update cran to 0.4.1

mcveanlab · Jul 24, 2017 · e094eae · e094eae
1 parent 3cae090
commit e094eae
Show file tree

Hide file tree

Showing 21 changed files with 101 additions and 23 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,5 +30,5 @@ Suggests:
 SystemRequirements: C++11
 VignetteBuilder: knitr
 LinkingTo: Rcpp
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
 Date: 2017-07-19
diff --git a/R/DEploidR.R b/R/DEploidR.R
@@ -127,6 +127,7 @@ extractPLAF <- function ( plafFileName ){
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
 #' panelFile = system.file("extdata", "labStrains.test.panel.txt", package = "DEploid")
 #' refFile = system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
@@ -135,6 +136,7 @@ extractPLAF <- function ( plafFileName ){
 #' PG0390CoverageTxt.deconv = dEploid(paste("-ref", refFile, "-alt", altFile,
 #'     "-plaf", plafFile, "-noPanel"))
 #' plotProportions( PG0390CoverageTxt.deconv$Proportions, "PG0390-C proportions" )
+#' }
 #'
 plotProportions <- function (proportions, title = "Components",
                        cex.lab = 1, cex.main = 1, cex.axis = 1 ){
@@ -338,6 +340,7 @@ plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
 #' PG0390CoverageVcf = extractCoverageFromVcf(vcfFile)
 #' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
@@ -346,6 +349,7 @@ plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
 #' prop = PG0390CoverageVcf.deconv$Proportions[dim(PG0390CoverageVcf.deconv$Proportions)[1],]
 #' expWSAF = t(PG0390CoverageVcf.deconv$Haps) %*% prop
 #' plotObsExpWSAF(obsWSAF, expWSAF)
+#' }
 #'
 plotObsExpWSAF <- function (obsWSAF, expWSAF,
                       title = "WSAF(observed vs expected)",

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -29,24 +29,26 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
 #' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
 #' set.seed(1234)
 #' PG0390.deconv = dEploid(paste("-vcf", vcfFile, "-plaf", plafFile, "-noPanel"))
+#' }
 #'
 dEploid <- function(args) {
-    .Call('DEploid_dEploid', PACKAGE = 'DEploid', args)
+    .Call(`_DEploid_dEploid`, args)
 }
 
 test_RRG_sample <- function() {
-    .Call('DEploid_test_RRG_sample', PACKAGE = 'DEploid')
+    .Call(`_DEploid_test_RRG_sample`)
 }
 
 test_RRG_sampleUnitExpo <- function() {
-    .Call('DEploid_test_RRG_sampleUnitExpo', PACKAGE = 'DEploid')
+    .Call(`_DEploid_test_RRG_sampleUnitExpo`)
 }
 
 test_RRG_sampleExpoExpoLimit <- function(lambda, b, limit) {
-    .Call('DEploid_test_RRG_sampleExpoExpoLimit', PACKAGE = 'DEploid', lambda, b, limit)
+    .Call(`_DEploid_test_RRG_sampleExpoExpoLimit`, lambda, b, limit)
 }
 
diff --git a/R/dEploid.R b/R/dEploid.R
@@ -1 +1,24 @@
+#' Deconvolute Mixed Genomes with Unknown Proportions
+#'
+#' Traditional phasing programs are limited to diploid organisms.
+#' Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo
+#' (MCMC) approaches, and builds a generic framework that allows haplotype searches
+#' in a multiple infection setting. This package is primarily developed as part of
+#' the Pf3k project, which is a global collaboration using the latest
+#' sequencing technologies to provide a high-resolution view of natural variation
+#' in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from
+#' patient blood sample, which often contains more than one parasite strain, with
+#' unknown proportions. This package is used for deconvoluting mixed haplotypes,
+#' and reporting the mixture proportions from each sample.
+#'
+#' @author
+#' Zhu Sha
+#'
+#' Maintainer: Joe Zhu \email{sha.joe.zhu@gmail.com}
+#'
+#' @name DEploid-package
+#' @docType package
+#'
+#' @importFrom Rcpp evalCpp
+#' @useDynLib _DEploid_dEploid
 NULL
diff --git a/buildLocally.sh b/buildLocally.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 PKG_NAME=$( cat DESCRIPTION | grep "Package:" | sed -e "s/Package: //g")
-Rscript -e "roxygen2::roxygenize(\"../${PKG_NAME}\")"
+Rscript -e "roxygen2::roxygenize(\"../${PKG_NAME}-r\")"
 
