CRAN Package Check Results for Package copula

Last updated on 2020-01-27 00:48:00 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.999-19.1 49.60 1097.50 1147.10 OK
r-devel-linux-x86_64-debian-gcc 0.999-19.1 44.14 743.36 787.50 ERROR
r-devel-linux-x86_64-fedora-clang 0.999-19.1 1323.97 NOTE
r-devel-linux-x86_64-fedora-gcc 0.999-19.1 1020.55 OK
r-devel-windows-ix86+x86_64 0.999-19.1 125.00 956.00 1081.00 NOTE --no-vignettes
r-devel-windows-ix86+x86_64-gcc8 0.999-19.1 128.00 961.00 1089.00 NOTE --no-vignettes
r-patched-linux-x86_64 0.999-19.1 46.13 969.38 1015.51 OK
r-patched-solaris-x86 0.999-19.1 1509.50 NOTE
r-release-linux-x86_64 0.999-19.1 41.99 965.88 1007.87 OK
r-release-windows-ix86+x86_64 0.999-19.1 82.00 1013.00 1095.00 NOTE --no-vignettes
r-release-osx-x86_64 0.999-19.1 NOTE
r-oldrel-windows-ix86+x86_64 0.999-19.1 82.00 834.00 916.00 NOTE --no-vignettes
r-oldrel-osx-x86_64 0.999-19.1 NOTE

Additional issues

LTO

Check Details

Version: 0.999-19.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘sfsmisc’
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.999-19.1
Check: examples
Result: ERROR
    Running examples in ‘copula-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: pairsRosenblatt
    > ### Title: Plots for Graphical GOF Test via Pairwise Rosenblatt Transforms
    > ### Aliases: pairsRosenblatt pairsColList
    > ### Keywords: hplot multivariate
    >
    > ### ** Examples
    >
    > ## 2-dim example {d = 2} ===============
    > ##
    > ## "t" Copula with 22. degrees of freedom; and (pairwise) tau = 0.5
    > nu <- 2.2 # degrees of freedom
    > ## Define the multivariate distribution
    > tCop <- ellipCopula("t", param=iTau(ellipCopula("t", df=nu), tau = 0.5),
    + dim=2, df=nu)
    > set.seed(19)
    > X <- qexp(rCopula(n = 400, tCop))
    >
    > ## H0 (wrongly): a Normal copula, with correct tau
    > copH0 <- ellipCopula("normal", param=iTau(ellipCopula("normal"), tau = 0.5))
    >
    > ## create array of pairwise copH0-transformed data columns
    > cu.u <- pairwiseCcop(pobs(X), copula = copH0)
    >
    > ## compute pairwise matrix of p-values and corresponding colors
    > pwIT <- pairwiseIndepTest(cu.u, N=200) # (d,d)-matrix of test results
    pairwiseIndepTest( (n=400, d=2)): indepTestSim(*, N=200) .. 1 simulate_empirical() working with double array J of size 320000 | | 0%
     | | 1%
     |= | 2%
     |== | 3%
     |== | 4%
     |=== | 5%
     |==== | 6%
     |==== | 7%
     |===== | 8%
     |====== | 9%
     |======= | 10%
     |======= | 11%
     |======== | 12%
     |========= | 13%
     |========= | 14%
     |========== | 15%
     |=========== | 16%
     |=========== | 17%
     |============ | 18%
     |============= | 19%
     |============== | 20%
     |============== | 21%
     |=============== | 22%
     |================ | 23%
     |================ | 24%
     |================= | 25%
     |================== | 26%
     |================== | 27%
     |=================== | 28%
     |==================== | 28%
     |===================== | 30%
     |===================== | 31%
     |====================== | 32%
     |======================= | 33%
     |======================= | 34%
     |======================== | 35%
     |========================= | 36%
     |========================= | 37%
     |========================== | 38%
     |=========================== | 39%
     |============================ | 40%
     |============================ | 41%
     |============================= | 42%
     |============================== | 43%
     |============================== | 44%
     |=============================== | 45%
     |================================ | 46%
     |================================ | 47%
     |================================= | 48%
     |================================== | 49%
     |=================================== | 50%
     |=================================== | 51%
     |==================================== | 52%
     |===================================== | 53%
     |===================================== | 54%
     |====================================== | 55%
     |======================================= | 56%
     |======================================= | 56%
     |======================================== | 57%
     |========================================= | 59%
     |========================================== | 60%
     |========================================== | 61%
     |=========================================== | 62%
     |============================================ | 63%
     |============================================ | 64%
     |============================================= | 65%
     |============================================== | 66%
     |============================================== | 67%
     |=============================================== | 68%
     |================================================ | 69%
     |================================================= | 70%
     |================================================= | 71%
     |================================================== | 72%
     |=================================================== | 73%
     |=================================================== | 74%
     |==================================================== | 75%
     |===================================================== | 76%
     |===================================================== | 77%
     |====================================================== | 78%
     |======================================================= | 79%
     |======================================================== | 80%
     |======================================================== | 81%
     |========================================================= | 82%
     |========================================================== | 83%
     |========================================================== | 84%
     |=========================================================== | 85%
     |============================================================ | 86%
     |============================================================ | 87%
     |============================================================= | 88%
     |============================================================== | 89%
     |=============================================================== | 90%
     |=============================================================== | 91%
     |================================================================ | 92%
     |================================================================= | 93%
     |================================================================= | 94%
     |================================================================== | 95%
     |=================================================================== | 96%
     |=================================================================== | 97%
     |==================================================================== | 98%
     |===================================================================== | 99%
     |======================================================================| 100%
    2 *Sim done
    >
    > round(pmat <- pviTest(pwIT), 3) # pick out p-values
     [,1] [,2]
    [1,] NA 0.007
    [2,] 0.032 NA
    > ## .286 and .077
    > pairsRosenblatt(cu.u, pvalueMat= pmat)
    Loading required namespace: colorspace
    Error in loadNamespace(name) : there is no package called ‘sfsmisc’
    Calls: pairsRosenblatt ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.999-19.1
Check: tests
Result: ERROR
     Running ‘Stirling-etc.R’ [11s/16s]
     Running ‘copula-play.R’ [25s/35s]
     Running ‘dC-dc-ex.R’ [4s/5s]
     Running ‘estim-ex.R’ [7s/9s]
     Running ‘explicitCop-ex.R’ [17s/25s]
     Running ‘fitting-ex.R’ [11s/15s]
     Running ‘fixedPar-ex.R’ [8s/12s]
     Running ‘ggraph-tst.R’ [2s/4s]
     Running ‘khoudraji-ex.R’ [18s/27s]
     Running ‘misc.R’ [2s/3s]
     Running ‘mixCop-tst.R’ [2s/4s]
     Running ‘moments.R’ [3s/5s]
     Running ‘nac-experi.R’ [13s/17s]
     Running ‘retstable-ex.R’ [4s/5s]
     Running ‘rstable-ex.R’ [5s/7s]
     Running ‘tail-pcopula.R’ [2s/3s]
     Comparing ‘tail-pcopula.Rout’ to ‘tail-pcopula.Rout.save’ ... OK
    Running the tests in ‘tests/ggraph-tst.R’ failed.
    Complete output:
     > require(copula)
     Loading required package: copula
     > doX <- FALSE # no "doExtras" -- be fast
     >
     > demo(gof_graph)
    
