Running examples in ‘coxed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: baseline.plot
> ### Title: Plot the simulated baseline functions
> ### Aliases: baseline.plot
> 
> ### ** Examples
> 
> simdata <- sim.survdata(N=1000, T=100, num.data.frames=1)
> baseline.plot(simdata$baseline)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
coxaalen: no visible global function definition for ‘terms’
coxaalen: no visible global function definition for ‘model.matrix’
coxaalen: no visible binding for global variable ‘frame’
coxaalen: no visible global function definition for ‘update.formula’
coxaalen: no visible global function definition for ‘capture.output’
coxdual: no visible global function definition for ‘terms’
coxdual: no visible global function definition for ‘model.matrix’
coxdual: no visible binding for global variable ‘frame’
coxdual: no visible global function definition for ‘update.formula’
coxdual: no visible global function definition for ‘as.formula’
coxdual: no visible global function definition for ‘capture.output’
frame.assign: no visible global function definition for ‘model.matrix’
linapprox: no visible global function definition for ‘approx’
print.coxinterval: no visible global function definition for ‘pchisq’
print.summary.coxinterval : f: no visible global function definition
  for ‘printCoefmat’
step2stepfun : f: no visible global function definition for ‘stepfun’
summary.coxinterval : f: no visible global function definition for
  ‘pchisq’
summary.coxinterval : f: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  approx as.formula capture.output frame model.matrix pchisq
  printCoefmat qnorm stepfun terms update.formula
Consider adding
  importFrom("graphics", "frame")
  importFrom("stats", "approx", "as.formula", "model.matrix", "pchisq",
             "printCoefmat", "qnorm", "stepfun", "terms",
             "update.formula")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
comp.graph: no visible global function definition for ‘qnorm’
comp.graph: no visible global function definition for ‘plot’
comp.graph: no visible global function definition for ‘polygon’
comp.graph: no visible global function definition for ‘lines’
cox.ridge: no visible global function definition for ‘terms’
cox.ridge: no visible global function definition for ‘model.extract’
cox.ridge: no visible global function definition for ‘model.matrix’
cox.ridge: no visible binding for global variable ‘hat’
Undefined global functions or variables:
  hat lines model.extract model.matrix plot polygon qnorm terms
Consider adding
  importFrom("graphics", "lines", "plot", "polygon")
  importFrom("stats", "hat", "model.extract", "model.matrix", "qnorm",
             "terms")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
coxr: no visible global function definition for ‘model.extract’
coxr: no visible global function definition for ‘model.matrix’
coxr.draw: no visible global function definition for ‘plot’
coxr.draw: no visible global function definition for ‘lines’
coxr.draw: no visible global function definition for ‘points’
coxr.fit: no visible global function definition for ‘quantile’
gen_data: no visible global function definition for ‘rnorm’
gen_data: no visible global function definition for ‘rexp’
plot.coxr: no visible global function definition for ‘quantile’
plot.coxr: no visible global function definition for ‘par’
plot.coxr: no visible global function definition for ‘mtext’
plot.coxr: no visible global function definition for ‘title’
plot.coxr: no visible global function definition for ‘split.screen’
plot.coxr: no visible global function definition for ‘screen’
plot.coxr: no visible global function definition for ‘close.screen’
print.coxr: no visible global function definition for ‘pnorm’
print.coxr: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq plot
  pnorm points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par", "plot",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘coxrt-vignette.Rmd’ using rmarkdown
Quitting from lines 64-85 (coxrt-vignette.Rmd) 
Error: processing vignette 'coxrt-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘coxrt-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘coxrt-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
CumInt : fn: no visible global function definition for ‘integrate’
RND0: no visible global function definition for ‘runif’
coxseiInt: no visible global function definition for ‘approxfun’
coxseiInt : js: no visible global function definition for ‘tail’
coxseiest: no visible global function definition for ‘approxfun’
coxseiest : loglik : ll: no visible global function definition for
  ‘tail’
coxseiest: no visible global function definition for ‘optim’
coxseiest2: no visible global function definition for ‘approxfun’
coxseiest2: no visible global function definition for ‘optim’
coxseiest3: no visible global function definition for ‘approxfun’
coxseiest3: no visible global function definition for ‘optim’
coxseiexp: no visible global function definition for ‘approxfun’
coxseiexp: no visible global function definition for ‘optim’
coxseiexp : js: no visible global function definition for ‘tail’
coxseiexp: no visible global function definition for ‘pnorm’
coxseiexp: no visible global function definition for ‘stepfun’
coxseifit.ex: no visible global function definition for ‘approxfun’
coxseifit.ex: no visible global function definition for ‘optim’
coxseifit.ex : js: no visible global function definition for ‘tail’
coxseifit.ex: no visible global function definition for ‘pnorm’
coxseifit.ex: no visible global function definition for ‘stepfun’
coxseisim : int.at.lasttm: no visible global function definition for
  ‘tail’
plot.coxsei: no visible global function definition for ‘plot’
print.summary.coxsei: no visible global function definition for
  ‘printCoefmat’
summary.coxsei: no visible global function definition for ‘coef’
Undefined global functions or variables:
  approxfun coef integrate optim plot pnorm printCoefmat runif stepfun
  tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "approxfun", "coef", "integrate", "optim", "pnorm",
             "printCoefmat", "runif", "stepfun")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
src/Makevars: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Running examples in ‘cpr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bsplineD
> ### Title: B-spline Derivatives
> ### Aliases: bsplineD
> 
> ### ** Examples
> 
> 
> set.seed(42)
> 
> xvec <- seq(0.1, 9.9, length = 1000)
> iknots <- sort(runif(rpois(1, 3), 1, 9))
> bknots <- c(0, 10)
> 
> # basis matrix and the first and second derivatives thereof, for cubic (order =
> # 4) b-splines
> bmat  <- bsplines(xvec, iknots, bknots = bknots)
> bmat1 <- bsplineD(xvec, iknots, bknots = bknots, derivative = 1)
> bmat2 <- bsplineD(xvec, iknots, bknots = bknots, derivative = 2)
> 
> # control polygon ordinates
> theta <- runif(length(iknots) + 4L, -5, 5)
> 
> # plot data
> plot_data <-
+   dplyr::data_frame(x = xvec,
+                     Spline = as.numeric(bmat %*% theta),
+                     "First Derivative" = as.numeric(bmat1 %*% theta),
+                     "Second Derivative" = as.numeric(bmat2 %*% theta))
Warning: `data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
> plot_data <- tidyr::gather(plot_data, key = key, value = value, -x)
> 
> ggplot2::ggplot(plot_data) +
+ ggplot2::aes(x = x, y = value, color = key) +
+ ggplot2::geom_line() +
+ ggplot2::geom_hline(yintercept = 0) +
+ ggplot2::geom_vline(xintercept = iknots, linetype = 3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cpr-pkg.Rmd’ using rmarkdown
Quitting from lines 93-95 (cpr-pkg.Rmd) 
Error: processing vignette 'cpr-pkg.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cpr-pkg.Rmd’

