v 0.2.3, CRAN release

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: solarius
 Type: Package
-Title: An R interface to SOLAR program
-Version: 0.2.2
-Date: 2015-05-06
+Title: An R Interface to SOLAR
+Version: 0.2.3
+Date: 2015-05-08
 Authors@R: c(
     person("Andrey", "Ziyatdinov", email = "[email protected]", role = c("cre", "aut")),
     person("Helena", "Brunel", role = "aut"),
@@ -14,11 +14,12 @@ Maintainer: Andrey Ziyatdinov <[email protected]>
 Description: 
   SOLAR is the standard software program to perform linkage and association mappings 
   of the quantitative trait loci (QTLs) in pedigrees of arbitrary size and complexity.
-  solarius allows the user to exploit the variance component methods implemented in SOLAR.
+  This package allows the user to exploit the variance component methods implemented in SOLAR.
   It automates such routine operations as formatting pedigree and phenotype data.
   It also parses the model output and contains summary and plotting functions for exploration of the results.
   In addition, solarius enables parallel computing of the linkage and association analyses,
   that makes the calculation of genome-wide scans more efficient.
+  See <http://solar.txbiomedgenetics.org/> for more information about SOLAR.
 License: GPL (>= 3)
 URL: https://github.com/ugcd/solarius
 LazyData: false
@@ -32,7 +33,7 @@ Suggests:
     scales,
     Matrix,
     gdata,
-    doMC,
+    doParallel,
     iterators,
     parallel,
     qqman

R/classSolarAssoc.R

@@ -72,7 +72,7 @@ plot.solarAssoc.old <- function(x,
   #if(!ret) {
   #  stop("`ggplot2` package is required for plotting")
   #}
-  ret <- require(scales)
+  ret <- requireNamespace("scales", quietly = TRUE)
   if(!ret) {
     stop("`scales` package is required for plotting")
   }

R/plot.lib.R

@@ -25,9 +25,17 @@ plotPed <- function(data, ped)
   stopifnot(!missing(data))
   stopifnot(class(data) == "data.frame")
   stopifnot(!missing(ped))
-
-  stopifnot(require(kinship2))
-
+
+  # load required R package kinship2
+  stopifnot(requireNamespace("kinship2", quietly = TRUE))
+
+  ret <- NULL # R CMD check: no visible binding
+  cmd <- "ret <- require(kinship2)"
+  eval(parse(text = cmd))
+  if(!ret) {
+    stop("`kinship2` package is required for plotting pedigrees.")
+  }
+
   renames <- matchIdNames(names(data))
   data <- rename(data, renames)
   stopifnot(all(c("ID", "FA", "MO", "SEX", "FAMID") %in% names(data)))
@@ -60,7 +68,7 @@ plotPed <- function(data, ped)
 
   # make `pedigree` object
   ped <- with(df, 
-    pedigree(id = ID, dadid = FA, momid = MO, sex = SEX, famid = FAMID, missid = ""))  
+    kinship2::pedigree(id = ID, dadid = FA, momid = MO, sex = SEX, famid = FAMID, missid = ""))  
 
   plot(ped[1])
 }
@@ -111,7 +119,7 @@ plotPed <- function(data, ped)
 #' @export
 plotManh <- function(A, alpha = 0.05, main, ...)
 {
-  stopifnot(require(qqman))
+  stopifnot(requireNamespace("qqman", quietly = TRUE))
 
   stopifnot(all(c("chr", "pSNP", "pos") %in% names(A$snpf)))
 
@@ -153,7 +161,7 @@ plotManh <- function(A, alpha = 0.05, main, ...)
 #' @export
 plotQQ <- function(A, df = 1, main, ...)
 {
-  stopifnot(require(qqman))
+  stopifnot(requireNamespace("qqman", quietly = TRUE))
 
   # get p-values
   stopifnot("pSNP" %in% names(A$snpf))
@@ -234,7 +242,7 @@ plotKinship2 <- function(x, y = c("image", "hist"))
 #' @export imageKinship2
 imageKinship2 <- function(x)
 { 
-  stopifnot(require(Matrix))
+  stopifnot(requireNamespace("Matrix", quietly = TRUE))
 
   Matrix::image(Matrix::Matrix(x))
 }

R/solarAssoc.R

@@ -506,11 +506,10 @@ run_assoc <- function(out, dir)
   trun_assoc$solar <- proc.time()
   parallel <- (cores > 1)
   if(parallel) {
-    ret <- require(doMC)
-    if(!ret) {
-      stop("`doMC` package is required for parallel calculations")
-    }
-    doMC::registerDoMC(cores)
+    # load required R package doParallel
+    stopifnot(requireNamespace("doParallel", quietly = TRUE))
+
+    doParallel::registerDoParallel(cores = cores)
   }
 
   ### case 1

R/solarMultipoint.R

@@ -301,11 +301,10 @@ run_multipoint <- function(out, dir)
   trun_multipoint$solar <- proc.time()
   parallel <- (cores > 1)
   if(parallel) {
-    ret <- require(doMC)
-    if(!ret) {
-      stop("`doMC` package is required for parallel calculations")
-    }
-    doMC::registerDoMC(cores)
+ # load required R package doParallel
+    stopifnot(requireNamespace("doParallel", quietly = TRUE))
+
+    doParallel::registerDoParallel(cores = cores)
   }
 
   if(cores == 1) {

R/support.lib.R

@@ -179,11 +179,10 @@ read_map_files <- function(files, cores = 1)
 {
   parallel <- (cores > 1)
   if(parallel) {
-    ret <- require(doMC)
-    if(!ret) {
-      stop("Error in `read_map_files`: `doMC` package is required for parallel calculations")
-    }
-    doMC::registerDoMC(cores)
+    # load required R package doParallel
+    stopifnot(requireNamespace("doParallel", quietly = TRUE))
+
+    doParallel::registerDoParallel(cores = cores)
   }
 
   map.list <- llply(files, function(f) try({
@@ -217,7 +216,7 @@ kmat2phi2 <- function(kmat, dir, kin2.gz = "kin2.gz")
 
 kf2phi2 <- function(kf, dir, kin2.gz = "kin2.gz")
 {
-  stopifnot(require(gdata))
+  #stopifnot(requireNamespace("gdata", quietly = TRUE))
 
   pedindex.out <- file.path(dir, "pedindex.out")
   pf <- read_pedindex(pedindex.out)

R/transforms.lib.R

@@ -174,7 +174,7 @@ transform_trait_inormal <- function(x, mean = 0, sd = 1)
   of <- of[with(of, order(sample)), ]
 
   ### duplicated values
-  y <- NULL # due to R CMD check: no visible binding for global variable ‘y’
+  y <- NULL # due to R CMD check: no visible binding
   of <- ddply(of, .(x), mutate, 
     y = median(y, na.rm = TRUE))