    
     demo(gof_graph)
     ---- ~~~~~~~~~
    
     > ## Copyright (C) 2012 Marius Hofert and Martin Maechler
     > ##
     > ## This program is free software; you can redistribute it and/or modify it under
     > ## the terms of the GNU General Public License as published by the Free Software
     > ## Foundation; either version 3 of the License, or (at your option) any later
     > ## version.
     > ##
     > ## This program is distributed in the hope that it will be useful, but WITHOUT
     > ## ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
     > ## FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
     > ## details.
     > ##
     > ## You should have received a copy of the GNU General Public License along with
     > ## this program; if not, see <http://www.gnu.org/licenses/>.
     >
     >
     > ### setup ######################################################################
     >
     > require(copula)
    
     > doPDF <- !dev.interactive(orNone=TRUE)
    
     > if(!(exists("setSeeds") && is.logical(as.logical(setSeeds))))
     + setSeeds <- TRUE # for reproducibility
    
     > ## maybe set to FALSE *before* running this demo
     >
     > if(interactive()) readline(
     + "NOTE: Set doX <- TRUE before running this demo 'realistically' ok? ")
    
     > if(!(exists("doX") && is.logical(as.logical(doX))))
     + print(doX <- copula:::doExtras())
    
     > if(!doX)
     + cat("** doX is FALSE ==> unrealistically small N, but speed for testing.\n")
     ** doX is FALSE ==> unrealistically small N, but speed for testing.
    