SUMMARY: processing the following file failed:
  ‘cpr-pkg.Rmd’

Error: Vignette re-building failed.
Execution halted
QR.cd: no visible global function definition for ‘quantile’
QR.lasso.cd: no visible global function definition for ‘quantile’
cqr.cd: no visible global function definition for ‘quantile’
cqr.lasso.cd: no visible global function definition for ‘quantile’
cqr.lasso.mm: no visible global function definition for ‘quantile’
cqr.mm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Running examples in ‘cr17-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCuminc
> ### Title: Cumulative incidences curves
> ### Aliases: plotCuminc
> 
> ### ** Examples
> 
> fitC <- fitCuminc(time = LUAD$time, risk = LUAD$event, group = LUAD$gender, cens = "alive")
19 cases omitted due to missing values
> plotCuminc(ci = fitC, cens = "alive", target = 1200)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 117-121 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
distance.comoving: no visible global function definition for
  ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘cranly.Rmd’ using rmarkdown
Quitting from lines 62-68 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cranly.Rmd’

--- re-building ‘dependence_trees.Rmd’ using rmarkdown
--- finished re-building ‘dependence_trees.Rmd’

--- re-building ‘glms.Rmd’ using rmarkdown
Quitting from lines 58-61 (glms.Rmd) 
Error: processing vignette 'glms.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘glms.Rmd’

SUMMARY: processing the following files failed:
  ‘cranly.Rmd’ ‘glms.Rmd’

Error: Vignette re-building failed.
Execution halted
crantastic.submitInstalledPackages: no visible global function
  definition for ‘installed.packages’
postData: no visible global function definition for ‘make.socket’
postData: no visible global function definition for ‘write.socket’
postData: no visible global function definition for ‘read.socket’
postData: no visible global function definition for ‘close.socket’
Undefined global functions or variables:
  close.socket installed.packages make.socket read.socket write.socket
Consider adding
  importFrom("utils", "close.socket", "installed.packages",
             "make.socket", "read.socket", "write.socket")
to your NAMESPACE file.
cm.CVaR: no visible global function definition for ‘quantile’
cm.hist: no visible global function definition for ‘hist’
cm.quantile: no visible global function definition for ‘qnorm’
cm.rnorm: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  hist qnorm quantile rnorm
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 74-79 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘cRegulome-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cor_joy
> ### Title: A joy plot of correlation of microRNA or tf sets
> ### Aliases: cor_joy
> 
> ### ** Examples
> 
> # locate the testset file and connect
> fl <- system.file('extdata', 'cRegulome.db', package = 'cRegulome')
> conn <- RSQLite::dbConnect(RSQLite::SQLite(), fl)
> 
> # enter a custom query with different arguments
> dat <- get_mir(conn,
+                mir = c('hsa-let-7g', 'hsa-let-7i'),
+                study = 'STES')
> 
> # make a cmicroRNA object   
> cmir <- cmicroRNA(dat)
> 
> # print object
> cor_joy(cmir)
Picking joint bandwidth of 0.0445
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [9s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cRegulome)
  > 
  > test_check("cRegulome")
  ── 1. Error: cor_upset works (@test-methods.plots.R#42)  ───────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: cor_upset(cmir) at testthat/test-methods.plots.R:42
  2: cor_upset.cmicroRNA(cmir)
  3: upset(dat, ...)
  4: Make_base_plot(Main_bar, Matrix, Sizes, labels, mb.ratio, att.x, att.y, New_data, 
         expression, att.pos, first.col, att.color, AllQueryData, attribute.plots, legend, 
         query.legend, BoxPlots, Set_names, set.metadata, set.metadata.plots)
  5: NoAttBasePlot(legend, size_plot_height, Main_bar_plot, Matrix_plot, hratios, Size_plot, 
         query_legend, set_metadata, set_metadata_plots)
  6: grid.draw(arrangeGrob(Main_bar_plot, Matrix_plot, heights = hratios))
  7: grid.draw.gTree(arrangeGrob(Main_bar_plot, Matrix_plot, heights = hratios))
  8: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  9: drawGTree(x)
  10: grid.draw(x$children[[i]], recording = FALSE)
  ...
  29: pushvpgp(x)
  30: pushgrobvp(x$vp)
  31: pushgrobvp.viewport(x$vp)
  32: pushViewport(vp, recording = FALSE)
  33: lapply(vps, push.vp, recording)
  34: FUN(X[[i]], ...)
  35: push.vp.vpTree(X[[i]], ...)
  36: push.vp(vp$parent, recording)
  37: push.vp.viewport(vp$parent, recording)
  38: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 133 SKIPPED: 0 FAILED: 1
  1. Error: cor_upset works (@test-methods.plots.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
makeX_eset: no visible global function definition for ‘model.matrix’
normFit: no visible binding for global variable ‘lm’
normFit: no visible binding for global variable ‘sd’
normFit: no visible global function definition for ‘lm’
normPred: no visible binding for global variable ‘predict’
normPred: no visible global function definition for ‘predict’
normPred: no visible binding for global variable ‘median’
plot.nFit: no visible global function definition for ‘par’
plot.nFit: no visible global function definition for ‘barplot’
plot.nFit: no visible global function definition for ‘legend’
show_nfit: no visible global function definition for ‘anova’
show_nfit: no visible global function definition for ‘residuals’
show_nfit: no visible global function definition for ‘fitted’
standardsFit: no visible binding for global variable ‘lm’
standardsFit: no visible global function definition for ‘resid’
standardsFit: no visible global function definition for
  ‘compareVersion’
standardsPred: no visible global function definition for ‘predict’
makeX,ExpressionSet-character: no visible global function definition
  for ‘model.matrix’
plot,nFit: no visible global function definition for ‘par’
plot,nFit: no visible global function definition for ‘barplot’
plot,nFit: no visible global function definition for ‘legend’
show,nFit: no visible global function definition for ‘anova’
show,nFit: no visible global function definition for ‘residuals’
show,nFit: no visible global function definition for ‘fitted’
Undefined global functions or variables:
  anova barplot compareVersion fitted legend lm median model.matrix par
  predict resid residuals sd
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "anova", "fitted", "lm", "median", "model.matrix",
             "predict", "resid", "residuals", "sd")
  importFrom("utils", "compareVersion")
to your NAMESPACE file.
Running examples in ‘crmPack-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DataMixture-class
> ### Title: Class for the data with mixture sharing
> ### Aliases: DataMixture-class .DataMixture
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## decide on the dose grid:
> doseGrid <- 1:80
> 
> ## and MCMC options:
> options <- McmcOptions()
> 
> ## the classic model would be:
> model <- LogisticLogNormal(mean = c(-0.85, 1),
+                            cov = matrix(c(1, -0.5, -0.5, 1), nrow = 2),
+                            refDose = 50)
> 
> nodata <- Data(doseGrid=doseGrid)
> 
> priorSamples <- mcmc(nodata, model, options)
> plot(priorSamples, model, nodata)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘chron’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
collateDaily: no visible global function definition for ‘read.table’
collateDaily: no visible global function definition for ‘write.table’
collateHourly: no visible global function definition for ‘read.table’
collateHourly: no visible global function definition for ‘write.table’
downloadCRN: no visible global function definition for ‘download.file’
getUrlsCRN: no visible global function definition for ‘getURL’
writeDataset: no visible global function definition for ‘read.table’
writeDataset: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  download.file getURL read.table write.table
Consider adding
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
get.plan: no visible global function definition for ‘menu’
Undefined global functions or variables:
  menu
Consider adding
  importFrom("utils", "menu")
to your NAMESPACE file.
crossmatchtest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Running examples in ‘Crossover-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot
> ### Title: Plots information about the search algorithm and its process.
> ### Aliases: plot plot,CrossoverSearchResult,missing-method
> 
> ### ** Examples
> 
> 
> ## Not run: 
> ##D x <- searchCrossOverDesign(s=9, p=5, v=4, model=4)
> ##D plot(x)
> ## End(Not run)
> 
> x <- searchCrossOverDesign(s=9, p=5, v=4, model=4, n=c(50,10), jumps=c(10, 10))
> plot(x, show.jumps=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Crossover.Rnw’ using knitr
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data

