[Genabel-commits] r2065 - in pkg/DatABEL: . R man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Mar 8 11:15:40 CET 2017 

Author: lckarssen
Date: 2017-03-08 11:15:39 +0100 (Wed, 08 Mar 2017)
New Revision: 2065

Modified:
   pkg/DatABEL/DESCRIPTION
   pkg/DatABEL/NAMESPACE
   pkg/DatABEL/R/get_temporary_file_name.R
   pkg/DatABEL/man/DatABEL-package.Rd
   pkg/DatABEL/man/apply2dfo.Rd
   pkg/DatABEL/man/databel-class.Rd
   pkg/DatABEL/man/databel.Rd
   pkg/DatABEL/man/databel2matrix.Rd
   pkg/DatABEL/man/databel2text.Rd
   pkg/DatABEL/man/extract_text_file_columns.Rd
   pkg/DatABEL/man/get_temporary_file_name.Rd
   pkg/DatABEL/man/make_empty_fvf.Rd
   pkg/DatABEL/man/matrix2databel.Rd
   pkg/DatABEL/man/process_lm_output.Rd
   pkg/DatABEL/man/text2databel.Rd
Log:
Fix build warning in DatABEL

This commit adds an @importFrom roxygen statement to the
get_temporary_file_name() function in DatABEL. Running R CMD build
gave the following warning:

get_temporary_file_name: no visible global function definition for
  ?\226?\128?\152runif?\226?\128?\153
  Undefined global functions or variables:
    runif
    Consider adding
      importFrom("stats", "runif")
      to your NAMESPACE file.

This commit solves that problem. I also ran devtools::document() to
update the documentation and DESCRIPTION and NAMESPACE files.




Modified: pkg/DatABEL/DESCRIPTION
===================================================================
--- pkg/DatABEL/DESCRIPTION	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/DESCRIPTION	2017-03-08 10:15:39 UTC (rev 2065)
@@ -20,3 +20,4 @@
     genome-wide association analyses e.g. using GenABEL, MixABEL and
     ProbABEL.
 License: GPL (>= 2)
+RoxygenNote: 5.0.1

Modified: pkg/DatABEL/NAMESPACE
===================================================================
--- pkg/DatABEL/NAMESPACE	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/NAMESPACE	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.0): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method(as.double,databel)
 export("cachesizeMb<-")
@@ -26,4 +26,5 @@
 exportClasses(databel)
 exportMethods(show)
 import(methods)
+importFrom(stats,runif)
 useDynLib(DatABEL)

Modified: pkg/DatABEL/R/get_temporary_file_name.R
===================================================================
--- pkg/DatABEL/R/get_temporary_file_name.R	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/R/get_temporary_file_name.R	2017-03-08 10:15:39 UTC (rev 2065)
@@ -9,6 +9,8 @@
 #' *FVI files too
 #' @export
 #'
+#' @importFrom stats runif
+#'
 
 get_temporary_file_name <- function(path=".", withFVext=TRUE)
 {

Modified: pkg/DatABEL/man/DatABEL-package.Rd
===================================================================
--- pkg/DatABEL/man/DatABEL-package.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/DatABEL-package.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/DatABEL-package.R
 \docType{package}
 \name{DatABEL-package}

Modified: pkg/DatABEL/man/apply2dfo.Rd
===================================================================
--- pkg/DatABEL/man/apply2dfo.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/apply2dfo.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/apply2dfo.R
 \name{apply2dfo}
 \alias{apply2dfo}
@@ -76,6 +76,7 @@
 rm(tA, tB, tC, tD)
 gc()
 unlink("tmp*")
+
 }
 \author{
 Yurii Aulchenko

Modified: pkg/DatABEL/man/databel-class.Rd
===================================================================
--- pkg/DatABEL/man/databel-class.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/databel-class.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/databel_class.R
 \docType{class}
 \name{databel-class}

Modified: pkg/DatABEL/man/databel.Rd
===================================================================
--- pkg/DatABEL/man/databel.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/databel.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/databel.R
 \name{databel}
 \alias{databel}

Modified: pkg/DatABEL/man/databel2matrix.Rd
===================================================================
--- pkg/DatABEL/man/databel2matrix.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/databel2matrix.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/databel2matrix.R
 \name{databel2matrix}
 \alias{databel2matrix}

Modified: pkg/DatABEL/man/databel2text.Rd
===================================================================
--- pkg/DatABEL/man/databel2text.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/databel2text.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/databel2text.R
 \name{databel2text}
 \alias{databel2text}

Modified: pkg/DatABEL/man/extract_text_file_columns.Rd
===================================================================
--- pkg/DatABEL/man/extract_text_file_columns.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/extract_text_file_columns.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/extract_text_file_columns.R
 \name{extract_text_file_columns}
 \alias{extract_text_file_columns}

Modified: pkg/DatABEL/man/get_temporary_file_name.Rd
===================================================================
--- pkg/DatABEL/man/get_temporary_file_name.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/get_temporary_file_name.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/get_temporary_file_name.R
 \name{get_temporary_file_name}
 \alias{get_temporary_file_name}

Modified: pkg/DatABEL/man/make_empty_fvf.Rd
===================================================================
--- pkg/DatABEL/man/make_empty_fvf.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/make_empty_fvf.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/make_empty_fvf.R
 \name{make_empty_fvf}
 \alias{make_empty_fvf}

Modified: pkg/DatABEL/man/matrix2databel.Rd
===================================================================
--- pkg/DatABEL/man/matrix2databel.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/matrix2databel.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/matrix2databel.R
 \name{matrix2databel}
 \alias{matrix2databel}

Modified: pkg/DatABEL/man/process_lm_output.Rd
===================================================================
--- pkg/DatABEL/man/process_lm_output.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/process_lm_output.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/apply2dfo_util.R
 \name{process_lm_output}
 \alias{process_lm_output}
@@ -35,6 +35,7 @@
 sex <- 1*(runif(10)>.5)
 trait <- rnorm(10)+sex+as(b[,2],"vector")+as(b[,2],"vector")*sex*5
 apply2dfo(trait~SNP*sex,dfodata=b,anFUN="lm",procFUN="process_lm_output")
+
 }
 \seealso{
 \link{apply2dfo}

Modified: pkg/DatABEL/man/text2databel.Rd
===================================================================
--- pkg/DatABEL/man/text2databel.Rd	2017-01-25 06:34:38 UTC (rev 2064)
+++ pkg/DatABEL/man/text2databel.Rd	2017-03-08 10:15:39 UTC (rev 2065)
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/text2databel.R
 \name{text2databel}
 \alias{text2databel}
@@ -75,6 +75,7 @@
 \code{write.table(...,col.names=TRUE,row.names=TRUE)}.
 }
 \examples{
+
 cat("this is an example which you can run if you can write to the
 file system\\n")
 
@@ -156,6 +157,7 @@
 if (!identical(data, as(x, "matrix"))) stop("not identical data")
 
 }
+
 }
 \author{
 Yurii Aulchenko

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