     > (N <- if(doX) 256 else 32)# be fast when run as "check"
     [1] 32
    
     > ### Example 1: 5d Gumbel copula ################################################
     >
     > ## setup
     > n <- if(doX) 1000 else 250 # sample size
    
     > d <- 5 # dimension
    
     > family <- "Gumbel" # copula family
    
     > tau <- 0.5
    
     > if(setSeeds) set.seed(1)
    
     > ## define and sample the copula (= H0 copula), build pseudo-observations
     > cop <- getAcop(family)
    
     > th <- cop@iTau(tau) # correct parameter value
    
     > copH0 <- onacopulaL(family, list(th, 1:d)) # define H0 copula
    
     > U. <- pobs(rCopula(n, cop=copH0))
    
     > ## create array of pairwise copH0-transformed data columns
     > cu.u <- pairwiseCcop(U., copH0)
    
     > stopifnot(is.array(cu.u), dim(cu.u) == c(n,d,d)) # check
    
     > ## compute pairwise matrix of p-values and corresponding colors
     > pwIT <- pairwiseIndepTest(cu.u, N=N, verbose=interactive()) # (d,d)-matrix of test results
    
     > round(pmat <- pviTest(pwIT), 3) # pick out p-values
     [,1] [,2] [,3] [,4] [,5]
     [1,] NA 0.924 0.530 0.379 0.985
     [2,] 0.682 NA 0.439 0.439 0.682
     [3,] 0.924 0.652 NA 0.652 0.924
     [4,] 0.682 0.742 0.439 NA 0.712
     [5,] 0.924 0.682 0.924 0.864 NA
    
     > ## Here (with seed=1): no significant ones, smallest = 0.0603
     > str(cc <- pairsColList(pmat)) # compute corresponding colors
     Loading required namespace: colorspace
     List of 4
     $ fgColMat : chr [1:5, 1:5] "#000000" "#000000" "#000000" "#000000" ...
     $ bgColMat : chr [1:5, 1:5] "transparent" "#F4EFC8" "#F4EFC8" "#F4EFC8" ...
     $ bucketCols : chr [1:6] "#0066CC" "#995CD8" "#D35DD3" "#FFAD8B" ...
     $ pvalueBuckets: num [1:7] 1e-04 1e-03 1e-02 5e-02 1e-01 ...
    
     > ## which pairs violate H0? [none, here]
     > which(pmat < 0.05, arr.ind=TRUE)
     row col
    
     > ## check whether p-values are uniform -- only if we have "many" (~ d^2)
     > if(d > 10){
     + n. <- d*(d-1)
     + qqplot(qunif(ppoints(n.)), sort(pmat), main = paste("n = ",n.))
     + abline(0,1)
     + }
    
     > ## Artificially more extreme P-values: {to see more}
     > pm.0 <- pmat
    
     > pm.0[1,2] <- 5.0e-3
    
     > pm.0[3,2] <- 0.03
    
     > pm.0[5,2] <- 0.9e-3
    
     > ### Example 1 b): Plots ########################################################
     >
     > ## 1a) plain (too large plot symbols here)
     > pairsRosenblatt(cu.u, pvalueMat=pmat)
     Error in loadNamespace(name) : there is no package called 'sfsmisc'
     Calls: demo ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
     In addition: Warning message:
     In indepTestSim(n, p = 2, m = 2, N = N, verbose = idT.verbose, ...) :
     N should be at least 100
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.999-19.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘AC_Liouville.Rmd’ using rmarkdown
    Loading required package: copula
    --- finished re-building ‘AC_Liouville.Rmd’
    
    --- re-building ‘AR_Clayton.Rmd’ using rmarkdown
    Loading required package: copula
    --- finished re-building ‘AR_Clayton.Rmd’
    
    --- re-building ‘GIG.Rmd’ using rmarkdown
    Loading required package: tools
    Loading required namespace: Runuran
    Loading required package: copula
    Loading required package: bbmle
    Loading required package: stats4
    Loading required package: lattice
    Loading required package: grid
    --- finished re-building ‘GIG.Rmd’
    
    --- re-building ‘HAXC.Rmd’ using rmarkdown
    --- finished re-building ‘HAXC.Rmd’
    
    --- re-building ‘NALC.Rmd’ using rmarkdown
    Loading required package: gsl
    Loading required package: copula
    
    Attaching package: 'copula'
    
    The following objects are masked from 'package:gsl':
    
     psi, sinc
    
    --- finished re-building ‘NALC.Rmd’
    
