[Genabel-commits] r1978 - in pkg/MixABEL: . R man

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

Author: lckarssen
Date: 2015-05-15 19:17:37 +0200 (Fri, 15 May 2015)
New Revision: 1978

Modified:
   pkg/MixABEL/DESCRIPTION
   pkg/MixABEL/NAMESPACE
   pkg/MixABEL/R/MixABEL-package.R
   pkg/MixABEL/R/fastmixmod.R
   pkg/MixABEL/R/fgls.R
   pkg/MixABEL/man/FastMixedModel.Rd
   pkg/MixABEL/man/GWFGLS.Rd
Log:
Moved DatABEL from MixABEL's Depends to Suggests (in the DESCRIPTION file) as it is only needed for the examples. Also moved some of the other packages from Depends to Imports.
This also leads to some changes in the (roxygen) documentation and examples.

Now MixABEL finishes the CRAN checks without NOTEs, ERRORs, or WARNINGs.


Modified: pkg/MixABEL/DESCRIPTION
===================================================================
--- pkg/MixABEL/DESCRIPTION	2015-05-15 16:54:51 UTC (rev 1977)
+++ pkg/MixABEL/DESCRIPTION	2015-05-15 17:17:37 UTC (rev 1978)
@@ -5,9 +5,9 @@
 Date: 2015-05-01
 Author: Yurii Aulchenko, William Astle, Erik Roos, Marcel Kempenaar
 Maintainer: Yurii Aulchenko <yurii.aulchenko at gmail.com>
-Depends: R (>= 2.4.0), MASS, mvtnorm, GenABEL (>= 1.5-8), DatABEL (>= 0.1-5)
-Suggests: RUnit
-Imports: Rcpp (>= 0.11.0)
+Depends: R (>= 2.4.0), GenABEL (>= 1.5-8)
+Suggests: RUnit, DatABEL (>= 0.1-5), GenABEL.data
+Imports: Rcpp (>= 0.11.0), mvtnorm, MASS
 LinkingTo: Rcpp
 Description: Provides methods for fast mixed models for association
              analysis in samples of related individuals.

Modified: pkg/MixABEL/NAMESPACE
===================================================================
--- pkg/MixABEL/NAMESPACE	2015-05-15 16:54:51 UTC (rev 1977)
+++ pkg/MixABEL/NAMESPACE	2015-05-15 17:17:37 UTC (rev 1978)
@@ -4,7 +4,6 @@
 export(FastMixedModel)
 export(GWFGLS)
 export(summaryFGLS)
-import(DatABEL)
 import(GenABEL)
 import(MASS)
 import(mvtnorm)

Modified: pkg/MixABEL/R/MixABEL-package.R
===================================================================
--- pkg/MixABEL/R/MixABEL-package.R	2015-05-15 16:54:51 UTC (rev 1977)
+++ pkg/MixABEL/R/MixABEL-package.R	2015-05-15 17:17:37 UTC (rev 1978)
@@ -10,7 +10,7 @@
 #' @name MixABEL-package
 #' @aliases "MixABEL"
 #' @useDynLib MixABEL
-#' @import DatABEL GenABEL MASS mvtnorm
+#' @import GenABEL MASS mvtnorm
 #' @importFrom Rcpp evalCpp
 
 "MixABEL-package" <- function() {}

Modified: pkg/MixABEL/R/fastmixmod.R
===================================================================
--- pkg/MixABEL/R/fastmixmod.R	2015-05-15 16:54:51 UTC (rev 1977)
+++ pkg/MixABEL/R/fastmixmod.R	2015-05-15 17:17:37 UTC (rev 1978)
@@ -28,7 +28,7 @@
 #'
 #' @examples
 #' require(mvtnorm)
-#' data(ge03d2.clean)
+#' data(ge03d2.clean, package="GenABEL.data")
 #' df <- ge03d2.clean[1:250,autosomal(ge03d2.clean)]
 #' NSNPS <- nsnps(df)
 #' modh2 <- 0.8

Modified: pkg/MixABEL/R/fgls.R
===================================================================
--- pkg/MixABEL/R/fgls.R	2015-05-15 16:54:51 UTC (rev 1977)
+++ pkg/MixABEL/R/fgls.R	2015-05-15 17:17:37 UTC (rev 1978)
@@ -221,6 +221,7 @@
 #' library(MASS)
 #' library(mvtnorm)
 #' library(GenABEL)
+#' library(DatABEL)
 #' data(ge03d2.clean)
 #' NIDS <- 100
 #' df <- ge03d2.clean[1:NIDS,autosomal(ge03d2.clean)]

Modified: pkg/MixABEL/man/FastMixedModel.Rd
===================================================================
--- pkg/MixABEL/man/FastMixedModel.Rd	2015-05-15 16:54:51 UTC (rev 1977)
+++ pkg/MixABEL/man/FastMixedModel.Rd	2015-05-15 17:17:37 UTC (rev 1978)
@@ -32,7 +32,7 @@
 }
 \examples{
 require(mvtnorm)
-data(ge03d2.clean)
+data(ge03d2.clean, package="GenABEL.data")
 df <- ge03d2.clean[1:250,autosomal(ge03d2.clean)]
 NSNPS <- nsnps(df)
 modh2 <- 0.8
@@ -69,9 +69,9 @@
 
 time0.fmm <- proc.time()
 fmm <- FastMixedModel(Response=res,
-						Explan=expl,
-						Kin = gkin,
-						Cov=covariates)
+                                             Explan=expl,
+                                             Kin = gkin,
+                                             Cov=covariates)
 time.fmm <- proc.time() - time0.fmm
 
 time.h2

Modified: pkg/MixABEL/man/GWFGLS.Rd
===================================================================
--- pkg/MixABEL/man/GWFGLS.Rd	2015-05-15 16:54:51 UTC (rev 1977)
+++ pkg/MixABEL/man/GWFGLS.Rd	2015-05-15 17:17:37 UTC (rev 1978)
@@ -75,6 +75,7 @@
 library(MASS)
 library(mvtnorm)
 library(GenABEL)
+library(DatABEL)
 data(ge03d2.clean)
 NIDS <- 100
 df <- ge03d2.clean[1:NIDS,autosomal(ge03d2.clean)]