[Genabel-commits] r942 - in branches/ProbABEL-pacox/v.0.1-3: . doc src

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

Author: lckarssen
Date: 2012-08-27 18:38:39 +0200 (Mon, 27 Aug 2012)
New Revision: 942

Modified:
   branches/ProbABEL-pacox/v.0.1-3/Makefile
   branches/ProbABEL-pacox/v.0.1-3/doc/CHANGES.LOG
   branches/ProbABEL-pacox/v.0.1-3/src/main.cpp
   branches/ProbABEL-pacox/v.0.1-3/src/version.h
Log:
Final preparation for the release of the ProbABEL pacoxfix branch. 
For the pacoxph module this branch is the only working one as pacoxph in TRUNK doesn't function. 

- Updated version number and data
- Updated Makefile to make .tar.gz file with appropriate name and subdir
- Minor addition to copyright notice when running the binary. 


Modified: branches/ProbABEL-pacox/v.0.1-3/Makefile
===================================================================
--- branches/ProbABEL-pacox/v.0.1-3/Makefile	2012-08-23 15:41:11 UTC (rev 941)
+++ branches/ProbABEL-pacox/v.0.1-3/Makefile	2012-08-27 16:38:39 UTC (rev 942)
@@ -1,5 +1,6 @@
 
-VERSION = 0.1-3-fixcox
+VERSION = 0.1-3-pacoxph-fix-1
+BUILDDIRLNK = ProbABEL-$(VERSION)
 SRCDIR = src
 BINDIR = bin
 DOCDIR = doc
@@ -34,9 +35,12 @@
 
 clean:
 	rm -f $(BINDIR)/* $(SRCDIR)/*~ $(SRCDIR)/*.o $(DOCDIR)/*~ *.zip *.tar.gz
+	rm -f ../$(BUILDDIRLNK)
 
 linux_distrib: clean
-	cd .. ; tar --exclude-vcs -czvf ProbABEL_$(VERSION).tar.gz ProbABEL
+	ln -s $(PWD) ../$(BUILDDIRLNK)
+	cd .. ; tar --exclude-vcs -czhvf ProbABEL_$(VERSION).tar.gz $(BUILDDIRLNK)
+	rm ../$(BUILDDIRLNK)
 
 win_distrib: all
 	cd .. ; zip -r9 ProbABEL_$(VERSION)_win.zip ProbABEL

Modified: branches/ProbABEL-pacox/v.0.1-3/doc/CHANGES.LOG
===================================================================
--- branches/ProbABEL-pacox/v.0.1-3/doc/CHANGES.LOG	2012-08-23 15:41:11 UTC (rev 941)
+++ branches/ProbABEL-pacox/v.0.1-3/doc/CHANGES.LOG	2012-08-27 16:38:39 UTC (rev 942)
@@ -1,3 +1,16 @@
+***** v.0.1-3-pacoxph-fix (2012-08-27)
+
+This release fixes bug #1846 in the Cox Proportional Hazards
+module. Now using genotype dosages or probabilities give the same
+results (as they should).
+Thanks to Dr. Kiemeney from the Radboud University Medical Centre in
+Nijmegen for sponsoring this fix. The copyright of this fix is theirs
+(see SVN r902). 
+
+Note that building the binaries for palinear and palogist is disabled
+in the Makefile as (much) newer versions of these can be found in
+ProbABEL v.0.2 (and later). 
+
 ***** v.0.1-3 (2009.11.25)
 
 This version is courtesy of Han Chen (Nov 9, 2009). The modifications allow

Modified: branches/ProbABEL-pacox/v.0.1-3/src/main.cpp
===================================================================
--- branches/ProbABEL-pacox/v.0.1-3/src/main.cpp	2012-08-23 15:41:11 UTC (rev 941)
+++ branches/ProbABEL-pacox/v.0.1-3/src/main.cpp	2012-08-27 16:38:39 UTC (rev 942)
@@ -182,7 +182,9 @@
 	while (next_option != -1);
 
 
-	fprintf(stdout,"ProbABEL v. %s (%s) (C) Yurii Aulchenko, Maksim Struchalin, EMCR\n\n",VERSION,DATE);
+	fprintf(stdout, 
+		"ProbABEL v. %s (%s) (C) Yurii Aulchenko, Maksim Struchalin, EMCR, and others\n\n", 
+		VERSION, DATE);
 	if (neco[0]!=1 || neco[1]!=1 || neco[2]!=1)
 	{
 		print_usage(program_name,1);

Modified: branches/ProbABEL-pacox/v.0.1-3/src/version.h
===================================================================
--- branches/ProbABEL-pacox/v.0.1-3/src/version.h	2012-08-23 15:41:11 UTC (rev 941)
+++ branches/ProbABEL-pacox/v.0.1-3/src/version.h	2012-08-27 16:38:39 UTC (rev 942)
@@ -1,3 +1,2 @@
-#define VERSION "0.1-3"
-#define DATE "Nov 11, 2009"
-
+#define VERSION "0.1-3-pacoxph-fix-1"
+#define DATE "Aug 27, 2012"