From 10cc3c77d5f6d385807f019b7894d4b87820cab4 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 15 Sep 2018 11:59:49 +0000
Subject: Using Guix container to build with gcc and clang

---
 INSTALL.md             | 12 ++++++++++++
 Makefile               | 14 ++++++++++----
 src/mathfunc.cpp       | 15 ---------------
 test/dev_test_suite.sh |  2 +-
 test/test_suite.sh     |  2 +-
 5 files changed, 24 insertions(+), 21 deletions(-)

diff --git a/INSTALL.md b/INSTALL.md
index be4469f..db7a6e5 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -53,6 +53,18 @@ 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
 
+Even better you can create a container in the source tree and run
+
+    guix environment -C guix --ad-hoc gcc gdb gfortran:lib gsl eigen openblas zlib bash ld-wrapper perl
+    make clean
+    make GUIX=$GUIX_ENVIRONMENT check -j 4
+
+and for the Clang edition
+
+    guix environment -C guix --ad-hoc clang gcc gdb gfortran:lib gsl eigen openblas zlib bash ld-wrapper perl
+    make clean
+    make GUIX=$GUIX_ENVIRONMENT CXX=clang++ check -j 4
+
 #### GNU Guix reproducible build system
 
 One of the challenges of developing software is dealing with
diff --git a/Makefile b/Makefile
index 047911f..97bbc68 100644
--- a/Makefile
+++ b/Makefile
@@ -76,15 +76,15 @@ ifeq ($(SYS), WIN)
 else
   OPENBLAS_INCLUDE_PATH = /usr/local/opt/openblas/include
   ifeq ($(SYS), MAC)
-  EIGEN_INCLUDE_PATH = /usr/local/include/eigen3
+    EIGEN_INCLUDE_PATH = /usr/local/include/eigen3
   else
-  EIGEN_INCLUDE_PATH = /usr/include/eigen3
+    EIGEN_INCLUDE_PATH = /usr/include/eigen3
   endif
   ifdef GUIX
     # Effectively disable paths for GNU Guix
     OPENBLAS_INCLUDE_PATH = .
     EIGEN_INCLUDE_PATH = $(GUIX)/include/eigen3
-    RPATH = -Xlinker --rpath=$(GUIX)/lib
+    # RPATH = -Xlinker --rpath=$(GUIX)/lib
     PROFILE =$(realpath $(GUIX))
   endif
 endif
@@ -106,7 +106,8 @@ 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$(EIGEN_INCLUDE_PATH) -Wl,-L/usr/local/opt/openblas/lib
+  # GCC_FLAGS=-O3 -std=c++11 -stdlib=libc++ -isystem$(OPENBLAS_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Wl,-L/usr/local/opt/openblas/lib
+  GCC_FLAGS=-O3 -std=c++11 -isystem$(OPENBLAS_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Wl,-L/usr/local/opt/openblas/lib
 endif
 
 ifdef WITH_OPENBLAS
@@ -119,6 +120,11 @@ ifdef WITH_OPENBLAS
   endif
 endif
 
+ifeq ($(CXX), clang++)
+  # CPPFLAGS += -isystem$(GUIX)/include/c++ -isystem$(GUIX)/include/c++/x86_64-unknown-linux-gnu
+  CPPFLAGS += -I$(GUIX)/include/c++ -I$(GUIX)/include/c++/x86_64-unknown-linux-gnu -L$(GUIX)/lib
+endif
+
 ifdef DEBUG
   CPPFLAGS += -g -Og $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc $(RPATH)
 else
diff --git a/src/mathfunc.cpp b/src/mathfunc.cpp
index 8acbd52..21d5c09 100644
--- a/src/mathfunc.cpp
+++ b/src/mathfunc.cpp
@@ -604,18 +604,3 @@ double UcharToDouble02(const unsigned char c) { return (double)c * 0.01; }
 unsigned char Double02ToUchar(const double dosage) {
   return (int)(dosage * 100);
 }
-
-/*
-void uchar_matrix_get_row(const vector<vector<unsigned char>> &X,
-                          const size_t i_row, VectorXd &x_row) {
-  if (i_row < X.size()) {
-    for (size_t j = 0; j < x_row.size(); j++) {
-      x_row(j) = UcharToDouble02(X[i_row][j]);
-    }
-  } else {
-    std::cerr << "Error return genotype vector...\n";
-    exit(1);
-  }
-}
-
-*/
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh
index 381d20a..9c2850e 100755
--- a/test/dev_test_suite.sh
+++ b/test/dev_test_suite.sh
@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/bin/sh
 
 gemma=../bin/gemma
 # gemmaopts="-debug -strict"
diff --git a/test/test_suite.sh b/test/test_suite.sh
index faddd43..0162d08 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/bin/sh
 
 gemma=../bin/gemma
 gemmaopts="-debug"
-- 
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