Add Eigen 3.2.1 to ProbABEL

This is a temporary workaround for Issue #11.
The full Eigen tar-ball is included as src/3.2.1.tar.bz2 and
src/eigen-3.2.1/ contains only the header files.

configure.ac

@@ -75,17 +75,30 @@ AC_CHECK_HEADERS([float.h inttypes.h libintl.h limits.h stddef.h \
 # Option that lets the user specify a path to the EIGEN include files.
 AC_ARG_WITH([eigen-include-path],
     [AS_HELP_STRING([--with-eigen-include-path],
-      [location of the Eigen headers, defaults to /usr/include/eigen3])],
-    [CPPFLAGS+=" -I${withval}"],
-    [CPPFLAGS+=' -I/usr/include/eigen3'])
-
-# Check for the EIGEN header files
-AC_CHECK_HEADERS([Eigen/Dense Eigen/LU])
-
-if test x$ac_cv_header_Eigen_Dense = xno; then
-  AC_MSG_ERROR([Could not find the Eigen header files. Did you specify \
---with-eigen-include-path correctly?])
+      [location of the Eigen headers, defaults to src/eigen-3.2.1])],
+    [EIGEN_PATH=${withval}; EXTERNAL_EIGEN=yes],
+    [EIGEN_PATH="src/eigen-3.2.1"])
+
+# Inform AutoMake that an eigen path has been specified using the
+# --with-eigen-include-dir option so that AutoMake doesn't prepend
+# ${top_srcdir} to the path
+AM_CONDITIONAL([EXTERNAL_EIGEN], test -n "$EXTERNAL_EIGEN")
+
+AC_SUBST(EIGEN_PATH)
+
+# Check for the EIGEN header files (make backup of CPPFLAGS first)
+CPPFLAGS_BACKUP=${CPPFLAGS}
+if test -z "$EXTERNAL_EIGEN"; then
+  CPPFLAGS+=" -I${srcdir}/${EIGEN_PATH}"
+else
+  CPPFLAGS+=" -I${EIGEN_PATH}"
 fi
+AC_CHECK_HEADERS([Eigen/Dense Eigen/LU],
+                 [],
+                 [AC_MSG_ERROR([Could not find the Eigen header files. \
+Did you specify --with-eigen-include-path correctly?])]
+                 )
+CPPFLAGS=${CPPFLAGS_BACKUP}
 
 
 # Checks for typedefs, structures, and compiler characteristics.

doc/COPYING

@@ -1,4 +1,18 @@
-		    GNU GENERAL PUBLIC LICENSE
+ProbABEL consists of two parts:
+1) The ProbABEL source code, which is licensed under the GPL
+2) The source code for the Eigen library v.3.2.1
+   (http://eigen.tuxfamily.org), which is licensed under the MPL 2.0.
+
+Note: the MPL allows distribution of unmodified MPL source code in a
+GPL-ed larger work (see
+https://www.mozilla.org/en-US/MPL/2.0/combining-mpl-and-gpl/)
+
+The licence text for the MPL can be found in the file
+lib/eigen-3.2.1/COPYING.MPL2
+The licence text for the GPL is reproduced below.
+
+
+                    GNU GENERAL PUBLIC LICENSE
 		       Version 2, June 1991
 
  Copyright (C) 1989, 1991 Free Software Foundation, Inc.

doc/ChangeLog

@@ -1,11 +1,13 @@
 ***** v.0.5.0 (2016.)
 * ProbABEL now depends on the Eigen library. The option to compile without
-  Eigen has been removed.
+  Eigen has been removed. Eigen 3.2.1 is included with ProbABEL. The
+  directory src/eigen-3.2.1 contains header files we need. The full Eigen
+  source code tar-ball is included as src/3.2.1.tar.bz2.
 * Fixed Issue #15: Coxph interactions not working; when using the
   --interaction option the name of the model was wrong (e.g. for
   --interaction=1, the interaction term was shown as mu * SNP_A1, which
   obviously is not what we meant to do).
-* Fixed issue Github #16: "Too many NANs for SNPs with low `Rsq` when some
+* Fixed Github issue #16: "Too many NANs for SNPs with low `Rsq` when some
   commandline options are specified"
 * Added --flipmaf command line option to palinear, pacoxph and palogist.
   If this option is selected, ProbABEL will 'flip' the alleles A1 and A2

doc/INSTALL

@@ -7,9 +7,13 @@ The ProbABEL manual (in .tex or .pdf format) also contains detailed
 ** The Eigen library
    ProbABEL has one external dependency that has to be met before
    compilation will succeed: it depends on the Eigen library
-   (http://eigen.tuxfamily.org) for fast matrix manipulation. On
-   Debian/Ubuntu systems the Eigen library can be installed in the
-   following way: apt-get install libeigen3-dev
+   (http://eigen.tuxfamily.org) for fast matrix manipulation.
+
+   Eigen v3.2.1 is distributed with the ProbABEL source code, so by
+   default no extra steps are needed.
+
+   Alternatively, on Debian/Ubuntu systems the Eigen library can be
+   installed in the following way: apt-get install libeigen3-dev
 