Attaching package: 'TH.data'

The following object is masked from 'package:MASS':

    geyser

Quitting from lines 23-29 (./childs/Search.Rnw) 
Quitting from lines NA-239 (./childs/Search.Rnw) 
Error: processing vignette 'Crossover.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Crossover.Rnw’

SUMMARY: processing the following file failed:
  ‘Crossover.Rnw’

Error: Vignette re-building failed.
Execution halted
BootC : BSs: no visible global function definition for ‘lm’
BootC : BSs: no visible global function definition for ‘vcov’
BootC: no visible global function definition for ‘boot’
BootC: no visible global function definition for ‘boot.ci’
DeltaC: no visible global function definition for ‘lm’
DeltaC: no visible global function definition for ‘vcov’
FiellerC: no visible global function definition for ‘lm’
FiellerC: no visible global function definition for ‘vcov’
nonLinearC: no visible global function definition for ‘nls’
Undefined global functions or variables:
  boot boot.ci lm nls vcov
Consider adding
  importFrom("stats", "lm", "nls", "vcov")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘CrossScreening-vignette.Rnw’ using knitr
Warning in wilcox.test.default(d.lead, alternative = "greater") :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(d.lead, alternative = "greater") :
  cannot compute exact p-value with zeroes
Quitting from lines 364-367 (CrossScreening-vignette.Rnw) 
Error: processing vignette 'CrossScreening-vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CrossScreening-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘CrossScreening-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
Warning: no function found corresponding to methods exports from ‘CR’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
curerate : cr: no visible global function definition for ‘rbinom’
curerate : cr: no visible global function definition for ‘rexp’
curerate : cr: no visible global function definition for ‘runif’
curerate: no visible global function definition for ‘new’
showcr: no visible global function definition for ‘show’
Undefined global functions or variables:
  new rbinom rexp runif show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "rbinom", "rexp", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
crrp: no visible global function definition for ‘approx’
gcrrp: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx
Consider adding
  importFrom("stats", "approx")
to your NAMESPACE file.
crrc: no visible binding for global variable ‘na.omit’
crrs: no visible binding for global variable ‘na.omit’
mycrr: no visible binding for global variable ‘na.omit’
mycrr.test: no visible binding for global variable ‘na.omit’
print.crrs: no visible global function definition for ‘pnorm’
psh.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  na.omit pchisq pnorm
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pnorm")
to your NAMESPACE file.
crrstep : crr.makecov1: no visible global function definition for
  ‘model.matrix’
crrstep : crr.dropterm: no visible global function definition for
  ‘terms’
crrstep : crr.dropterm: no visible global function definition for
  ‘as.formula’
crrstep : crr.addterm: no visible global function definition for
  ‘terms’
crrstep : crr.addterm: no visible global function definition for
  ‘as.formula’
crrstep: no visible global function definition for ‘as.formula’
crrstep: no visible global function definition for ‘terms’
crrstep: no visible global function definition for ‘model.frame’
crrstep: no visible binding for global variable ‘na.pass’
crrstep: no visible global function definition for ‘update’
crrstep: no visible global function definition for ‘drop.terms’
Undefined global functions or variables:
  as.formula drop.terms model.frame model.matrix na.pass terms update
Consider adding
  importFrom("stats", "as.formula", "drop.terms", "model.frame",
             "model.matrix", "na.pass", "terms", "update")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘csp.Rmd’ using rmarkdown
Warning: Removed 1776 rows containing missing values (geom_path).
Quitting from lines 48-58 (csp.Rmd) 
Error: processing vignette 'csp.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘csp.Rmd’

SUMMARY: processing the following file failed:
  ‘csp.Rmd’

Error: Vignette re-building failed.
Execution halted
pielou: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘test.html’
Package in Depends field not imported from: ‘compiler’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
csSAM: no visible binding for global variable ‘quantile’
csSAM: no visible global function definition for ‘median’
csfit: no visible global function definition for ‘lsfit’
csfit: no visible global function definition for ‘ls.diag’
plotCsSAM: no visible global function definition for ‘pdf’
plotCsSAM: no visible global function definition for ‘par’
plotCsSAM: no visible global function definition for ‘plot’
plotCsSAM: no visible global function definition for ‘title’
plotCsSAM: no visible global function definition for ‘dev.off’
runSAM: no visible binding for global variable ‘median’
runSAM: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf plot quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
cstar: no visible global function definition for ‘vcov’
cstar : utility: no visible global function definition for ‘dt’
cstar : maximand: no visible global function definition for ‘integrate’
cstar: no visible global function definition for ‘uniroot’
cstari : utility: no visible global function definition for ‘dt’
cstari : maximand: no visible global function definition for
  ‘integrate’
cstari: no visible global function definition for ‘uniroot’
cstarme : utility: no visible global function definition for ‘density’
cstarme : maximand: no visible global function definition for
  ‘integrate’
cstarme : maximand: no visible global function definition for ‘sd’
cstarme: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  density dt integrate sd uniroot vcov
Consider adding
  importFrom("stats", "density", "dt", "integrate", "sd", "uniroot",
             "vcov")
to your NAMESPACE file.
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘cubist.Rmd’ using rmarkdown
Quitting from lines 127-129 (cubist.Rmd) 
Error: processing vignette 'cubist.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cubist.Rmd’

