Change to genv

Author: snoweye

ChangeLog

@@ -1,3 +1,6 @@
+2015-11-01: Ver. 0.1-8
+  * Change SPMD.CT$* to .pbd_env$SPMD.CT$*.
+
 2014-06-21: Ver. 0.1-7
   * Migrate to MS-MPI.
   * Get rid of jss.cls and jss.bst.

DESCRIPTION

@@ -25,7 +25,7 @@ URL: http://r-pbd.org/
 BugReports: http://group.r-pbd.org/
 MailingList: Please send questions and comments regarding pbdR to
         [email protected]
-Packaged: 2015-09-17 18:39:55 UTC; snoweye
+Packaged: 2015-11-01 20:15:02 UTC; snoweye
 Author: Wei-Chen Chen [aut, cre],
   George Ostrouchov [aut]
 Maintainer: Wei-Chen Chen <[email protected]>

R/000_globalVariables.r

@@ -0,0 +1,11 @@
+### Do not delete this file and file name!!
+### This file should be loaded before all other *.r files.
+
+### This is to avoid the false positive messages from R CMD check.
+###   "no visible binding for global variable"
+### Suggested by Prof Brian Ripley
+### ?globalVariables
+
+if(getRversion() >= "2.15.1"){
+  utils::globalVariables(c(".pmclustEnv", ".PMC.CT"))
+}

R/00_pmclust.r

@@ -3,7 +3,7 @@
 pmclust <- function(X = NULL, K = 2, MU = NULL,
     algorithm = .PMC.CT$algorithm, RndEM.iter = .PMC.CT$RndEM.iter,
     CONTROL = .PMC.CT$CONTROL, method.own.X = .PMC.CT$method.own.X,
-    rank.own.X = .SPMD.CT$rank.source, comm = .SPMD.CT$comm){
+    rank.own.X = .pbd_env$SPMD.CT$rank.source, comm = .pbd_env$SPMD.CT$comm){
   if(comm.all(is.null(X))){
     # Check global matrix.
     A <- exists("X.spmd", envir = .GlobalEnv)
@@ -68,7 +68,7 @@ pmclust <- function(X = NULL, K = 2, MU = NULL,
 pkmeans <- function(X = NULL, K = 2, MU = NULL,
     algorithm = c("kmeans", "kmeans.dmat"),
     CONTROL = .PMC.CT$CONTROL, method.own.X = .PMC.CT$method.own.X,
-    rank.own.X = .SPMD.CT$rank.source, comm = .SPMD.CT$comm){
+    rank.own.X = .pbd_env$SPMD.CT$rank.source, comm = .pbd_env$SPMD.CT$comm){
   if(comm.all(is.null(X))){
     # Check global matrix.
     A <- exists("X.spmd", envir = .GlobalEnv)

R/00_pmclust_internal.r

@@ -3,7 +3,7 @@
 pmclust.internal <- function(X = NULL, K = 2, MU = NULL,
     algorithm = .PMC.CT$algorithm.gbd, RndEM.iter = .PMC.CT$RndEM.iter,
     CONTROL = .PMC.CT$CONTROL, method.own.X = .PMC.CT$method.own.X,
-    rank.own.X = .SPMD.CT$rank.source, comm = .SPMD.CT$comm){
+    rank.own.X = .pbd_env$SPMD.CT$rank.source, comm = .pbd_env$SPMD.CT$comm){
   # Check.
   if(! (algorithm[1] %in% .PMC.CT$algorithm.gbd)){
     comm.stop("The algorithm is not supported")

R/00_pmclust_internal_dmat.r

@@ -3,7 +3,7 @@
 pmclust.internal.dmat <- function(X = NULL, K = 2, MU = NULL,
     algorithm = .PMC.CT$algorithm.dmat, RndEM.iter = .PMC.CT$RndEM.iter,
     CONTROL = .PMC.CT$CONTROL, method.own.X = .PMC.CT$method.own.X,
-    rank.own.X = .SPMD.CT$rank.source, comm = .SPMD.CT$comm){
+    rank.own.X = .pbd_env$SPMD.CT$rank.source, comm = .pbd_env$SPMD.CT$comm){
   # Check.
   if(! (algorithm[1] %in% .PMC.CT$algorithm.dmat)){
     comm.stop("The algorithm is not supported.")