    If you install the eigen library by hand (e.g. after downloading
    the files from the aforementioned website) you have to specify the

doc/ProbABEL_manual.tex

@@ -157,12 +157,17 @@ \subsection{Precompiled packages}
   and install it from there. The PPA can be found at
   \url{https://launchpad.net/~l.c.karssen/+archive/genabel-ppa}. Instructions
   on how to add the PPA can also be found there.
-\item If your computer runs Debian Linux\footnote{At the moment \PA{}
-    is only available in Debian testing and unstable.} (and you have
+\item If your computer runs Debian Linux (and you have
   administrative rights on it), you can install ProbABEL like this:
   \begin{lstlisting}[basicstyle=\footnotesize\ttfamily,]
-user@server:~$ apt-get install probabel
+user@server:~$ sudo apt install probabel probabel-examples
   \end{lstlisting}
+  Note that since Debian has a relatively slow release cycle the
+  ProbABEL version in the Debian repositories may be relatively
+  old\footnote{The Debian package tracker
+    (\url{https://tracker.debian.org/pkg/probabel}) lists the \PA{}
+    versions currently in the Debian stable, testing and unstable
+    releases.}.
 \item Zip files with pre-compiled binaries (if available) can be found
   on the ProbABEL web page
   (\url{http://www.genabel.org/packages/ProbABEL}).
@@ -217,35 +222,25 @@ \subsection{Obtaining the source code and compiling it yourself}
 \end{lstlisting}
 
 Before continuing, it is important to mention that \PA{} needs the
-EIGEN library\footnote{EIGEN is a library for fast matrix
-  multiplication. In ProbABEL versions before v0.5.0 EIGEN was not
-  required (but still recommended).}. In order to download the
-library, go to \url{http://eigen.tuxfamily.org} and download the
-\texttt{tar.gz} file of the latest version of EIGEN (3.2.4 at the time
-of writing). Extract the files:
-\begin{lstlisting}[basicstyle=\footnotesize\ttfamily,]
-user@server:~$ tar -xzf 3.2.4.tar.gz
-\end{lstlisting}
-This will create a directory called \texttt{eigen-eigen} followed by a
-series of letters and digits. For simplicity we rename it to EIGEN
-\begin{lstlisting}[basicstyle=\footnotesize\ttfamily,]
-user@server:~$ mv eigen-eigen-10219c95fe65 EIGEN
-\end{lstlisting}
+Eigen library\footnote{Eigen is a library for fast matrix
+  multiplication. The Eigen website can be found at
+  \url{http://eigen.tuxfamily.org}. In ProbABEL versions before v0.5.0
+  Eigen was not required (but still recommended).}. The required
+source code for Eigen v3.2.1 is included in the ProbABEL
+\lstinline{.tar.gz} file in the \lstinline{src/eigen-3.2.1} directory.
 
 Now it's time to extract the \PA{} source code and move into the
 directory that is created:
 \begin{lstlisting}[basicstyle=\footnotesize\ttfamily,]
 user@server:~$ tar -xzf probabel-0.5.0.tar.gz
 user@server:~$ cd probabel-0.5.0
 \end{lstlisting}
-With the following command we will indicate where the EIGEN files can
-be found and where we want to install \PA{}. Let's install in a
-subdirectory of your home directory,
+With the following command we will indicate where we want to install
+\PA{}. Let's install in a subdirectory of your home directory,
 e.g.~\texttt{/home/yourusername/ProbABEL}:
 \begin{lstlisting}[basicstyle=\footnotesize\ttfamily,]
 user@server:~$ ./configure \
-   --prefix=/home/yourusername/ProbABEL/ \
-   --with-eigen-include-path=/home/yourusername/EIGEN
+   --prefix=/home/yourusername/ProbABEL/
 \end{lstlisting}
 This will be followed by a series of checks to see if all tools
 required for compilation and installation are present on your
@@ -1136,6 +1131,18 @@ \section{How to cite}
 %Iteratively re-weighted least squares are used to obtain parameters'
 %estimates.
 
+\section{Licence}
+\PA{} is licenced under the GNU Public Licence (GPL) v2.0, which
+means it is free/libre open source software, basically allowing you to
+the freedoms to run, study, share, and modify the software. The full
+text of the licence can be found in the file \lstinline{doc/COPYING}
+or on \url{https://gnu.org/licenses/old-licenses/gpl-2.0.html}.
+
+The Eigen library that is included with \PA{} is licenced under the
+Mozilla Public Licence (MPL) v2.0. The full text of this licence can
+be found in the file \lstinline{lib/eigen-3.2.1/COPYING.MPL2} or on
+\url{https://www.mozilla.org/en-US/MPL/2.0/}.
+
 \printindex
 
 \end{document}