SUMMARY: processing the following file failed:
  ‘cubist.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘BUGS.md’ ‘TODO.md’ ‘benchmarks’ ‘build_script.sh’ ‘doc’
  ‘iddply_dt.R’ ‘profiling’
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cci.nostrat: no visible global function definition for ‘quantile’
cci.nostrat: no visible global function definition for ‘plot’
cci.nostrat: no visible global function definition for ‘axis’
cci.nostrat: no visible global function definition for ‘lines’
cci.nostrat: no visible global function definition for ‘legend’
cci.strat: no visible global function definition for ‘plot’
cci.strat: no visible global function definition for ‘axis’
cci.strat: no visible global function definition for ‘lines’
cci.strat: no visible global function definition for ‘legend’
clfs.nostrat: no visible global function definition for ‘quantile’
clfs.nostrat: no visible global function definition for ‘plot’
clfs.nostrat: no visible global function definition for ‘axis’
clfs.nostrat: no visible global function definition for ‘lines’
clfs.nostrat: no visible global function definition for ‘legend’
clfs.strat: no visible global function definition for ‘plot’
clfs.strat: no visible global function definition for ‘axis’
clfs.strat: no visible global function definition for ‘lines’
clfs.strat: no visible global function definition for ‘legend’
pvals.2cat: no visible global function definition for ‘pchisq’
pvals.cat: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis legend lines pchisq plot quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
Running examples in ‘customLayout-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lay_grid
> ### Title: Use Layout object with grid graphics.
> ### Aliases: lay_grid layGrid
> 
> ### ** Examples
> 
> 
> library(ggplot2)
> 
> l1 <- lay_new(matrix(1:2, ncol = 1), heights = c(2, 3))
> l2 <- lay_new(matrix(1:2, ncol = 1), heights = c(1, 3))
> l3 <- lay_bind_col(l1, l2)
> 
> pl1 <- qplot(mpg, wt, data = mtcars)
> pl2 <- qplot(mpg, gear, data = mtcars)
> pl3 <- qplot(cyl, gear, data = mtcars)
> pl4 <- qplot(qsec, am, data = mtcars)
> 
> lay_grid(list(pl1, pl2, pl3, pl4), l3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: lay_grid ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Roadmap.Rmd’ using rmarkdown
--- finished re-building ‘Roadmap.Rmd’

--- re-building ‘customlayout-cookbook.Rmd’ using rmarkdown
Loading required package: MASS

Attaching package: 'cowplot'

The following object is masked from 'package:ggplot2':

    ggsave

Quitting from lines 30-86 (customlayout-cookbook.Rmd) 
Error: processing vignette 'customlayout-cookbook.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘customlayout-cookbook.Rmd’

--- re-building ‘layouts-for-officer-power-point-document.Rmd’ using rmarkdown
Quitting from lines 57-66 (layouts-for-officer-power-point-document.Rmd) 
Error: processing vignette 'layouts-for-officer-power-point-document.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘layouts-for-officer-power-point-document.Rmd’

SUMMARY: processing the following files failed:
  ‘customlayout-cookbook.Rmd’
  ‘layouts-for-officer-power-point-document.Rmd’

Error: Vignette re-building failed.
Execution halted
Cut: no visible global function definition for ‘cor’
MissSimulation: no visible global function definition for ‘rbinom’
cutoff: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor rbinom
Consider adding
  importFrom("stats", "cor", "rbinom")
to your NAMESPACE file.
Running examples in ‘cutoffR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HeatStruct
> ### Title: Structure Heatmap with Missing Value Demonstration
> ### Aliases: HeatStruct
> 
> ### ** Examples
> 
> data(hqmr.data)
> # use a subset of the hqmr.data
> # notice the gold chunks which represent missing values
> subdata <- hqmr.data[1000:1200, 1:30]
> HeatStruct(subdata)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘cutpointr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cutpoint
> ### Title: Extract the cutpoints from a ROC curve generated by cutpointr
> ### Aliases: cutpoint cutpoints
> 
> ### ** Examples
> 
> oc <- cutpointr(suicide, dsi, suicide, gender)
Assuming the positive class is yes
Assuming the positive class has higher x values
> plot_cutpointr(oc, cutpoint, accuracy)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cutpointr.Rmd’ using rmarkdown
Quitting from lines 59-60 (cutpointr.Rmd) 
Error: processing vignette 'cutpointr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cutpointr.Rmd’

SUMMARY: processing the following file failed:
  ‘cutpointr.Rmd’

Error: Vignette re-building failed.
Execution halted
delta.glm: no visible global function definition for ‘glm’
delta.glm: no visible global function definition for ‘residuals’
delta.glm: no visible global function definition for ‘fitted’
delta.glm: no visible global function definition for ‘predict.glm’
two.stage.model.outputs: no visible global function definition for ‘sd’
Undefined global functions or variables:
  fitted glm predict.glm residuals sd
Consider adding
  importFrom("stats", "fitted", "glm", "predict.glm", "residuals", "sd")
to your NAMESPACE file.
ci.cvAUC: no visible global function definition for ‘qnorm’
ci.pooled.cvAUC: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
calfun: no visible global function definition for ‘optim’
calfun: no visible global function definition for ‘cov’
calfun: no visible global function definition for ‘var’
Undefined global functions or variables:
  cov optim var
Consider adding
  importFrom("stats", "cov", "optim", "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘how_to_test_CVs.Rmd’ using rmarkdown
Quitting from lines 108-116 (how_to_test_CVs.Rmd) 
Error: processing vignette 'how_to_test_CVs.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘how_to_test_CVs.Rmd’

SUMMARY: processing the following file failed:
  ‘how_to_test_CVs.Rmd’

