[Genabel-commits] r1441 - pkg/ProbABEL/doc

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-12-02 15:49:15 +0100 (Mon, 02 Dec 2013)
New Revision: 1441

Modified:
   pkg/ProbABEL/doc/ChangeLog
   pkg/ProbABEL/doc/INSTALL
   pkg/ProbABEL/doc/ProbABEL_manual.tex
   pkg/ProbABEL/doc/packaging.txt
   pkg/ProbABEL/doc/pacoxph.1
   pkg/ProbABEL/doc/palinear.1
   pkg/ProbABEL/doc/palogist.1
Log:
Preparing for the next release of ProbABEL. 
Updated version numbers and dates. 
Small updates to the documentation. 


Modified: pkg/ProbABEL/doc/ChangeLog
===================================================================
--- pkg/ProbABEL/doc/ChangeLog	2013-12-02 11:00:13 UTC (rev 1440)
+++ pkg/ProbABEL/doc/ChangeLog	2013-12-02 14:49:15 UTC (rev 1441)
@@ -9,6 +9,11 @@
   slightly different place in the code to help debugging problems with the
   input data.
 * Fix a bug in the example scripts: an incorrect shell variable was used.
+* The extract-snp binary is no longer built by default (as it isn't
+  finished yet). Building can be enabled at compile time by giving the
+  --enable-extract-snp option to ./configure.
+* For developers: a start has been made on documenting the internal
+  functions using Doxygen.
 
 ***** v.0.4.1 (2013.08.29)
 * Fix bug #4854: When using mmscore, there is one (nan) column missing in

Modified: pkg/ProbABEL/doc/INSTALL
===================================================================
--- pkg/ProbABEL/doc/INSTALL	2013-12-02 11:00:13 UTC (rev 1440)
+++ pkg/ProbABEL/doc/INSTALL	2013-12-02 14:49:15 UTC (rev 1441)
@@ -47,12 +47,10 @@
   this file to probabel_config.cfg.
 
   To see options, run
-
 ./configure --help
 
   The most notable option is
 ./configure --prefix=/some/subdirectory
-
   to install ProbABEL in that subdirectory. Instead of using
   /usr/local/ as install root directory, it installs in /some/subdirectory.
 

Modified: pkg/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- pkg/ProbABEL/doc/ProbABEL_manual.tex	2013-12-02 11:00:13 UTC (rev 1440)
+++ pkg/ProbABEL/doc/ProbABEL_manual.tex	2013-12-02 14:49:15 UTC (rev 1441)
@@ -1,6 +1,6 @@
 \documentclass[12pt,a4paper]{article}
 
-\title{Manual for ProbABEL v0.4.1}
+\title{Manual for ProbABEL v0.4.2}
 \author{\emph{Current Programmers:} Lennart Karssen$^{1}$, Maarten
   Kooyman$^1$, \\
   Yurii Aulchenko$^{2}$ \\
@@ -294,7 +294,7 @@
 short explanation to the command line options:
 \begin{verbatim}
 user at server:~$ palogist --help
-probabel v. 0.4.1
+probabel v. 0.4.2
 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
 
 Using EIGEN version 3.1.2 for matrix operations
@@ -854,7 +854,7 @@
 \end{quote}
 A proper reference may look like
 \begin{quote}
-For the analysis of imputed data, we used the \PA{} v.0.4.1
+For the analysis of imputed data, we used the \PA{} v.0.4.2
 from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et al.}, 2010).
 \end{quote}
 

Modified: pkg/ProbABEL/doc/packaging.txt
===================================================================
--- pkg/ProbABEL/doc/packaging.txt	2013-12-02 11:00:13 UTC (rev 1440)
+++ pkg/ProbABEL/doc/packaging.txt	2013-12-02 14:49:15 UTC (rev 1441)
@@ -26,6 +26,7 @@
     DISTCHECK_CONFIGURE_FLAGS="--disable-palinear" make distcheck
     DISTCHECK_CONFIGURE_FLAGS="--disable-palogist" make distcheck
     DISTCHECK_CONFIGURE_FLAGS="--disable-pacoxph" make distcheck
+    DISTCHECK_CONFIGURE_FLAGS="--enable-extract-snp" make distcheck
 ** Building the package for the first time
    Now that we verified that the source code builds without problems,
    let's create the package.

Modified: pkg/ProbABEL/doc/pacoxph.1
===================================================================
--- pkg/ProbABEL/doc/pacoxph.1	2013-12-02 11:00:13 UTC (rev 1440)
+++ pkg/ProbABEL/doc/pacoxph.1	2013-12-02 14:49:15 UTC (rev 1441)
@@ -1,4 +1,4 @@
-.TH pacoxph 1 "29 August 2013"
+.TH pacoxph 1 "25 November 2013"
 .SH NAME
 pacoxph \- Perform Genome-Wide Association Analysis using a linear model
 .SH SYNOPSIS

Modified: pkg/ProbABEL/doc/palinear.1
===================================================================
--- pkg/ProbABEL/doc/palinear.1	2013-12-02 11:00:13 UTC (rev 1440)
+++ pkg/ProbABEL/doc/palinear.1	2013-12-02 14:49:15 UTC (rev 1441)
@@ -1,4 +1,4 @@
-.TH palinear 1 "29 August 2013"
+.TH palinear 1 "25 November 2013"
 .SH NAME
 palinear \- Perform Genome-Wide Association Analysis using a linear model
 .SH SYNOPSIS

Modified: pkg/ProbABEL/doc/palogist.1
===================================================================
--- pkg/ProbABEL/doc/palogist.1	2013-12-02 11:00:13 UTC (rev 1440)
+++ pkg/ProbABEL/doc/palogist.1	2013-12-02 14:49:15 UTC (rev 1441)
@@ -1,4 +1,4 @@
-.TH palogist 1 "29 August 2013"
+.TH palogist 1 "25 November 2013"
 .SH NAME
 palogist \- Perform Genome-Wide Association Analysis using a linear model
 .SH SYNOPSIS