[Genabel-commits] r1011 - in pkg/ProbABEL: . doc

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

Author: lckarssen
Date: 2012-11-07 00:00:13 +0100 (Wed, 07 Nov 2012)
New Revision: 1011

Modified:
   pkg/ProbABEL/configure.ac
   pkg/ProbABEL/doc/CHANGES.LOG
   pkg/ProbABEL/doc/ProbABEL_manual.tex
Log:
Bumped version number to 0.2.2 because of troubles when uploading v0.2.1 to the GenABEL PPA. It turns out you can't re-upload a new version of an orig.tar.gz file (to make sure every user has a clean upgrade path). In my first try the build failed because of the non-POSIX sh extensions in the test_probABEL.pl_chunks.sh script. These were subsequently fixed in SVN r999 and r1007 (the original uploaded orig.tar.gz file was based on SVN r997). 


Modified: pkg/ProbABEL/configure.ac
===================================================================
--- pkg/ProbABEL/configure.ac	2012-11-06 20:34:29 UTC (rev 1010)
+++ pkg/ProbABEL/configure.ac	2012-11-06 23:00:13 UTC (rev 1011)
@@ -2,8 +2,8 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.67])
-AC_INIT(ProbABEL, 0.2.1, genabel-devel at r-forge.wu-wien.ac.at)
-AM_INIT_AUTOMAKE(ProbABEL, 0.2.1)
+AC_INIT(ProbABEL, 0.2.2, genabel-devel at r-forge.wu-wien.ac.at)
+AM_INIT_AUTOMAKE(ProbABEL, 0.2.2)
 AC_CONFIG_SRCDIR([src/data.h])
 AC_CONFIG_HEADERS([src/config.h])
 

Modified: pkg/ProbABEL/doc/CHANGES.LOG
===================================================================
--- pkg/ProbABEL/doc/CHANGES.LOG	2012-11-06 20:34:29 UTC (rev 1010)
+++ pkg/ProbABEL/doc/CHANGES.LOG	2012-11-06 23:00:13 UTC (rev 1011)
@@ -1,3 +1,10 @@
+***** v.0.2.2 (2012.11.05)
+* No change in the code compared to v.0.2.1. Due to a mistake with the
+  Ubuntu packaging (which was based on SVN r997, which contained a
+  major bug in the tests and which was uploaded to the GenABEL PPA)
+  I'm releasing a new package based on the same source code as
+  ProbABEL v.0.2.1 (except for the version numbers of course).
+
 ***** v.0.2.1 (2012.11.05)
 * Fixed bug #2295: the inverse variance-covariance matrix (used with
   the --mmscore option) was incorrectly subsetted when NAs are present

Modified: pkg/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- pkg/ProbABEL/doc/ProbABEL_manual.tex	2012-11-06 20:34:29 UTC (rev 1010)
+++ pkg/ProbABEL/doc/ProbABEL_manual.tex	2012-11-06 23:00:13 UTC (rev 1011)
@@ -1,6 +1,6 @@
 \documentclass[12pt,a4paper]{article}
 
-\title{Manual for ProbABEL v0.2.1}
+\title{Manual for ProbABEL v0.2.2}
 \author{
 Maksim Struchalin$^{1}$, Lennart Karssen$^{1}$, Yurii Aulchenko$^{2}$ \\
 \\
@@ -89,7 +89,7 @@
 Currently, \PA{} implements linear, logistic regression,
 and Cox proportional hazards models. The corresponding analysis
 programs are called \texttt{palinear},  \texttt{palogist},
-and \texttt{pacoxph}\footnote{Please note that in ProbABEL v.0.2.1 the
+and \texttt{pacoxph}\footnote{Please note that in ProbABEL v.0.2.2 the
   \texttt{pacoxph} program is not built by default because it is still
 too buggy for production use. Instructions on how to compile the
 \texttt{pacoxph} module can be found in the \texttt{CHANGES.LOG} file
@@ -274,7 +274,7 @@
 To run linear regression, you should use the program called
 \texttt{palinear}; for logistic analysis use \texttt{palogist}, and
 for the Cox proportional hazards model use
-\texttt{pacoxph}\footnote{Please note that in ProbABEL v.0.2.1 the
+\texttt{pacoxph}\footnote{Please note that in ProbABEL v.0.2.2 the
   \texttt{pacoxph} program is not built by default because it is still
   too buggy for production use. Instructions on how to compile the
   \texttt{pacoxph} module can be found in the \texttt{CHANGES.LOG}
@@ -348,7 +348,7 @@
 \end{verbatim}
 
 To run a Cox proportional hazards model\footnote{Please note that in
-  ProbABEL v.0.2.1 the \texttt{pacoxph} program is not built by
+  ProbABEL v.0.2.2 the \texttt{pacoxph} program is not built by
   default because it is still too buggy for production
   use. Instructions on how to compile the \texttt{pacoxph} module can
   be found in the \texttt{CHANGES.LOG} file in the \texttt{doc/}
@@ -838,7 +838,7 @@
 \end{quote}
 A proper reference may look like
 \begin{quote}
-For the analysis of imputed data, we used the \PA{} v.0.2.1
+For the analysis of imputed data, we used the \PA{} v.0.2.2
 from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et al.}, 2010).
 \end{quote}