Error: Vignette re-building failed.
Execution halted
func.constructRegressionFormula: no visible global function definition
  for ‘as.formula’
func.crossValidationAnalysis: no visible global function definition for
  ‘glm’
func.crossValidationAnalysis: no visible global function definition for
  ‘predict’
func.crossValidationAnalysis: no visible global function definition for
  ‘write.table’
func.externalValidationAnalysis: no visible global function definition
  for ‘predict’
func.externalValidationAnalysis: no visible global function definition
  for ‘write.table’
func.linearRegressionAnalysis: no visible global function definition
  for ‘glm’
func.linearRegressionAnalysis: no visible global function definition
  for ‘predict’
func.linearRegressionAnalysis: no visible global function definition
  for ‘write.table’
func.sortDataColumns: no visible global function definition for
  ‘write.table’
mainfunc.q2: no visible global function definition for ‘write.table’
mainfunc.q2: no visible global function definition for ‘new’
mainfunc.stats: no visible global function definition for ‘write.table’
mainfunc.stats: no visible global function definition for ‘new’
Undefined global functions or variables:
  as.formula glm new predict write.table
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.formula", "glm", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cvimpute.by.wavelet: no visible global function definition for ‘sd’
cvimpute.by.wavelet: no visible global function definition for ‘mad’
cvimpute.image.by.wavelet: no visible global function definition for
  ‘sd’
cvimpute.image.by.wavelet: no visible global function definition for
  ‘mad’
cvwavelet.image.after.impute: no visible global function definition for
  ‘sd’
cvwavelet.image.after.impute: no visible global function definition for
  ‘mad’
Undefined global functions or variables:
  mad sd
Consider adding
  importFrom("stats", "mad", "sd")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
random.CV: no visible global function definition for ‘var’
regular.CV: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
create_clustering_problem: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Running examples in ‘cvxclustr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cvxclust
> ### Title: Convex Clustering Path via Variable Splitting Methods
> ### Aliases: cvxclust
> 
> ### ** Examples
> 
> ## Clusterpaths for Mammal Dentition
> data(mammals)
> X <- as.matrix(mammals[,-1])
> X <- t(scale(X,center=TRUE,scale=FALSE))
> n <- ncol(X)
> 
> ## Pick some weights and a sequence of regularization parameters.
> k <- 5
> phi <- 0.5
> w <- kernel_weights(X,phi)
> w <- knn_weights(w,k,n)
> gamma <- seq(0.0,43, length.out=100)
> 
> ## Perform clustering
> sol <- cvxclust(X,w,gamma)
Warning in cvxclust_ama(X, Lambda, ix - 1, M1 - 1, M2 - 1, s1, s2, w[w >  :
  The stepsize nu may be too large. Setting it to maximum of 1/n and 1/AnM.
> 
> ## Plot the cluster path
> library(ggplot2)
> svdX <- svd(X)
> pc <- svdX$u[,1:2,drop=FALSE]
> pc.df <- as.data.frame(t(pc)%*%X)
> nGamma <- sol$nGamma
> df.paths <- data.frame(x=c(),y=c(), group=c())
> for (j in 1:nGamma) {
+   pcs <- t(pc)%*%sol$U[[j]]
+   x <- pcs[1,]
+   y <- pcs[2,]
+   df <- data.frame(x=pcs[1,], y=pcs[2,], group=1:n)
+   df.paths <- rbind(df.paths,df)
+ }
> X_data <- as.data.frame(t(X)%*%pc)
> colnames(X_data) <- c("x","y")
> X_data$Name <- mammals[,1]
> data_plot <- ggplot(data=df.paths,aes(x=x,y=y))
> data_plot <- data_plot + geom_path(aes(group=group),colour='grey30',alpha=0.5)
> data_plot <- data_plot + geom_text(data=X_data,aes(x=x,y=y,label=Name),
+   position=position_jitter(h=0.125,w=0.125))
> data_plot <- data_plot + geom_point(data=X_data,aes(x=x,y=y),size=1.5)
> data_plot <- data_plot + xlab('Principal Component 1') + ylab('Principal Component 2')
> data_plot + theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
.mixgauss_init: no visible global function definition for ‘cov’
.mixgauss_init: no visible global function definition for ‘var’
Undefined global functions or variables:
  cov var
Consider adding
  importFrom("stats", "cov", "var")
to your NAMESPACE file.
cxxfun.from.dll: no visible global function definition for ‘new’
cxxfun.from.dso.bin: no visible global function definition for ‘new’
cxxfunctionplus: no visible global function definition for ‘getPlugin’
cxxfunctionplus: no visible global function definition for
  ‘cxxfunction’
cxxfunctionplus: no visible global function definition for ‘new’
show,cxxdso: no visible global function definition for ‘object.size’
Undefined global functions or variables:
  cxxfunction getPlugin new object.size
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package in Depends field not imported from: ‘fda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.for.sequence.endpoint.breaks: no visible global function
  definition for ‘na.omit’
get.breaks.vector: no visible global function definition for ‘na.omit’
get.cycle.breaks: no visible global function definition for ‘na.omit’
get.cycle.counts: no visible global function definition for ‘na.omit’
get.cycle.matrix: no visible global function definition for ‘na.omit’
get.cycle.minimums: no visible global function definition for ‘na.omit’
get.peaks: no visible global function definition for ‘embed’
get.trans: no visible global function definition for
  ‘create.bspline.basis’
get.trans: no visible global function definition for ‘smooth.basis’
get.trans: no visible global function definition for ‘deriv.fd’
get.trans: no visible global function definition for ‘eval.fd’
get.transition.locations: no visible global function definition for
  ‘na.omit’
get.transition.locations.FDiff: no visible global function definition
  for ‘na.omit’
get.window: no visible global function definition for ‘sd’
Undefined global functions or variables:
  create.bspline.basis deriv.fd embed eval.fd na.omit sd smooth.basis
Consider adding
  importFrom("stats", "embed", "na.omit", "sd")
to your NAMESPACE file.
cytoDiv: no visible global function definition for ‘colorRampPalette’
cytoDiv: no visible global function definition for ‘persp’
Undefined global functions or variables:
  colorRampPalette persp
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "persp")
to your NAMESPACE file.
Running examples in ‘cytofan-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_fan
> ### Title: Fan plots for trend and population visualizations
> ### Aliases: geom_fan stat_fan
> 
> ### ** Examples
> 
> # reformat dataset from short-wide to tall-skinny
> EuStockMarkets_ts <- lapply(colnames(EuStockMarkets),function(id) {
+   data.frame(id=id,value=as.numeric(EuStockMarkets[,id]))
+ })
> EuStockMarkets_ts <- do.call('rbind',EuStockMarkets_ts)
> 
> # plot the distribution of the different stock markets
> ggplot(EuStockMarkets_ts,aes(x=id,y=value))+
+   geom_fan()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cytofan_flow_cytometry.Rmd’ using rmarkdown
Quitting from lines 78-84 (cytofan_flow_cytometry.Rmd) 
Error: processing vignette 'cytofan_flow_cytometry.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cytofan_flow_cytometry.Rmd’

SUMMARY: processing the following file failed:
  ‘cytofan_flow_cytometry.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘cytometree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CytomeTree
> ### Title: Binary tree algorithm for cytometry data analysis.
> ### Aliases: CytomeTree
> 
> ### ** Examples
> 
> head(DLBCL)
  FL1 FL2 FL4 label
1 416 251 293     2
2 210  93 184     2
3 387 300 233     2
4 403 438 288     2
5 399 128 116     2
6 538 288 189     2
> 
> # number of cell event
> N <- nrow(DLBCL)
> 
> # Cell events
> cellevents <- DLBCL[, c("FL1", "FL2", "FL4")]
> 
> 
> # Manual partitioning of the set N (from FlowCAP-I)
> manual_labels <- DLBCL[, "label"]
> 
> 
> # Build the binary tree
> Tree <- CytomeTree(cellevents, minleaf = 1, t=.1)

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================================| 100%
> 
> 
> # Retreive the resulting partition of the set N
> Tree_Partition <- Tree$labels
> 
> 
> # Plot node distributions
> par(mfrow=c(1, 2))
> plot_nodes(Tree)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_nodes ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘autogating_cytometree.Rmd’ using rmarkdown
Loading required package: Rcpp
Quitting from lines 86-88 (autogating_cytometree.Rmd) 
Error: processing vignette 'autogating_cytometree.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘autogating_cytometree.Rmd’