    --- re-building ‘copula_GARCH.Rmd’ using rmarkdown
    Loading required package: copula
    Loading required package: rugarch
    Loading required package: parallel
    
    Attaching package: 'rugarch'
    
    The following object is masked from 'package:stats':
    
     sigma
    
    --- finished re-building ‘copula_GARCH.Rmd’
    
    --- re-building ‘dNAC.Rmd’ using rmarkdown
    Loading required package: copula
    Loading required package: grid
    Loading required package: lattice
    --- finished re-building ‘dNAC.Rmd’
    
    --- re-building ‘empiricial_copulas.Rmd’ using rmarkdown
    --- finished re-building ‘empiricial_copulas.Rmd’
    
    --- re-building ‘logL_visualization.Rmd’ using rmarkdown
    Loading required package: copula
    --- finished re-building ‘logL_visualization.Rmd’
    
    --- re-building ‘qrng.Rmd’ using rmarkdown
    Loading required package: stats4
    Loading required package: splines
    
    Attaching package: 'VGAM'
    
    The following objects are masked from 'package:copula':
    
     log1mexp, log1pexp, rlog
    
    Loading required package: rngWELL
    This is randtoolbox. For an overview, type 'help("randtoolbox")'.
    
    Attaching package: 'randtoolbox'
    
    The following object is masked from 'package:qrng':
    
     sobol
    
    --- finished re-building ‘qrng.Rmd’
    
    --- re-building ‘wild_animals.Rmd’ using rmarkdown
    Quitting from lines 290-294 (wild_animals.Rmd)
    Error: processing vignette 'wild_animals.Rmd' failed with diagnostics:
    there is no package called 'sfsmisc'
    --- failed re-building ‘wild_animals.Rmd’
    
    --- re-building ‘Frank-Rmpfr.Rnw’ using Sweave
    Loading required package: copula
    Loading required package: Rmpfr
    Loading required package: gmp
    
    Attaching package: 'gmp'
    
    The following objects are masked from 'package:copula':
    
     Eulerian, Eulerian.all, Stirling1, Stirling1.all, Stirling2,
     Stirling2.all
    
    The following objects are masked from 'package:base':
    
     %*%, apply, crossprod, matrix, tcrossprod
    
    C code of R package 'Rmpfr': GMP using 64 bits per limb
    
    
    Attaching package: 'Rmpfr'
    
    The following object is masked from 'package:gmp':
    
     outer
    
    The following object is masked from 'package:copula':
    
     Bernoulli
    
    The following objects are masked from 'package:stats':
    
     dbinom, dgamma, dnorm, dpois, pnorm
    
    The following objects are masked from 'package:base':
    
     cbind, pmax, pmin, rbind
    
    --- finished re-building ‘Frank-Rmpfr.Rnw’
    
    --- re-building ‘nacopula-pkg.Rnw’ using Sweave
    Loading required package: copula
    Loading required package: lattice
    Warning: 'pnacopula' is deprecated.
    Use 'pCopula' instead.
    See help("Deprecated")
    Warning: 'pnacopula' is deprecated.
    Use 'pCopula' instead.
    See help("Deprecated")
    Warning: 'pnacopula' is deprecated.
    Use 'pCopula' instead.
    See help("Deprecated")
    Warning: 'pnacopula' is deprecated.
    Use 'pCopula' instead.
    See help("Deprecated")
    --- finished re-building ‘nacopula-pkg.Rnw’
    
    --- re-building ‘rhoAMH-dilog.Rnw’ using Sweave
    Loading required package: copula
    Loading required package: sfsmisc
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called 'sfsmisc'
    
    Error: processing vignette 'rhoAMH-dilog.Rnw' failed with diagnostics:
     chunk 5 (label = ak-frac-do)
    Error in mat2tex(rbind(k = k, `$a_k$` = as.character(ak)), stdout()) :
     could not find function "mat2tex"
    
    --- failed re-building 'rhoAMH-dilog.Rnw'
    
    SUMMARY: processing the following files failed:
     ‘wild_animals.Rmd’ ‘rhoAMH-dilog.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.999-19.1
Check: installed package size
Result: NOTE
     installed size is 10.0Mb
     sub-directories of 1Mb or more:
     R 2.1Mb
     doc 5.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.999-19.1
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 9.8Mb
     sub-directories of 1Mb or more:
     R 2.1Mb
     doc 5.6Mb
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64