[Genabel-commits] r713 - in pkg/GenABEL: . R inst/unitTests src/GAlib

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

Author: yurii
Date: 2011-05-13 12:17:57 +0200 (Fri, 13 May 2011)
New Revision: 713

Added:
   pkg/GenABEL/inst/unitTests/runit.convert.snp.ped.R
Modified:
   pkg/GenABEL/CHANGES.LOG
   pkg/GenABEL/DESCRIPTION
   pkg/GenABEL/R/zzz.R
   pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp
   pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp
Log:
Fixing bug [1388], added regression test

Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG	2011-05-05 13:06:37 UTC (rev 712)
+++ pkg/GenABEL/CHANGES.LOG	2011-05-13 10:17:57 UTC (rev 713)
@@ -1,5 +1,7 @@
-*** v. 1.6-7 (2011.05.05)
+*** v. 1.6-7 (2011.05.13)
 
+Fixing bug [1388], added regression test
+
 upgrade version number
 
 fix in example of polygenic_hglm

Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION	2011-05-05 13:06:37 UTC (rev 712)
+++ pkg/GenABEL/DESCRIPTION	2011-05-13 10:17:57 UTC (rev 713)
@@ -2,7 +2,7 @@
 Type: Package
 Title: genome-wide SNP association analysis
 Version: 1.6-7
-Date: 2011-05-05
+Date: 2011-05-13
 Author: Yurii Aulchenko et al.
 Maintainer: Yurii Aulchenko <i.aoultchenko at erasmusmc.nl>
 Depends: R (>= 2.10.0), methods, MASS

Modified: pkg/GenABEL/R/zzz.R
===================================================================
--- pkg/GenABEL/R/zzz.R	2011-05-05 13:06:37 UTC (rev 712)
+++ pkg/GenABEL/R/zzz.R	2011-05-13 10:17:57 UTC (rev 713)
@@ -1,6 +1,6 @@
 .onLoad <- function(lib, pkg) {
 	GenABEL.version <- "1.6-7"
-	cat("GenABEL v.",GenABEL.version,"(May 05, 2011) loaded\n")
+	cat("GenABEL v.",GenABEL.version,"(May 13, 2011) loaded\n")
 	
 	# check for updates and news
 	address <- c(

Added: pkg/GenABEL/inst/unitTests/runit.convert.snp.ped.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.convert.snp.ped.R	                        (rev 0)
+++ pkg/GenABEL/inst/unitTests/runit.convert.snp.ped.R	2011-05-13 10:17:57 UTC (rev 713)
@@ -0,0 +1,30 @@
+### --- Test setup ---
+#
+# regression test
+#
+
+if(FALSE) {
+	## Not really needed, but can be handy when writing tests
+	library(RUnit)
+	library(GenABEL)
+}
+
+### do not run
+#stop("SKIP THIS TEST")
+###
+
+### ---- common functions and data -----
+
+#source(paste("../inst/unitTests/shared_functions.R"))
+#source(paste(path,"/shared_functions.R",sep=""))
+
+### --- Test functions ---
+
+test.convert.snp.ped <- function()
+{
+	pref <- "../inst/exdata/"
+	pedf <- paste(pref,"pedin.18",sep="")
+	mapf <- paste(pref,"map.18",sep="")
+	convert.snp.ped(pedfile=pedf,mapfile=mapf,out="tmp.raw")
+	unlink("tmp.raw")
+}
\ No newline at end of file


Property changes on: pkg/GenABEL/inst/unitTests/runit.convert.snp.ped.R
___________________________________________________________________
Added: svn:mime-type
   + text/plain

Modified: pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp	2011-05-05 13:06:37 UTC (rev 712)
+++ pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp	2011-05-13 10:17:57 UTC (rev 713)
@@ -26,7 +26,7 @@
 
 #include <R.h>
 
-#define MAXIDS 2000000
+#define MAXIDS 200000
 
 string replace_mrl(string in);
 string replace_mach(string in);

Modified: pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp	2011-05-05 13:06:37 UTC (rev 712)
+++ pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp	2011-05-13 10:17:57 UTC (rev 713)
@@ -26,7 +26,7 @@
 
 #include <R.h>
 
-#define MAXIDS 100000
+#define MAXIDS 200000
 
 string replace_mach(string in);