SUMMARY: processing the following file failed:
  ‘autogating_cytometree.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘D2C-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict,D2C-method
> ### Title: predict if there is a connection between node i and node j
> ### Aliases: predict,D2C-method
> 
> ### ** Examples
> 
> require(RBGL)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:randomForest’:

    combine

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

> require(gRbase)
Loading required package: gRbase
> require(foreach)
Loading required package: foreach
> data(example)
> ## load the D2C object
> testDAG<-new("simulatedDAG",NDAG=1, N=50,noNodes=5,
+            functionType = "linear", seed=1,sdn=c(0.25,0.5))
simulatedDAG: DAG number: 1 generated: #nodes= 5 # edges= 0 # samples= 50 
> ## creates a simulatedDAG object for testing
> plot(testDAG@list.DAGs[[1]])
Error in testDAG@list.DAGs[[1]] : subscript out of bounds
Calls: plot
Execution halted
Running examples in ‘DAAG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: errorsINx
> ### Title: Simulate data for straight line regression, with "errors in x".
> ### Aliases: errorsINx
> ### Keywords: datagen
> 
> ### ** Examples
> 
> library(lattice)
> errorsINx()
              Intercept Slope
No error in x      15.3 1.483
0.4sx              18.6 1.222
0.8sx              23.6 0.833
1.2sx              26.5 0.587
1.6sx              29.2 0.381
2sx                30.4 0.281
Error in unit(0.5 * shows, "strwidth", list(sep)) : 
  no string supplied for 'strwidth/height' unit
Calls: errorsINx ... strip -> do.call -> strip.default -> paste.and.draw -> unit
Execution halted
compareModels: no visible binding for global variable ‘fgl’
compareModels: no visible global function definition for ‘rlm’
compareModels: no visible global function definition for ‘lm’
compareModels: no visible global function definition for ‘predict’
compareModels: no visible global function definition for ‘resid’
plotSampDist: no visible global function definition for ‘par’
plotSampDist: no visible global function definition for ‘density’
plotSampDist: no visible global function definition for ‘plot’
plotSampDist: no visible global function definition for ‘lines’
plotSampDist: no visible global function definition for ‘legend’
plotSampDist: no visible global function definition for ‘qqnorm’
plotSampDist: no visible global function definition for ‘points’
plotSampDist: no visible global function definition for ‘mtext’
simulateSampDist: no visible binding for global variable ‘rnorm’
Undefined global functions or variables:
  density fgl legend lines lm mtext par plot points predict qqnorm
  resid rlm rnorm
Consider adding
  importFrom("graphics", "legend", "lines", "mtext", "par", "plot",
             "points")
  importFrom("stats", "density", "lm", "predict", "qqnorm", "resid",
             "rnorm")
to your NAMESPACE file.
Running examples in ‘dabestr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dabest
> ### Title: Differences between Groups with Bootstrap Confidence Intervals
> ### Aliases: dabest
> 
> ### ** Examples
> 
> # Performing unpaired (two independent groups) analysis.
> unpaired_mean_diff <- dabest(iris, Species, Petal.Width,
+                              idx = c("setosa", "versicolor"),
+                              paired = FALSE)
Warning: Some components of ... were not used: ..1
> 
> # Display the results in a user-friendly format.
> unpaired_mean_diff
DABEST (Data Analysis with Bootstrap Estimation) v0.2.0
=======================================================

Variable: Petal.Width 

Unpaired mean difference of versicolor (n=50) minus setosa (n=50)
 1.08 [95CI  1.01; 1.14]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

> 
> # Produce an estimation plot.
> plot(unpaired_mean_diff)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bootstrap-confidence-intervals.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 72-106 (bootstrap-confidence-intervals.Rmd) 
Error: processing vignette 'bootstrap-confidence-intervals.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bootstrap-confidence-intervals.Rmd’

--- re-building ‘robust-statistical-visualization.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 110-166 (robust-statistical-visualization.Rmd) 
Error: processing vignette 'robust-statistical-visualization.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘robust-statistical-visualization.Rmd’

--- re-building ‘using-dabestr.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 82-83 (using-dabestr.Rmd) 
Error: processing vignette 'using-dabestr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-dabestr.Rmd’

SUMMARY: processing the following files failed:
  ‘bootstrap-confidence-intervals.Rmd’
  ‘robust-statistical-visualization.Rmd’ ‘using-dabestr.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘dae-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: designPlotlabels
> ### Title: Plots labels on a two-way grid using 'ggplot2'
> ### Aliases: designPlotlabels
> ### Keywords: aplot hplot design
> 
> ### ** Examples
> 
> Treatments <- factor(rep(1:6, times = 5))
> RCBD.lay <- designRandomize(allocated = Treatments,
+                             recipient = list(Blocks = 5, Units = 6),
+                             nested.recipients = list(Units = "Blocks"),
+                             seed = 74111)
> designPlotlabels(RCBD.lay, labels = "Treatments", 
+                  grid.x = "Units", grid.y = "Blocks",
+                  colour.column = "Treatments", size = 5)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: designPlotlabels ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package in Depends field not imported from: ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
allCombs: no visible global function definition for ‘combn’
brute.search: no visible global function definition for ‘na.omit’
dag.draw: no visible global function definition for ‘plot’
dag.draw: no visible global function definition for ‘text’
dag.init: no visible global function definition for
  ‘installed.packages’
dag.legend: no visible global function definition for ‘text’
dag.letter: no visible global function definition for ‘text’
dag.move: no visible global function definition for ‘identify’
dag.move: no visible global function definition for ‘locator’
dag.sim: no visible global function definition for ‘rnorm’
dag.sim: no visible global function definition for ‘rbinom’
dag.sim : <anonymous>: no visible global function definition for
  ‘rbinom’
garrows: no visible global function definition for ‘arrows’
smoothArc: no visible global function definition for ‘points’
summary_dagRdag: no visible global function definition for ‘na.omit’
viv: no visible global function definition for ‘na.omit’
write.paths: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows combn identify installed.packages locator na.omit plot points
  rbinom rnorm text
Consider adding
  importFrom("graphics", "arrows", "identify", "locator", "plot",
             "points", "text")
  importFrom("stats", "na.omit", "rbinom", "rnorm")
  importFrom("utils", "combn", "installed.packages")
to your NAMESPACE file.
Running examples in ‘DALEX-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: model_feature_response
> ### Title: Marginal Response for a Single Variable
> ### Aliases: model_feature_response model_feature_response.explainer
> ###   model_feature_response.default
> 
> ### ** Examples
> 
> library("DALEX")
> 
> HR_glm_model <- glm(status == "fired" ~ ., data = HR, family = "binomial")
> explainer_glm <- explain(HR_glm_model, data = HR)
> expl_glm <- model_feature_response(explainer_glm, "age", "pdp")
> head(expl_glm)
         x         y var type label
1 20.00389 0.3690356 age  pdp    lm
2 20.80378 0.3688270 age  pdp    lm
3 21.60368 0.3686184 age  pdp    lm
4 22.40357 0.3684098 age  pdp    lm
5 23.20346 0.3682013 age  pdp    lm
6 24.00336 0.3679928 age  pdp    lm
> plot(expl_glm)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘dalmatian-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: traceplots
> ### Title: Traceplots (Generic)
> ### Aliases: traceplots
> 
> ### ** Examples
> 
> 
> ## Load output from previously run model
> load(system.file("Pied_Flycatchers_1","pfresults.RData",package="dalmatian"))
> 
> ## Generate traceplots
> pftraceplots <- traceplots(pfresults)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: traceplots ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pied-flycatchers-1.Rmd’ using rmarkdown
Quitting from lines 133-142 (pied-flycatchers-1.Rmd) 
Error: processing vignette 'pied-flycatchers-1.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pied-flycatchers-1.Rmd’

