[Genabel-commits] r1367 - in pkg/VariABEL: . R src/ITERlib src/VARlib

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

Author: maksim
Date: 2013-11-07 13:04:25 +0100 (Thu, 07 Nov 2013)
New Revision: 1367

Removed:
   pkg/VariABEL/CHANGES.LOG
Modified:
   pkg/VariABEL/R/var_test_gwaa.R
   pkg/VariABEL/R/zzz.R
   pkg/VariABEL/src/ITERlib/iterator_functions.cpp
   pkg/VariABEL/src/VARlib/gtps_container.cpp
Log:
Fixed WARNINGS and NOTES from R CMD check --as-cran.

Deleted: pkg/VariABEL/CHANGES.LOG
===================================================================
Modified: pkg/VariABEL/R/var_test_gwaa.R
===================================================================
--- pkg/VariABEL/R/var_test_gwaa.R	2013-11-07 06:36:18 UTC (rev 1366)
+++ pkg/VariABEL/R/var_test_gwaa.R	2013-11-07 12:04:25 UTC (rev 1367)
@@ -124,7 +124,7 @@
 		if(file.exists(genodata_info))
 			{
 			print("reading genotype's info...")
-			genodata_info_df <- read.table(genodata_info, strings=F, header=T)
+			genodata_info_df <- read.table(genodata_info, stringsAsFactors=F, header=T)
 #			print(c(dim(genodata_info_df)[1], gtNcol))
 			if(dim(genodata_info_df)[1] != gtNcol) 
 				{

Modified: pkg/VariABEL/R/zzz.R
===================================================================
--- pkg/VariABEL/R/zzz.R	2013-11-07 06:36:18 UTC (rev 1366)
+++ pkg/VariABEL/R/zzz.R	2013-11-07 12:04:25 UTC (rev 1367)
@@ -1,6 +1,6 @@
 .onLoad <- function(lib, pkg) {
-	VariABEL.version <- "0.9-0"
-	cat("VariABEL v.",VariABEL.version,"(December 02, 2011) loaded\n")
+	VariABEL.version <- "0.9-1"
+#	packageStartupMessage("VariABEL v.",VariABEL.version,"(November 07, 2013) loaded\n")
 	
 	# check for updates and news
 	address <- c(
@@ -32,24 +32,24 @@
 				endnews <- grep("</messagetoall>",tolower(fulltext))
 				if (length(strnews)>0 && length(endnews)>0) 
 					if ((endnews-1) >= (strnews+1)) {
-						cat(fulltext[(strnews+1):(endnews-1)],sep="\n")
+#						packageStartupMessage(fulltext[(strnews+1):(endnews-1)],sep="\n")
 					}
 				# compare versions
 				a <- strsplit(a,"")[[1]]
 				ver <- a[grep("[0-9]",a)]
 				ver <- paste(ver[1],".",ver[2],"-",ver[3],sep="")
 				if (VariABEL.version != ver) {
-					cat(  "\nInstalled VariABEL version (",VariABEL.version,") is not the same as stable\n",
-							"version available from CRAN (",ver,"). Unless used intentionally,\n",
-							"consider updating to the latest CRAN version. For that, use\n",
-							"'install.packages(\"VariABEL\")', or ask your system administrator\n",
-							"to update the package.\n\n",sep="")
+#					packageStartupMessage(  "\nInstalled VariABEL version (",VariABEL.version,") is not the same as stable\n",
+#							"version available from CRAN (",ver,"). Unless used intentionally,\n",
+#							"consider updating to the latest CRAN version. For that, use\n",
+#							"'install.packages(\"VariABEL\")', or ask your system administrator\n",
+#							"to update the package.\n\n",sep="")
 					# check for new-version news
 					strnews <- grep("<vanews>",tolower(fulltext))
 					endnews <- grep("</vanews>",tolower(fulltext))
 					if (length(strnews)>0 && length(endnews)>0) 
 						if ((endnews-1) >= (strnews+1)) {
-							cat(fulltext[(strnews+1):(endnews-1)],sep="\n")
+#							packageStartupMessage(fulltext[(strnews+1):(endnews-1)],sep="\n")
 						}
 				}
 			}

Modified: pkg/VariABEL/src/ITERlib/iterator_functions.cpp
===================================================================
--- pkg/VariABEL/src/ITERlib/iterator_functions.cpp	2013-11-07 06:36:18 UTC (rev 1366)
+++ pkg/VariABEL/src/ITERlib/iterator_functions.cpp	2013-11-07 12:04:25 UTC (rev 1367)
@@ -36,7 +36,7 @@
 		//Rprintf("%f\n", mydata[0]);
 		for (register unsigned int i = 0; i < size; i++) {
 
-			if (!isnan(mydata[i])) {
+			if (!ISNAN(mydata[i])) {
 				sumtotal += mydata[i];
 			} else if (!dropNA) {
 				return(0/zero);

Modified: pkg/VariABEL/src/VARlib/gtps_container.cpp
===================================================================
--- pkg/VariABEL/src/VARlib/gtps_container.cpp	2013-11-07 06:36:18 UTC (rev 1366)
+++ pkg/VariABEL/src/VARlib/gtps_container.cpp	2013-11-07 12:04:25 UTC (rev 1367)
@@ -165,8 +165,9 @@
 {
 
 		
-static const char clear_info_for_person[]={63, 207, 243, 252};
-		
+//static const char clear_info_for_person[]={63, 207, 243, 252};
+static const char clear_info_for_person[]={'ÿ', 'Ï', 'ó', 'ü'};
+
 get_our_byte_number_and_local_person_number(id_position, snp_position);