 # Building package
 R CMD build  .

diff --git a/man/DEploid-package.Rd b/man/DEploid-package.Rd
diff --git a/man/computeObsWSAF.Rd b/man/computeObsWSAF.Rd
diff --git a/man/dEploid.Rd b/man/dEploid.Rd
diff --git a/man/extractCoverageFromTxt.Rd b/man/extractCoverageFromTxt.Rd
diff --git a/man/extractCoverageFromVcf.Rd b/man/extractCoverageFromVcf.Rd
diff --git a/man/extractPLAF.Rd b/man/extractPLAF.Rd
diff --git a/man/haplotypePainter.Rd b/man/haplotypePainter.Rd
diff --git a/man/histWSAF.Rd b/man/histWSAF.Rd
diff --git a/man/plotAltVsRef.Rd b/man/plotAltVsRef.Rd
diff --git a/man/plotObsExpWSAF.Rd b/man/plotObsExpWSAF.Rd
diff --git a/man/plotProportions.Rd b/man/plotProportions.Rd
diff --git a/man/plotWSAFvsPLAF.Rd b/man/plotWSAFvsPLAF.Rd
diff --git a/src/Makevars.win b/src/Makevars.win
@@ -1,4 +1,4 @@
-OBJECTS.dEploidr = dEploidr.o test_exports.o RcppExports.o
+OBJECTS.dEploidr = dEploidr.o test_exports.o RcppExports.o init.o
 
 OBJECTS.dEploid = DEploid/panel.o \
     DEploid/ibd.o \
@@ -18,5 +18,5 @@ OBJECTS.dEploid = DEploid/panel.o \
 
 OBJECTS = $(OBJECTS.dEploidr) $(OBJECTS.dEploid)
 CXX_STD = CXX11
-PKG_CXXFLAGS = -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -DVERSION="\"R\"" -DRBUILD
+PKG_CXXFLAGS = -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -DVERSION="\"R\"" -DRBUILD
 PKG_LIBS = -lz
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -7,7 +7,7 @@ using namespace Rcpp;
 
 // dEploid
 List dEploid(std::string args);
-RcppExport SEXP DEploid_dEploid(SEXP argsSEXP) {
+RcppExport SEXP _DEploid_dEploid(SEXP argsSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
@@ -18,7 +18,7 @@ END_RCPP
 }
 // test_RRG_sample
 double test_RRG_sample();
-RcppExport SEXP DEploid_test_RRG_sample() {
+RcppExport SEXP _DEploid_test_RRG_sample() {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
@@ -28,7 +28,7 @@ END_RCPP
 }
 // test_RRG_sampleUnitExpo
 double test_RRG_sampleUnitExpo();
-RcppExport SEXP DEploid_test_RRG_sampleUnitExpo() {
+RcppExport SEXP _DEploid_test_RRG_sampleUnitExpo() {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
@@ -38,7 +38,7 @@ END_RCPP
 }
 // test_RRG_sampleExpoExpoLimit
 double test_RRG_sampleExpoExpoLimit(double lambda, double b, double limit);
-RcppExport SEXP DEploid_test_RRG_sampleExpoExpoLimit(SEXP lambdaSEXP, SEXP bSEXP, SEXP limitSEXP) {
+RcppExport SEXP _DEploid_test_RRG_sampleExpoExpoLimit(SEXP lambdaSEXP, SEXP bSEXP, SEXP limitSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;

diff --git a/src/dEploidr.cpp b/src/dEploidr.cpp
@@ -127,10 +127,12 @@ class RMcmcSample {
 //' @export
 //'
 //' @examples
+//' \dontrun{
 //' vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
 //' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
 //' set.seed(1234)
 //' PG0390.deconv = dEploid(paste("-vcf", vcfFile, "-plaf", plafFile, "-noPanel"))
+//' }
 //'
 // [[Rcpp::export]]
 List dEploid(std::string args) {

diff --git a/src/init.c b/src/init.c
@@ -0,0 +1,28 @@
+#include <R.h>
+#include <Rinternals.h>
+#include <stdlib.h> // for NULL
+#include <R_ext/Rdynload.h>
+
+/* FIXME:
+   Check these declarations against the C/Fortran source code.
+*/
+
+/* .Call calls */
+extern SEXP _DEploid_dEploid(SEXP);
+extern SEXP _DEploid_test_RRG_sample();
+extern SEXP _DEploid_test_RRG_sampleExpoExpoLimit(SEXP, SEXP, SEXP);
+extern SEXP _DEploid_test_RRG_sampleUnitExpo();
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_DEploid_dEploid",                      (DL_FUNC) &_DEploid_dEploid,                      1},
+    {"_DEploid_test_RRG_sample",              (DL_FUNC) &_DEploid_test_RRG_sample,              0},
+    {"_DEploid_test_RRG_sampleExpoExpoLimit", (DL_FUNC) &_DEploid_test_RRG_sampleExpoExpoLimit, 3},
+    {"_DEploid_test_RRG_sampleUnitExpo",      (DL_FUNC) &_DEploid_test_RRG_sampleUnitExpo,      0},
+    {NULL, NULL, 0}
+};
+
+void R_init_DEploid(DllInfo *dll)
+{
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}