rerun revdep_check()

revdep/README.md

@@ -2,21 +2,29 @@
 
 |field    |value                        |
 |:--------|:----------------------------|
-|version  |R version 3.5.2 (2018-12-20) |
+|version  |R version 3.6.3 (2020-02-29) |
 |os       |Windows 7 x64 SP 1           |
 |system   |x86_64, mingw32              |
 |ui       |RStudio                      |
 |language |(EN)                         |
 |collate  |English_United States.1252   |
 |ctype    |English_United States.1252   |
 |tz       |America/New_York             |
-|date     |2019-05-29                   |
+|date     |2020-10-29                   |
 
 # Dependencies
 
-|package |old   |new |<U+0394>  |
-|:-------|:-----|:---|:--|
-|matlib  |0.9.1 |NA  |*  |
+|package       |old   |new        |<U+0394>  |
+|:-------------|:-----|:----------|:--|
+|matlib        |0.9.4 |0.9.4      |   |
+|digest        |NA    |0.6.27     |*  |
+|openxlsx      |NA    |4.2.3      |*  |
+|ps            |NA    |1.4.0      |*  |
+|quantreg      |NA    |5.75       |*  |
+|R6            |NA    |2.5.0      |*  |
+|RcppArmadillo |NA    |0.10.1.0.0 |*  |
+|rlang         |NA    |0.4.8      |*  |
+|sp            |NA    |1.4-4      |*  |
 
 # Revdeps
 

revdep/checks/MPkn/new/MPkn.Rcheck/00check.log

@@ -0,0 +1,90 @@
+* using log directory 'C:/Users/friendly/Dropbox/R/projects/matlib/revdep/checks/MPkn/new/MPkn.Rcheck'
+* using R version 3.6.3 (2020-02-29)
+* using platform: x86_64-w64-mingw32 (64-bit)
+* using session charset: ISO8859-1
+* using options '--no-manual --no-build-vignettes'
+* checking for file 'MPkn/DESCRIPTION' ... OK
+* checking extension type ... Package
+* this is package 'MPkn' version '0.1.0'
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: 'markovchain'
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking whether package 'MPkn' can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking 'build' directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking sizes of PDF files under 'inst/doc' ... OK
+* checking installed files from 'inst/doc' ... OK
+* checking files in 'vignettes' ... OK
+* checking examples ... ERROR
+Running examples in 'MPkn-Ex.R' failed
+The error most likely occurred in:
+
+> ### Name: MPkn-package
+> ### Title: Calculations of One Discrete Model in Several Time Steps
+> ### Aliases: MPkn-package
+> 
+> ### ** Examples
+> 
+> require(MPkn)
+> require(markovchain)
+Loading required package: markovchain
+Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
+  there is no package called 'markovchain'
+> options(digits = 14)
+> n = 12
+> k = 2
+> rz = 11
+> P = array(0, c(rz, rz))
+> for (i in 1:rz){
++   po = runif(rz)
++   P[i, ] = po/sum(po)
++ }
+> I = diag(1, rz, rz)
+> Myy = MUPkL(P, P, I, n, k, c(1:rz))
+> StSy = NULL
+> for (i in 1:rz) StSy = c(StSy, Myy$Navg[,,i][n])
+> mrkv = new("markovchain", transitionMatrix = P)
+Error in getClass(Class, where = topenv(parent.frame())) : 
+  "markovchain" is not a defined class
+Calls: new -> getClass
+Execution halted
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in 'inst/doc' ... OK
+* checking running R code from vignettes ... NONE
+  'Fundament.Rmd'using 'UTF-8'... OK
+* checking re-building of vignette outputs ... SKIPPED
+* DONE
+Status: 1 ERROR, 1 NOTE

revdep/checks/MPkn/new/MPkn.Rcheck/00install.out

@@ -0,0 +1,14 @@
+* installing *source* package 'MPkn' ...
+** package 'MPkn' successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** inst
+** byte-compile and prepare package for lazy loading
+** help
+*** installing help indices
+** building package indices
+** installing vignettes
+** testing if installed package can be loaded from temporary location
+** testing if installed package can be loaded from final location
+** testing if installed package keeps a record of temporary installation path
+* DONE (MPkn)

