no idea

snoweye · snoweye · commit f5cf0d06c25e · 2016-01-07T01:50:09.000-05:00
diff --git a/ChangeLog b/ChangeLog
@@ -1,4 +1,4 @@
-2015-11-01: Ver. 0.1-8
+2015-11-01: Ver. 0.1-7
   * Change SPMD.CT$* to .pbd_env$SPMD.CT$*.
 
 2014-06-21: Ver. 0.1-7
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,12 @@
 Package: pmclust
 Version: 0.1-7
-Date: 2014-05-24
+Date: 2016-06-07
 Title: Parallel Model-Based Clustering
 Authors@R: c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email =
         "wccsnow@gmail.com"), person("George", "Ostrouchov", role = "aut"))
-Depends: R (>= 3.0.0), methods, rlecuyer, pbdMPI (>= 0.2-3), MASS,
-        pbdSLAP (>= 0.1-9), pbdBASE (>= 0.3-0), pbdDMAT (>= 0.3-0)
+Depends: R (>= 3.0.0), pbdMPI (>= 0.3-1), pbdBASE (>= 0.4-3), pbdDMAT
+        (>= 0.4-0)
+Imports: methods, MASS
 Enhances: MixSim
 LazyLoad: yes
 LazyData: yes
@@ -25,8 +26,8 @@ URL: http://r-pbd.org/
 BugReports: http://group.r-pbd.org/
 MailingList: Please send questions and comments regarding pbdR to
         RBigData@gmail.com
-Packaged: 2015-11-01 20:15:02 UTC; snoweye
+NeedsCompilation: yes
+Packaged: 2016-01-07 06:47:13 UTC; snoweye
 Author: Wei-Chen Chen [aut, cre],
   George Ostrouchov [aut]
 Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
-NeedsCompilation: yes
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,23 @@
 useDynLib(pmclust)
 
-import(methods, rlecuyer, pbdMPI, MASS, pbdSLAP, pbdBASE, pbdDMAT)
+import(methods, MASS, pbdBASE, pbdDMAT)
+importFrom(pbdMPI,spmd.allgather.integer)
+importFrom(pbdMPI,spmd.allgather.object)
+importFrom(pbdMPI,spmd.allreduce.integer)
+importFrom(pbdMPI,spmd.allreduce.double)
+importFrom(pbdMPI,spmd.bcast.integer)
+importFrom(pbdMPI,spmd.bcast.object)
+importFrom(pbdMPI,spmd.comm.rank)
+importFrom(pbdMPI,spmd.comm.size)
+importFrom(pbdMPI,spmd.isend.double)
+importFrom(pbdMPI,spmd.recv.double)
+importFrom(pbdMPI,spmd.wait)
+importFrom(pbdMPI,comm.all)
+importFrom(pbdMPI,comm.any)
+importFrom(pbdMPI,comm.cat)
+importFrom(pbdMPI,comm.size)
+importFrom(pbdMPI,comm.stop)
+importFrom(pbdMPI,get.jid)
 
 # exportPattern("^[[:alpha:]]+")
 # exportPattern("^[\\.]")
diff --git a/R/01_as_dmat.r b/R/01_as_dmat.r
@@ -1,6 +1,6 @@
 ### Convert X.spmd to X.dmat
 
-as.dmat <- function(X.spmd, bldim = pbdDMAT::.BLDIM, ICTXT = pbdDMAT::.ICTXT,
+as.dmat <- function(X.spmd, bldim = .pbd_env$BLDIM, ICTXT = .pbd_env$ICTXT,
     comm = .pbd_env$SPMD.CT$comm){
   X.spmd <- load.balance(X.spmd, comm = comm)
 
diff --git a/demo/dmat_em.r b/demo/dmat_em.r
@@ -1,6 +1,6 @@
 ### Setup mpi environment.
-library(pbdDMAT, quietly = TRUE)
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pbdDMAT, quietly = TRUE))
+suppressMessages(library(pmclust, quietly = TRUE))
 init.grid()
 comm.set.seed(123, diff = TRUE)
 
diff --git a/demo/dmat_kmeans.r b/demo/dmat_kmeans.r
@@ -1,6 +1,6 @@
 ### Setup mpi environment.
-library(pbdDMAT, quietly = TRUE)
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pbdDMAT, quietly = TRUE))
+suppressMessages(library(pmclust, quietly = TRUE))
 init.grid()
 comm.set.seed(123, diff = TRUE)
 
