From b309569fe9497befa008ac2d2cbc04f2e861ce76 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 22 May 2020 11:07:44 -0500
Subject: Removing more eigenlib references

---
 INSTALL.md         |  9 +++++++--
 Makefile           | 13 +++----------
 VERSION            |  2 +-
 src/fastblas.cpp   |  8 +++++++-
 src/fastopenblas.h |  4 ++--
 src/version.h      |  8 ++++----
 6 files changed, 24 insertions(+), 20 deletions(-)

diff --git a/INSTALL.md b/INSTALL.md
index 4f7da49..4885ed0 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -17,7 +17,6 @@ dependencies:
 * GNU Science library (GSL) 1.x (GEMMA does not currently work with GSL >= 2).
 * blas/openblas
 * lapack
-* [Eigen3 library](http://eigen.tuxfamily.org/dox/)
 * zlib
 
 See below for installation on Guix.
@@ -51,10 +50,16 @@ using the following command
 
 To build GEMMA from source you can opt to install the build tools with GNU Guix
 
-    guix package -i make gcc linux-libre-headers gsl eigen openblas lapack glibc ld-wrapper
+    guix package -i make gcc linux-libre-headers gsl openblas lapack glibc ld-wrapper
+
+The current build container is
+
+    guix environment -C guix --ad-hoc gcc-toolchain gdb gsl openblas zlib bash ld-wrapper perl vim
 
 ### Install from source
 
+Note: Eigen is no longer required!
+
 Install listed dependencies and run
 
 	make -j 4
diff --git a/Makefile b/Makefile
index 191285a..246cf6f 100644
--- a/Makefile
+++ b/Makefile
@@ -76,15 +76,9 @@ GCC_FLAGS              = -DHAVE_INLINE -pthread -Wall -std=gnu++11 # extra flags
 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), OSX)
-    EIGEN_INCLUDE_PATH = /usr/local/include/eigen3
-  else
-    EIGEN_INCLUDE_PATH = /usr/include/eigen3
-  endif
   ifndef GUIX
     ifdef GUIX_ENVIRONMENT
       GUIX=$(GUIX_ENVIRONMENT)
@@ -93,7 +87,6 @@ else
   ifdef GUIX
     # Effectively disable paths for GNU Guix
     OPENBLAS_INCLUDE_PATH = .
-    # EIGEN_INCLUDE_PATH = $(GUIX)/include/eigen3
     # RPATH = -Xlinker --rpath=$(GUIX)/lib
     ifdef FORCE_STATIC
       LIBS = -L$(GUIX)/lib
@@ -118,7 +111,7 @@ else
 endif
 
 ifeq ($(CPP), clang++)
-  GCC_FLAGS=-std=c++11 -isystem$(OPENBLAS_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH)
+  GCC_FLAGS=-std=c++11 -isystem$(OPENBLAS_INCLUDE_PATH) 
   ifdef GUIX
     CPPFLAGS += -I$(GUIX)/include/c++ -I$(GUIX)/include/c++/x86_64-unknown-linux-gnu
   endif
@@ -147,9 +140,9 @@ debug check fast-check: CPPFLAGS += -g $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -Icontri
 
 profile: CPPFLAGS += -pg
 
-release: CPPFLAGS += -DNDEBUG -O3 $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+release: CPPFLAGS += -DNDEBUG -O3 $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
 
-static: CPPFLAGS += -DNDEBUG -O3 $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+static: CPPFLAGS += -DNDEBUG -O3 $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
 
 
 ifeq ($(SYS), WIN)
diff --git a/VERSION b/VERSION
index 359d7a7..85b51db 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.98.1
+0.98.2
diff --git a/src/fastblas.cpp b/src/fastblas.cpp
index e9e38d0..42c59ee 100644
--- a/src/fastblas.cpp
+++ b/src/fastblas.cpp
@@ -29,6 +29,7 @@
 #include "mathfunc.h"
 #include <string.h>
 #include "eigenlib.h"
+#include <cblas.h>
 
 const char *FastblasTrans = "T";
 const char *FastblasNoTrans = "N";
@@ -243,7 +244,12 @@ void fast_eigen_dgemm(const char *TransA, const char *TransB, const double alpha
  */
 
 #include <gsl/gsl_permutation.h>
-#include <gsl/gsl_linalg.h>
+// #include <gsl/gsl_linalg.h>
+
+extern "C" {
+  int gsl_linalg_LU_invert(const gsl_matrix * LU, const gsl_permutation * p, gsl_matrix * inverse);
+  int gsl_linalg_LU_decomp(gsl_matrix * A, gsl_permutation * p, int * signum);
+}
 
 void gsl_matrix_inv(gsl_matrix *m)  
 {  
diff --git a/src/fastopenblas.h b/src/fastopenblas.h
index 2fc743e..7f453da 100644
--- a/src/fastopenblas.h
+++ b/src/fastopenblas.h
@@ -25,11 +25,11 @@
 #include <iostream>
 extern "C"
 {
-  // #include <cblas.h>   // For OpenBlas / Atlas
+  #include <cblas.h>   // For OpenBlas / Atlas
 }
 // #include "gsl/gsl_matrix.h"
 
-void fast_cblas_dgemm(const enum CBLAS_ORDER Order,
+void fast_cblas_dgemm(const enum CBLAS_ORDER ,
                       const enum CBLAS_TRANSPOSE TransA,
                       const enum CBLAS_TRANSPOSE TransB,
                       const size_t M,
diff --git a/src/version.h b/src/version.h
index cfb3ba9..d413933 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1,5 +1,5 @@
 // version.h generated by GEMMA scripts/gen_version_info.sh
-#define GEMMA_VERSION "0.98.1"
-#define GEMMA_DATE "2018-12-10"
-#define GEMMA_YEAR "2018"
-#define GEMMA_PROFILE ""
+#define GEMMA_VERSION "0.98.2"
+#define GEMMA_DATE "2020-05-22"
+#define GEMMA_YEAR "2020"
+#define GEMMA_PROFILE "/gnu/store/h9xwdvc7kqx7cvpvs6iascfdw5zgzhyd-profile"
-- 
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