--- re-building ‘pied-flycatchers-2.Rmd’ using rmarkdown
Quitting from lines 123-138 (pied-flycatchers-2.Rmd) 
Error: processing vignette 'pied-flycatchers-2.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pied-flycatchers-2.Rmd’

--- re-building ‘weights-1-simulate.Rmd’ using rmarkdown
Quitting from lines 36-71 (weights-1-simulate.Rmd) 
Error: processing vignette 'weights-1-simulate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘weights-1-simulate.Rmd’

SUMMARY: processing the following files failed:
  ‘pied-flycatchers-1.Rmd’ ‘pied-flycatchers-2.Rmd’
  ‘weights-1-simulate.Rmd’

Error: Vignette re-building failed.
Execution halted
DAMOCLES_ML: no visible global function definition for ‘flush.console’
DAMOCLES_bootstrap: no visible global function definition for
  ‘cophenetic’
DAMOCLES_bootstrap: no visible global function definition for ‘sd’
DAMOCLES_bootstrap: no visible global function definition for
  ‘quantile’
DAMOCLES_sim: no visible global function definition for ‘na.omit’
DAMOCLES_sim: no visible global function definition for ‘runif’
DAMOCLES_sim: no visible global function definition for ‘lines’
DAMOCLES_sim: no visible global function definition for ‘rnorm’
DAMOCLES_sim: no visible global function definition for ‘dexp’
DAMOCLES_sim: no visible global function definition for ‘dist’
DAMOCLES_simplex: no visible global function definition for
  ‘flush.console’
Undefined global functions or variables:
  cophenetic dexp dist flush.console lines na.omit quantile rnorm runif
  sd
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "cophenetic", "dexp", "dist", "na.omit",
             "quantile", "rnorm", "runif", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘dams.Rmd’ using rmarkdown
Loading required package: dams
Loading required package: ggplot2
Loading required package: maps
Loading required package: mapproj
Quitting from lines 74-75 (dams.Rmd) 
Error: processing vignette 'dams.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dams.Rmd’

SUMMARY: processing the following file failed:
  ‘dams.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘IntroTutorial_dartR.Rmd’ using rmarkdown
Quitting from lines 936-938 (IntroTutorial_dartR.Rmd) 
Error: processing vignette 'IntroTutorial_dartR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘IntroTutorial_dartR.Rmd’

SUMMARY: processing the following file failed:
  ‘IntroTutorial_dartR.Rmd’

Error: Vignette re-building failed.
Execution halted
drawAimSpot: no visible global function definition for ‘points’
drawBoard: no visible global function definition for ‘par’
drawBoard: no visible global function definition for ‘plot’
drawBoard: no visible global function definition for ‘points’
drawBoard: no visible global function definition for ‘text’
drawHeatmap: no visible global function definition for ‘heat.colors’
drawHeatmap: no visible global function definition for ‘par’
drawHeatmap: no visible global function definition for ‘image’
drawHeatmap: no visible global function definition for ‘rect’
generalExpScores: no visible global function definition for ‘fft’
simpleExpScores: no visible global function definition for ‘mvfft’
simpleExpScores: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft heat.colors image mvfft par plot points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "points", "rect",
             "text")
  importFrom("stats", "fft", "mvfft")
to your NAMESPACE file.
dashboard_open: no visible global function definition for ‘write.csv’
dashboard_open: no visible global function definition for
  ‘capture.output’
dctable: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output write.csv
Consider adding
  importFrom("utils", "capture.output", "write.csv")
to your NAMESPACE file.
datadict.profile: no visible global function definition for
  ‘txtProgressBar’
datadict.profile: no visible global function definition for
  ‘setTxtProgressBar’
datadict_profile: no visible global function definition for
  ‘txtProgressBar’
datadict_profile: no visible global function definition for
  ‘setTxtProgressBar’
heatmap.quality: no visible global function definition for
  ‘colorRampPalette’
heatmap.quality: no visible global function definition for ‘heatmap’
heatmap_quality: no visible global function definition for
  ‘colorRampPalette’
heatmap_quality: no visible global function definition for ‘heatmap’
is.oneOf: no visible global function definition for ‘read.csv’
is_one_of: no visible global function definition for ‘read.csv’
pkg.version: no visible global function definition for ‘citation’
pkg_version: no visible global function definition for ‘citation’
ruleCoverage: no visible global function definition for ‘dotchart’
ruleCoverage: no visible global function definition for ‘abline’
rule_coverage: no visible global function definition for ‘dotchart’
rule_coverage: no visible global function definition for ‘abline’
scoreSum: no visible global function definition for ‘plot’
score_sum: no visible global function definition for ‘plot’
shortSummary: no visible global function definition for ‘sd’
short_summary: no visible global function definition for ‘sd’
Undefined global functions or variables:
  abline citation colorRampPalette dotchart heatmap plot read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart", "plot")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Package suggested but not available for checking: ‘Rhipe’
Found the following assignments to the global environment:
File ‘DataEntry/R/Export.R’:
  assign(svalue(edObnm), d, envir = .GlobalEnv)
Error(s) in re-building vignettes:
  ...
--- re-building ‘dataexplorer-intro.Rmd’ using rmarkdown
Quitting from lines 115-116 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dataexplorer-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘dataexplorer-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending_dataMaid.Rmd’ using rmarkdown
Quitting from lines 526-527 (extending_dataMaid.Rmd) 
Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘extending_dataMaid.Rmd’

SUMMARY: processing the following file failed:
  ‘extending_dataMaid.Rmd’

Error: Vignette re-building failed.
Execution halted
Package in Depends field not imported from: ‘DBI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onLoad : <anonymous>: no visible global function definition for
  ‘read.table’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbConnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbListTables’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbExistsTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbReadTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbWriteTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbDisconnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbRemoveTable’
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.