diff --git a/demo/ex_MixSim.r b/demo/ex_MixSim.r
@@ -1,5 +1,5 @@
 ### Setup environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ### Generate an example data.
diff --git a/demo/ex_aecm.r b/demo/ex_aecm.r
@@ -1,5 +1,5 @@
 ### Setup mpi environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ### Generate an example data.
diff --git a/demo/ex_apecm.r b/demo/ex_apecm.r
@@ -1,5 +1,5 @@
 ### Setup mpi environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ### Generate an example data.
diff --git a/demo/ex_apecma.r b/demo/ex_apecma.r
@@ -1,5 +1,5 @@
 ### Setup mpi environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ### Generate an example data.
diff --git a/demo/ex_em.r b/demo/ex_em.r
@@ -1,5 +1,5 @@
 ### Setup mpi environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ### Generate an example data.
diff --git a/demo/ex_kmeans.r b/demo/ex_kmeans.r
@@ -1,5 +1,5 @@
 ### Setup mpi environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ### Generate an example data.
diff --git a/demo/gbd_aecm.r b/demo/gbd_aecm.r
@@ -1,5 +1,5 @@
 ### Setup mpi environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ### Generate an example data.
diff --git a/demo/gbd_apecm.r b/demo/gbd_apecm.r
@@ -1,5 +1,5 @@
 ### Setup mpi environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ### Generate an example data.
diff --git a/demo/gbd_apecma.r b/demo/gbd_apecma.r
@@ -1,5 +1,5 @@
 ### Setup mpi environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ### Generate an example data.
diff --git a/demo/gbd_em.r b/demo/gbd_em.r
@@ -1,5 +1,5 @@
 ### Setup mpi environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ### Generate an example data.
diff --git a/demo/gbd_kmeans.r b/demo/gbd_kmeans.r
@@ -1,5 +1,5 @@
 ### Setup mpi environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ### Generate an example data.
diff --git a/demo/io_csv.r b/demo/io_csv.r
@@ -1,5 +1,5 @@
 ### Setup environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 if(comm.size() != 4){
   comm.stop("4 processors are needed.")
diff --git a/demo/iris_common.r b/demo/iris_common.r
@@ -1,5 +1,5 @@
 ### Setup environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 
 ### Load data
 X <- as.matrix(iris[, -5])
@@ -8,7 +8,7 @@ X <- as.matrix(iris[, -5])
 X.std <- scale(X)
 
 ### Clustering
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ret.mb1 <- pmclust(X.std, K = 3, method.own.X = "common")
diff --git a/demo/iris_dmat.r b/demo/iris_dmat.r
@@ -1,6 +1,6 @@
 ### Setup environment.
-library(pbdDMAT, quietly = TRUE)
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pbdDMAT, quietly = TRUE))
+suppressMessages(library(pmclust, quietly = TRUE))
 init.grid()
 
 ### Load data
@@ -13,7 +13,7 @@ X.dmat <- as.ddmatrix(X)
 X.std <- scale(X.dmat)
 
 ### Clustering
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ret.mb1 <- pmclust(X.std, K = 3)
diff --git a/demo/iris_gbdr.r b/demo/iris_gbdr.r
@@ -1,5 +1,5 @@
 ### Setup environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 
 ### Load data
 X <- as.matrix(iris[, -5])
@@ -17,7 +17,7 @@ std <- sqrt(allreduce(colSums(X.std^2 / (N - 1))))
 X.std <- sweep(X.std, 2, std, FUN = "/")
 
 ### Clustering
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ret.mb1 <- pmclust(X.std, K = 3)
diff --git a/demo/iris_single.r b/demo/iris_single.r
@@ -1,5 +1,5 @@
 ### Setup environment.
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 
 X.std <- NULL
 if(comm.rank() == .pbd_env$SPMD.CT$rank.source){
@@ -11,7 +11,7 @@ if(comm.rank() == .pbd_env$SPMD.CT$rank.source){
 }
 
 ### Clustering
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 ret.mb1 <- pmclust(X.std, K = 3, method.own.X = "single")
diff --git a/inst/CITATION b/inst/CITATION
@@ -2,20 +2,22 @@ citHeader("To cite pmclust in a publication use:")
 
 citEntry(
   entry = "Misc",
-  title = "pmclust: Parallel Model-Based Clustering",
+  title = "{pmclust}: Parallel Model-Based Clustering",
   author = personList(as.person("W.-C. Chen"), as.person("G. Ostrouchov")),
   year = "2012",
-  note = "R Package, URL http://cran.r-project.org/package=pmclust",
+  note = "R Package",
+  url = "http://cran.r-project.org/package=pmclust",
   textVersion = "W.-C. Chen, G. Ostrouchov (2012). pmclust: Parallel Model-Based Clustering. R Package, URL http://cran.r-project.org/package=pmclust",
   key = "Chen2012pmclustpackage"
 )
 
