[Genabel-commits] r1306 - pkg/ProbABEL/doc

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

Author: lckarssen
Date: 2013-08-25 20:51:34 +0200 (Sun, 25 Aug 2013)
New Revision: 1306

Modified:
   pkg/ProbABEL/doc/ChangeLog
   pkg/ProbABEL/doc/QuickStart.txt
   pkg/ProbABEL/doc/TODO
   pkg/ProbABEL/doc/packaging.txt
Log:
Small updates in the ProbABEL documentation.


Modified: pkg/ProbABEL/doc/ChangeLog
===================================================================
--- pkg/ProbABEL/doc/ChangeLog	2013-08-25 14:41:36 UTC (rev 1305)
+++ pkg/ProbABEL/doc/ChangeLog	2013-08-25 18:51:34 UTC (rev 1306)
@@ -1,4 +1,4 @@
-***** v.0.4.0 (2013.08)
+***** v.0.4.0 (2013.08.25)
 * The output files now contain a chi^2 column with the chi^2 value based
   on the LRT when not using --mmscore. When using -mmscore, the chi^2
   values are calculated from the Wald statistic (not implemented for the
@@ -31,6 +31,8 @@
   but not distributed in .deb or .tar.gz
 * Fixed bug #2529: ProbABEL doesn't warn when a required file is not
   specified on the command line
+* Fix small bug where running "pa{linear,logist,coxph} -h" complained
+  about a missing argument.
 
 
 ***** v.0.3.0 (2013.01.01)

Modified: pkg/ProbABEL/doc/QuickStart.txt
===================================================================
--- pkg/ProbABEL/doc/QuickStart.txt	2013-08-25 14:41:36 UTC (rev 1305)
+++ pkg/ProbABEL/doc/QuickStart.txt	2013-08-25 18:51:34 UTC (rev 1306)
@@ -1,18 +1,9 @@
-Read INSTALL file and compile the program
-
-Go to "example" directory
-
-Run binary trait analysis by 
-
-sh example_bt.sh
-
-Run quantitative trait analysis with
-
-sh example_qt.sh
-
-Run complete analysis including preparing the files with
-
-sh example_all.sh
-
-Inspect sh files to understand how to run the programs.
-
+- Read the doc/INSTALL file for instructions on how to compile the program.
+- Go to the "example" directory
+- Run a binary trait analysis by typing:
+   sh example_bt.sh
+- Run a quantitative trait analysis with
+   sh example_qt.sh
+- Run complete analysis including preparing the files with
+   sh example_all.sh
+- Inspect the .sh files to understand how to run the programs.

Modified: pkg/ProbABEL/doc/TODO
===================================================================
--- pkg/ProbABEL/doc/TODO	2013-08-25 14:41:36 UTC (rev 1305)
+++ pkg/ProbABEL/doc/TODO	2013-08-25 18:51:34 UTC (rev 1306)
@@ -1,2 +1,3 @@
 * Repeated measurements / GEE
 * Robust variances for Cox
+* Add p-values to the output

Modified: pkg/ProbABEL/doc/packaging.txt
===================================================================
--- pkg/ProbABEL/doc/packaging.txt	2013-08-25 14:41:36 UTC (rev 1305)
+++ pkg/ProbABEL/doc/packaging.txt	2013-08-25 18:51:34 UTC (rev 1306)
@@ -20,7 +20,7 @@
    package is built. But first we need to check whether the source
    builds correctly for various settings of the ./configure
    options. Run the following:
-    DISTCHECK_CONFIGURE_FLAGS="--disable-eigen" make distcheck
+    DISTCHECK_CONFIGURE_FLAGS="--without-eigen" make distcheck
     DISTCHECK_CONFIGURE_FLAGS="--disable-palinear" make distcheck
     DISTCHECK_CONFIGURE_FLAGS="--disable-palogist" make distcheck
     DISTCHECK_CONFIGURE_FLAGS="--disable-pacoxph" make distcheck
@@ -28,13 +28,12 @@
    Now that we verified that the source code builds without problems,
    let's create the package.
     mkdir /tmp/PA-deb
-    cp probabel-0.3.0.tar.gz /tmp/PA-deb
+    cp probabel-0.4.0.tar.gz /tmp/PA-deb
     cd /tmp/PA-deb
-    tar -xzf probabel-0.3.0.tar.gz
-    cd probabel-0.3.0
+    tar -xzf probabel-0.4.0.tar.gz
+    cd probabel-0.4.0
     dh_make --single --email youremail at example.com \
-     --file ../probabel-0.3.0.tar.gz --copyright gpl2 \
-
+     --file ../probabel-0.4.0.tar.gz --copyright gpl2
    Hit the enter key to confirm the settings. Several files need to be
    edited.
    - debian/control
@@ -58,9 +57,14 @@
    is part of the devscripts package):
     debuild -i -us -uc -b
 ** Uploading to an Ubuntu PPA (Personal Package Archive)
+   First, make sure you've set the correct version of the
+   distribution you are packaging for in the debian/changelog file
+   (use the dch command). E.g. for Ubuntu 12.04 (Precise) this should
+   be
+     probabel (0.4.0-0ubuntu1~precise1) precise; urgency=low
    Building a package for upload to a PPA is almost the same as shown above:
     debuild -i -S -kYOURKEYID
    where YOURKEYID is the ID of the gpg key you use for signing your
    package (this key should be known by launchpad).
    To upload the package created above to the GenABEL PPA simply type:
-    dput ppa:l.c.karssen/genabel-ppa ../probabel_0.3.0-1_source.changes
+    dput ppa:l.c.karssen/genabel-ppa ../probabel_0.4.0-0ubuntu1~precise1_source.changes