diff --git a/src/io.h b/src/gemma_io.h
index dd1d5c0..dd1d5c0 100644
--- a/src/io.h
+++ b/src/gemma_io.h
diff --git a/src/lm.h b/src/lm.h
index 030e6f9..bcec0ab 100644
--- a/src/lm.h
+++ b/src/lm.h
@@ -21,7 +21,7 @@
 
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "param.h"
 
 using namespace std;
diff --git a/src/lmm.cpp b/src/lmm.cpp
index 4198fab..c0a9785 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -43,7 +43,7 @@
 // #include "eigenlib.h"
 
 #include "gzstream.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "fastblas.h"
 #include "lapack.h"
 #include "lmm.h"
diff --git a/src/lmm.h b/src/lmm.h
index e9740d5..f603599 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -23,7 +23,7 @@
 
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "param.h"
 #include <functional>
 #include <tuple>
diff --git a/src/main.cpp b/src/main.cpp
index 706ac35..deadc63 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -58,7 +58,11 @@ int main(int argc, char *argv[]) {
 
   ifstream check_dir((cPar.path_out).c_str());
   if (!check_dir) {
-    mkdir((cPar.path_out).c_str(), S_IRWXU | S_IRGRP | S_IROTH);
+    #ifdef WINDOWS
+      mkdir((cPar.path_out).c_str());
+    #else
+      mkdir((cPar.path_out).c_str(), S_IRWXU | S_IRGRP | S_IROTH);
+    #endif
   }
 
   if (!is_quiet_mode())
diff --git a/src/mvlmm.cpp b/src/mvlmm.cpp
index eee562d..14f8b4a 100644
--- a/src/mvlmm.cpp
+++ b/src/mvlmm.cpp
@@ -39,7 +39,7 @@
 
 #include "fastblas.h"
 #include "gzstream.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "lmm.h"
 #include "mvlmm.h"
diff --git a/src/mvlmm.h b/src/mvlmm.h
index 4329ad1..b92bd5e 100644
--- a/src/mvlmm.h
+++ b/src/mvlmm.h
@@ -21,7 +21,7 @@
 
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "param.h"
 
 using namespace std;
diff --git a/src/param.cpp b/src/param.cpp
index bf6c195..cd4274a 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -35,7 +35,7 @@
 #include "gsl/gsl_vector.h"
 
 #include "eigenlib.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "mathfunc.h"
 #include "param.h"
 
diff --git a/src/prdt.cpp b/src/prdt.cpp
index fc0abe8..42912a8 100644
--- a/src/prdt.cpp
+++ b/src/prdt.cpp
@@ -32,8 +32,7 @@
 #include <vector>
 
 #include "gzstream.h"
-#include "io.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "mathfunc.h"
 #include "prdt.h"
diff --git a/src/varcov.cpp b/src/varcov.cpp
index e9c7295..055d3b1 100644
--- a/src/varcov.cpp
+++ b/src/varcov.cpp
@@ -37,7 +37,7 @@
 #include "gsl/gsl_vector.h"
 
 #include "gzstream.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "mathfunc.h"
 #include "param.h"
diff --git a/src/varcov.h b/src/varcov.h
index 47b4f9d..fa707d5 100644
--- a/src/varcov.h
+++ b/src/varcov.h
@@ -21,7 +21,7 @@
 
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "param.h"
 
 using namespace std;
diff --git a/src/vc.cpp b/src/vc.cpp
index 1a16c07..416a3e4 100644
--- a/src/vc.cpp
+++ b/src/vc.cpp
@@ -45,7 +45,7 @@
 
 #include "eigenlib.h"
 #include "gzstream.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "lmm.h"
 #include "mathfunc.h"
diff --git a/src/vc.h b/src/vc.h
index 49397bb..3586433 100644
--- a/src/vc.h
+++ b/src/vc.h
@@ -21,7 +21,7 @@
 
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "param.h"
 
 using namespace std;