 citEntry(
   entry = "Manual",
-  title = "A Quick Guide to the pmclust Package",
+  title = "A Quick Guide to the {pmclust} Package",
   author = personList(as.person("W.-C. Chen"), as.person("G. Ostrouchov")),
   year = "2012",
-  note = "R Vignette, URL http://cran.r-project.org/package=pmclust",
+  note = "R Vignette",
+  url = "http://cran.r-project.org/package=pmclust",
   textVersion = "W.-C. Chen, G. Ostrouchov (2014). A Quick Guide for the pmclust Package. R Vignette, URL http://cran.r-project.org/package=pmclust",
   key = "Chen2012pmclustvignette"
 )
diff --git a/inst/doc/pmclust-guide.pdf b/inst/doc/pmclust-guide.pdf
diff --git a/man/50-as.dmat.spmd.Rd b/man/50-as.dmat.spmd.Rd
@@ -8,7 +8,7 @@
   GBD row-major to ddmatrix vice versa.
 }
 \usage{
-  as.dmat(X.spmd, bldim = pbdDMAT::.BLDIM, ICTXT = pbdDMAT::.ICTXT,
+  as.dmat(X.spmd, bldim = .pbd_env$BLDIM, ICTXT = .pbd_env$ICTXT,
           comm = .pbd_env$SPMD.CT$comm)
 
   as.gbd(X.dmat, comm = .pbd_env$SPMD.CT$comm)
diff --git a/tests/dmat_em.r b/tests/dmat_em.r
@@ -1,6 +1,6 @@
 ### Setup mpi environment.
-library(pbdDMAT, quietly = TRUE)
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pbdDMAT, quietly = TRUE))
+suppressMessages(library(pmclust, quietly = TRUE))
 init.grid()
 comm.set.seed(123, diff = TRUE)
 
diff --git a/tests/dmat_kmeans.r b/tests/dmat_kmeans.r
@@ -1,6 +1,6 @@
 ### Setup mpi environment.
-library(pbdDMAT, quietly = TRUE)
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pbdDMAT, quietly = TRUE))
+suppressMessages(library(pmclust, quietly = TRUE))
 init.grid()
 comm.set.seed(123, diff = TRUE)
 
diff --git a/tests/iris_em_dmat.r b/tests/iris_em_dmat.r
@@ -2,7 +2,7 @@
 # Run: mpiexec -np 4 Rscript iris_dmat.r
 
 rm(list = ls())                                       # Clean environment
-library(pbdDMAT, quietly = TRUE)                      # Load library
+suppressMessages(library(pbdDMAT, quietly = TRUE))                      # Load library
 init()
 init.grid()
 
@@ -17,7 +17,7 @@ X.dmat <- as.ddmatrix(X)
 X.std <- scale(X.dmat)
 
 ### Clustering
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 X.dmat <- X.std
diff --git a/tests/iris_em_spmd.r b/tests/iris_em_spmd.r
@@ -2,7 +2,7 @@
 # Run: mpiexec -np 4 Rscript iris_dmat.r
 
 rm(list = ls())                                       # Clean environment
-library(pbdDMAT, quietly = TRUE)                      # Load library
+suppressMessages(library(pbdDMAT, quietly = TRUE))                      # Load library
 init.grid()
 if(comm.size() >= 150 )
   comm.stop("Too many processors.")
@@ -20,7 +20,7 @@ jid <- get.jid(nrow(X.std))
 X.std <- X.std[jid,]
 
 ### Clustering
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 X.spmd <- X.std
diff --git a/tests/iris_kmeans_dmat.r b/tests/iris_kmeans_dmat.r
@@ -2,7 +2,7 @@
 # Run: mpiexec -np 4 Rscript iris_dmat.r
 
 rm(list = ls())                                       # Clean environment
-library(pbdDMAT, quietly = TRUE)                      # Load library
+suppressMessages(library(pbdDMAT, quietly = TRUE))                      # Load library
 init.grid()
 
 ### Load data
@@ -16,7 +16,7 @@ X.dmat <- as.ddmatrix(X)
 X.std <- scale(X.dmat)
 
 ### Clustering
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 X.dmat <- X.std
diff --git a/tests/iris_kmeans_spmd.r b/tests/iris_kmeans_spmd.r
@@ -2,7 +2,7 @@
 # Run: mpiexec -np 4 Rscript iris_dmat.r
 
 rm(list = ls())                                       # Clean environment
-library(pbdDMAT, quietly = TRUE)                      # Load library
+suppressMessages(library(pbdDMAT, quietly = TRUE))                      # Load library
 init.grid()
 if(comm.size() >= 150)
   comm.stop("Too many processors.")
@@ -20,7 +20,7 @@ jid <- get.jid(nrow(X.std))
 X.std <- X.std[jid,]
 
 ### Clustering
-library(pmclust, quietly = TRUE)
+suppressMessages(library(pmclust, quietly = TRUE))
 comm.set.seed(123, diff = TRUE)
 
 X.spmd <- X.std

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-2015-11-01: Ver. 0.1-8`
	`1`	`+2015-11-01: Ver. 0.1-7`
`2`	`2`	`* Change SPMD.CT$* to .pbd_env$SPMD.CT$*.`
`3`	`3`
`4`	`4`	`2014-06-21: Ver. 0.1-7`