revdep/checks/MPkn/new/MPkn.Rcheck/MPkn-Ex.R

@@ -0,0 +1,206 @@
+pkgname <- "MPkn"
+source(file.path(R.home("share"), "R", "examples-header.R"))
+options(warn = 1)
+options(pager = "console")
+library('MPkn')
+
+base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
+base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
+cleanEx()
+nameEx("MPKlMatrix")
+### * MPKlMatrix
+
+flush(stderr()); flush(stdout())
+
+### Name: MPKlMatrix
+### Title: Creates a matrix of specified row of output 'MUPkLo'
+### Aliases: MPKlMatrix
+### Keywords: MPKlMatrix
+
+### ** Examples
+
+A <- array(c(0.9, 0.6, 0.8, 0.05, 0.2, 0.05, 0.05, 0.2, 0.15), c(3, 3))
+P <- array(c(0.9, 0.6, 0.8, 0.05, 0.2, 0.05, 0.05, 0.2, 0.15), c(3, 3))
+U <- array(c(0.8, 0.8, 0.7, 0.06, 0.02, 0.2, 0.14, 0.18, 0.1), c(3, 3))
+sta <- c(1, 2, 3)
+k <- c(1, 0, 1, 0)
+n <- c(5, 7, 12, 17)
+Mx <- MUPkLo(A, P, U, n, k, sta)
+M100 = MPKlMatrix(Mx, step = 100, nc = 3, sta = c(1, 2, 3))
+
+
+
+cleanEx()
+nameEx("MPkn-package")
+### * MPkn-package
+
+flush(stderr()); flush(stdout())
+
+### Name: MPkn-package
+### Title: Calculations of One Discrete Model in Several Time Steps
+### Aliases: MPkn-package
+
+### ** Examples
+
+require(MPkn)
+require(markovchain)
+options(digits = 14)
+n = 12
+k = 2
+rz = 11
+P = array(0, c(rz, rz))
+for (i in 1:rz){
+  po = runif(rz)
+  P[i, ] = po/sum(po)
+}
+I = diag(1, rz, rz)
+Myy = MUPkL(P, P, I, n, k, c(1:rz))
+StSy = NULL
+for (i in 1:rz) StSy = c(StSy, Myy$Navg[,,i][n])
+mrkv = new("markovchain", transitionMatrix = P)
+StSx = steadyStates(mrkv)
+print("MPkn");  print(StSy)
+print("markovchain"); print(StSx)
+
+
+
+
+cleanEx()
+nameEx("MUPkL")
+### * MUPkL
+
+flush(stderr()); flush(stdout())
+
+### Name: MUPkL
+### Title: Calculations of one discrete model in several time steps
+### Aliases: MUPkL
+### Keywords: MUPkL
+
+### ** Examples
+
+A <- array(c(2, 3, 1, 4, 2, 1, 3, 1, 2), c(3, 3))
+P <- array(c(0.9, 0.6, 0.8, 0.05, 0.2, 0.05, 0.05, 0.2, 0.15),
+					 c(3, 3))
+U <- array(c(0.8, 0.8, 0.7, 0.06, 0.02, 0.2, 0.14, 0.18, 0.1),
+					 c(3, 3))
+sta <- c(1, 3)
+k <- 3
+n <- 8
+M33 <- MUPkL(A, P, U, n, k, sta)
+print(M33$N)
+k <- 1
+n <- 24
+M11 <- MUPkL(A, P, U, n, k, sta)
+print(M11$N)
+k <- 0
+n <- 6
+M00 <- MUPkL(A, P, U, n, k, sta)
+print(M00$N)
+
+
+
+cleanEx()
+nameEx("MUPkLo")
+### * MUPkLo
+
+flush(stderr()); flush(stdout())
+
+### Name: MUPkLo
+### Title: Calculations of one discrete model in several time steps
+### Aliases: MUPkLo
+### Keywords: MUPkLo
+
+### ** Examples
+
+A = array(c(-2, -3, 1, 4, -2, 1, 3, -1, -2), c(3, 3))
+P <- array(c(0.9, 0.6, 0.8, 0.05, 0.2, 0.05, 0.05, 0.2, 0.15), c(3, 3))
+U <- array(c(0.8, 0.8, 0.7, 0.06, 0.02, 0.2, 0.14, 0.18, 0.1), c(3, 3))
+sta <- 3
+Ao <- A
+k <- c(1, 0, 1, 0)
+n <- c(5, 7, 12, 17)
+# Steps, in which will compute the value of the Mx:
+# 1, 2, 3, 4, 5, 10, 20, 21,  22, 23, 24, 25, 50, 100, 200, 400, 800
+Mx <- MUPkLo(A, P, U, n, k, sta)
+print(Mx)
+A <- Ao
+Mb <- MUPkLo(A, P, U, n = 100, k = 1, sta)
+Mb[100,,]
+
+
+
+cleanEx()
+nameEx("matrix.powerni")
+### * matrix.powerni
+
+flush(stderr()); flush(stdout())
+
+### Name: matrix.powerni
+### Title: Matrix Power of Non Integer
+### Aliases: matrix.powerni
+### Keywords: matrix.powerni
+
+### ** Examples
+
+require(MPkn)
+require(matrixcalc)
+matmult <- function(A, B){
+	C = matrix(numeric(4), 2, 2)
+	for (i in 1:2){
+		for (j in 1:2){ C[i, j] = sum(A[i, ]*B[, j])}
+	}
+	return(C)
+}
+I = diag(1, 2, 2)
+P = matrix(c(0.9, 0.3, 0.1, 0.7), 2, 2)
+M1 = P
+M2 = matmult((I + P), M1)
+M4 = matmult((I + t(matrix.power(P, 2))), M2)
+M8 = matmult((I + t(matrix.power(P, 4))), M4)
+M16 = matmult((I + t(matrix.power(P, 8))), M8)
+## =====================
+Q = list()
+Q[[1]] = M1
+Q[[2]] = matmult(M2, matrix.inverse(M1)) - I
+Q[[3]] = matrix.powerni(matmult(M4, matrix.inverse(M2)) - I, 1/2)
+Q[[4]] = matrix.powerni(matmult(M8, matrix.inverse(M4)) - I, 1/4)
+Q[[5]] = matrix.powerni(matmult(M16, matrix.inverse(M8)) - I, 1/8)
+print("Q"); print(Q)
+S = as.matrix(Q[[1]], 2, 2)
+for (i in 2:5){
+  S = S + as.matrix(Q[[i]], 2, 2)
+}
+Qs = S/5
+print("Qs"); print(Qs)
+
+
+
+cleanEx()
+nameEx("radekW")
+### * radekW
+
+flush(stderr()); flush(stdout())
+
+### Name: radekW
+### Title: The Numbers of Rows of the Output Matrix
+### Aliases: radekW
+### Keywords: radekW
+
+### ** Examples
+
+  radekW(n = c(3, 5, 8, 9, 11), k = c(1, 0, 1, 0, 0))
+
+
+
+### * <FOOTER>
+###
+cleanEx()
+options(digits = 7L)
+base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
+grDevices::dev.off()
+###
+### Local variables: ***
+### mode: outline-minor ***
+### outline-regexp: "\\(> \\)?### [*]+" ***
+### End: ***
+quit('no')