R/01_as_dmat.r

@@ -1,7 +1,7 @@
 ### Convert X.spmd to X.dmat
 
 as.dmat <- function(X.spmd, bldim = pbdDMAT::.BLDIM, ICTXT = pbdDMAT::.ICTXT,
-    comm = .SPMD.CT$comm){
+    comm = .pbd_env$SPMD.CT$comm){
   X.spmd <- load.balance(X.spmd, comm = comm)
 
   N.spmd <- nrow(X.spmd)

R/01_as_spmd.r

@@ -1,6 +1,6 @@
 ### Convert X.dmat to X.spmd
 
-as.spmd <- function(X.dmat, comm = .SPMD.CT$comm){
+as.spmd <- function(X.dmat, comm = .pbd_env$SPMD.CT$comm){
   COMM.SIZE <- comm.size(comm)
 
   ### check data.
@@ -12,7 +12,7 @@ as.spmd <- function(X.dmat, comm = .SPMD.CT$comm){
 
   ### block-cyclic in context 2.
   bldim.new <- c(ceiling(nrow(X.dmat) / COMM.SIZE), ncol(X.dmat))
-  X.dmat <- pbdDMAT::dmat.reblock(X.dmat, bldim = bldim.new, ICTXT = 2)
+  X.dmat <- pbdDMAT::reblock(X.dmat, bldim = bldim.new, ICTXT = 2)
 
   ### copy to spmd.
   if(pbdBASE::base.ownany(dim(X.dmat), pbdDMAT::bldim(X.dmat), ICTXT = 2)){

R/02_convert_data.r

@@ -1,7 +1,7 @@
 ### For general methods.
 
 convert.data <- function(X, method.own.X = .PMC.CT$method.own.X,
-    rank.own.X = .SPMD.CT$rank.source, comm = .SPMD.CT$comm){
+    rank.own.X = .pbd_env$SPMD.CT$rank.source, comm = .pbd_env$SPMD.CT$comm){
   COMM.SIZE <- spmd.comm.size(comm)
   COMM.RANK <- spmd.comm.rank(comm)
 

R/02_load_balance.r

@@ -1,6 +1,6 @@
 ### This file contains functions to load balance of data X.spmd.
 
-balance.info <- function(X.spmd, comm = .SPMD.CT$comm,
+balance.info <- function(X.spmd, comm = .pbd_env$SPMD.CT$comm,
     spmd.major = 1, method = c("block.cyclic", "block0")){
   COMM.SIZE <- spmd.comm.size(comm)
   COMM.RANK <- spmd.comm.rank(comm)
@@ -64,7 +64,7 @@ balance.info <- function(X.spmd, comm = .SPMD.CT$comm,
 } # End of balance.info()
 
 
-load.balance <- function(X.spmd, bal.info = NULL, comm = .SPMD.CT$comm,
+load.balance <- function(X.spmd, bal.info = NULL, comm = .pbd_env$SPMD.CT$comm,
     spmd.major = 1){
   COMM.RANK <- spmd.comm.rank(comm)
   if(is.null(bal.info)){
@@ -149,7 +149,7 @@ load.balance <- function(X.spmd, bal.info = NULL, comm = .SPMD.CT$comm,
 } # End of load.balance().
 
 
-unload.balance <- function(new.X.spmd, bal.info, comm = .SPMD.CT$comm){
+unload.balance <- function(new.X.spmd, bal.info, comm = .pbd_env$SPMD.CT$comm){
   rev.bal.info <- list(send = data.frame(org = bal.info$recv$belong,
                                          belong = bal.info$recv$org),
                        recv = data.frame(org = bal.info$send$belong,