[Genabel-commits] r1887 - in branches/ProbABEL-v0.4.3-coxfix/ProbABEL: . doc

Fri Nov 7 16:34:52 CET 2014

Author: lckarssen
Date: 2014-11-07 16:34:52 +0100 (Fri, 07 Nov 2014)
New Revision: 1887

Modified:
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/ChangeLog
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/ProbABEL_manual.tex
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/pacoxph.1
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/palinear.1
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/palogist.1
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/probabel.1
Log:
Update version number in ProbABEL 0.4.3 coxfix branch to 0.4.4. Also update release date in man pages and manual.


Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac
===================================================================

--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac	2014-11-07 14:54:30 UTC (rev 1886)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac	2014-11-07 15:34:52 UTC (rev 1887)
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.67])
-AC_INIT(ProbABEL, 0.4.3-coxfix2, genabel-devel at r-forge.wu-wien.ac.at)
+AC_INIT(ProbABEL, 0.4.4, genabel-devel at r-forge.wu-wien.ac.at)
 AM_INIT_AUTOMAKE([silent-rules subdir-objects])
 AM_SILENT_RULES([yes])
 AC_CONFIG_SRCDIR([src/data.h])

Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/ChangeLog
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/ChangeLog	2014-11-07 14:54:30 UTC (rev 1886)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/ChangeLog	2014-11-07 15:34:52 UTC (rev 1887)
@@ -1,3 +1,14 @@
+***** v.0.4.4 (2014.11.07)
+* Fixed bug #5729 in the Cox PH module. Some checks for problems with the
+  regression were incorrectly implemented. Thanks to Matthias Wuttke from
+  the University Medical Centre Freiburg, Anne Grotenhuis from the Radboud
+  Medical Centre Nijmegen, and Luba Pardo and Joris Verkouteren from the
+  Erasmus Medical Centre Rotterdam for their time and effort in reporting
+  the bug, helping to identify the problem and testing the fix.
+* Backported fix of bug #5982: ProbABEL's make install fails on MacOS X
+  and FreeBSD with sed error. Thanks to forum user mmold for reporting the bug.
+
+
 ***** v.0.4.3 (2014.04.01)
 * Speed-up of a factor of ~ 2 for linear, logistic and Cox regression when
   using filevector input files.

Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/ProbABEL_manual.tex	2014-11-07 14:54:30 UTC (rev 1886)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/ProbABEL_manual.tex	2014-11-07 15:34:52 UTC (rev 1887)
@@ -1,6 +1,6 @@
 \documentclass[12pt,a4paper]{article}
 
-\title{Manual for ProbABEL v0.4.3}
+\title{Manual for ProbABEL v0.4.4}
 \author{\emph{Current Programmers:} Lennart Karssen$^{1,2}$, Maarten
   Kooyman$^2$, \\
   Yurii Aulchenko$^{1,3}$ \\
@@ -11,7 +11,7 @@
   $^{2}${\small Erasmus MC, Rotterdam}\\
   $^{3}${\small Institute of Cytology and Genetics SD RAS, Novosibirsk}
 }
-\date{April 1, 2014}
+\date{November 7, 2014}
 
 
 \usepackage[utf8]{inputenc}
@@ -237,8 +237,8 @@
 Now it's time to extract the \PA{} source code and move into the
 directory that is created:
 \begin{lstlisting}
-user at server:~$ tar -xzf probabel-0.4.3.tar.gz
-user at server:~$ cd probabel-0.4.3
+user at server:~$ tar -xzf probabel-0.4.4.tar.gz
+user at server:~$ cd probabel-0.4.4
 \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
@@ -463,7 +463,7 @@
 short explanation to the command line options:
 \begin{verbatim}
 user at server:~$ palogist --help
-probabel v. 0.4.3
+probabel v. 0.4.4
 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
 
 Using EIGEN version 3.1.2 for matrix operations
@@ -1028,7 +1028,7 @@
 \end{quote}
 A proper reference may look like
 \begin{quote}
-For the analysis of imputed data, we used \PA{} v.0.4.3
+For the analysis of imputed data, we used \PA{} v.0.4.4
 from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et al.}, 2010).
 \end{quote}
 

Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/pacoxph.1
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/pacoxph.1	2014-11-07 14:54:30 UTC (rev 1886)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/pacoxph.1	2014-11-07 15:34:52 UTC (rev 1887)
@@ -1,4 +1,4 @@
-.TH pacoxph 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH pacoxph 1 "7 November 2014" "ProbABEL 0.4.4"
 .SH NAME
 pacoxph \- Perform Genome-Wide Association Analysis using a linear model
 .SH SYNOPSIS

Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/palinear.1
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/palinear.1	2014-11-07 14:54:30 UTC (rev 1886)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/palinear.1	2014-11-07 15:34:52 UTC (rev 1887)
@@ -1,4 +1,4 @@
-.TH palinear 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH palinear 1 "7 November 2014" "ProbABEL 0.4.4"
 .SH NAME
 palinear \- Perform Genome-Wide Association Analysis using a linear model
 .SH SYNOPSIS

Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/palogist.1
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/palogist.1	2014-11-07 14:54:30 UTC (rev 1886)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/palogist.1	2014-11-07 15:34:52 UTC (rev 1887)
@@ -1,4 +1,4 @@
-.TH palogist 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH palogist 1 "7 November 2014" "ProbABEL 0.4.4"
 .SH NAME
 palogist \- Perform Genome-Wide Association Analysis using a linear model
 .SH SYNOPSIS

Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/probabel.1
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/probabel.1	2014-11-07 14:54:30 UTC (rev 1886)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/doc/probabel.1	2014-11-07 15:34:52 UTC (rev 1887)
@@ -1,4 +1,4 @@
-.TH ProbABEL 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH ProbABEL 1 "7 November 2014" "ProbABEL 0.4.4"
 .SH NAME
 probabel \- Wrapper around the three ProbABEL binaries, simplifying their use
 .SH SYNOPSIS