Found the following calls to attach():
File ‘datamap/R/datamap.R’:
  attach(.Call("CreateUserDB", map, PACKAGE = "datamap"), pos, 
    name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
checkDataQuality: no visible binding for global variable ‘quantile’
checkDataQuality: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  quantile write.csv
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Running examples in ‘datasauRus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: box_plots
> ### Title: Box plot data
> ### Aliases: box_plots
> ### Keywords: datasets
> 
> ### ** Examples
> 
> summary(box_plots)
      left              lines               normal          right       
 Min.   :-9.76964   Min.   :-9.769575   Min.   :-9.76   Min.   :-9.760  
 1st Qu.:-2.68999   1st Qu.:-2.689993   1st Qu.:-2.68   1st Qu.:-2.680  
 Median :-0.00999   Median :-0.007132   Median : 0.00   Median : 0.000  
 Mean   :-1.17780   Mean   :-0.831733   Mean   : 0.00   Mean   : 1.174  
 3rd Qu.: 2.67007   3rd Qu.: 2.670236   3rd Qu.: 2.68   3rd Qu.: 2.680  
 Max.   : 9.75025   Max.   : 9.756001   Max.   : 9.76   Max.   : 9.760  
     split          
 Min.   :-9.769886  
 1st Qu.:-2.689989  
 Median :-0.003099  
 Mean   :-0.003060  
 3rd Qu.: 2.680000  
 Max.   : 9.760000  
> 
> ## base plot
> 
> #save current settings
> state <- par("mar", "mfrow")
> 
> par(mfrow = c(5, 2), mar=c(1,2,2,1))
> 
> nms <- names(box_plots)
> 
> for (i in 1:5){
+   nm <- nms[i]
+   hist(box_plots[[nms[i]]],
+        breaks = 100,
+        main = nm)
+   boxplot(box_plots[[nms[i]]],
+           horizontal = TRUE)
+ }
> 
> 
> #reset settings
> par(state)
> 
> ## ggplot
> if(require(ggplot2)){
+   ggplot(box_plots, aes(x=left))+
+     geom_density()
+   ggplot(box_plots, aes(x=lines))+
+     geom_density()
+   ggplot(box_plots, aes(x=normal))+
+     geom_density()
+   ggplot(box_plots, aes(x=right))+
+     geom_density()
+   ggplot(box_plots, aes(x=split))+
+     geom_density()
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Datasaurus.Rmd’ using rmarkdown
Quitting from lines 47-55 (Datasaurus.Rmd) 
Error: processing vignette 'Datasaurus.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Datasaurus.Rmd’

SUMMARY: processing the following file failed:
  ‘Datasaurus.Rmd’

Error: Vignette re-building failed.
Execution halted
browse: no visible global function definition for ‘slot’
browse: no visible global function definition for ‘page’
default.options: no visible binding for global variable ‘object.size’
heat.view: no visible global function definition for ‘head’
heat.view: no visible global function definition for ‘tail’
whos: no visible global function definition for ‘slotNames’
whos : <anonymous> : <anonymous>: no visible global function definition
  for ‘slot’
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found the following calls to attach():
File ‘dataview/R/browse.R’:
  attach(x)
File ‘dataview/R/entry_view.R’:
  attach(x)
See section ‘Good practice’ in ‘?attach’.
Running examples in ‘DataVisualizations-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ClassBoxplot
> ### Title: Creates Boxplot plot for all classes
> ### Aliases: ClassBoxplot
> 
> ### ** Examples
> 
> ## Don't show: 
> data(ITS)
> #clustering only for testing
> Classification=c(rep(1,8805),rep(2,2389))
> DataVisualizations::ClassBoxplot(ITS,Classification)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DataVisualizations.Rmd’ using rmarkdown
Quitting from lines 40-43 (DataVisualizations.Rmd) 
Error: processing vignette 'DataVisualizations.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DataVisualizations.Rmd’

SUMMARY: processing the following file failed:
  ‘DataVisualizations.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘R.methodsS3’ ‘R.oo’ ‘akima’ ‘graphics’ ‘grid’ ‘lattice’ ‘locfit’
  ‘matlab’ ‘xtable’
  Please remove these calls from your code.
'library' or 'require' call to ‘R.matlab’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘R.methodsS3’ ‘R.oo’ ‘akima’ ‘grid’ ‘lattice’ ‘locfit’ ‘matlab’
  ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DAT : DATrun : calch: no visible global function definition for
  ‘preplot’
DAT : DATrun: no visible global function definition for ‘rot90’
DAT : DATrun: no visible global function definition for ‘median’
DAT : DATrun: no visible global function definition for ‘locfit.robust’
DAT : DATrun: no visible global function definition for ‘preplot’
DAT : DATrun: no visible global function definition for ‘dev.new’
DAT : DATrun: no visible global function definition for ‘image’
DAT : DATrun: no visible global function definition for ‘palette’
DAT : DATrun: no visible global function definition for
  ‘colorRampPalette’
DAT : DATrun: no visible global function definition for ‘text’
DAT : DATrun: no visible global function definition for ‘dev.set’
DAT : DATrun: no visible global function definition for ‘locator’
DAT : DATrun: no visible global function definition for ‘graphics.off’
DAT : DATrun: no visible global function definition for ‘pdf’
DAT : DATrun: no visible global function definition for ‘layout’
DAT : DATrun: no visible global function definition for ‘par’
DAT : DATrun: no visible global function definition for ‘plot’
DAT : DATrun: no visible global function definition for ‘frame’
DAT : DATrun: no visible global function definition for ‘lines’
DAT : DATrun: no visible global function definition for ‘dev.off’
DAT : DATrun: no visible global function definition for ‘writeMat’
DAT: no visible binding for global variable ‘DAT.simData’
Undefined global functions or variables:
  DAT.simData colorRampPalette dev.new dev.off dev.set frame
  graphics.off image layout lines locator locfit.robust median palette
  par pdf plot preplot rot90 text writeMat
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "dev.set", "graphics.off", "palette", "pdf")
  importFrom("graphics", "frame", "image", "layout", "lines", "locator",
             "par", "plot", "text")
  importFrom("stats", "median", "preplot")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘daymetr-vignette.Rmd’ using rmarkdown
Sitename set to default - tmp
Quitting from lines 85-92 (daymetr-vignette.Rmd) 
Error: processing vignette 'daymetr-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘daymetr-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘daymetr-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘RMySQL’ ‘gWidgets’
  Please remove these calls from your code.
dbEmpLikeGOF: no visible global function definition for ‘runif’
dbEmpLikeGOF: no visible global function definition for ‘var’
dbEmpLikeGOF: no visible global function definition for ‘rnorm’
emplikeGOFinternal: no visible global function definition for ‘var’
getCutoff: no visible binding for global variable ‘unifCut’
getCutoff: no visible binding for global variable ‘normCut’
getCutoff: no visible global function definition for ‘lm’
getCutoff: no visible binding for global variable ‘distEqCut’
getPval: no visible binding for global variable ‘unifCut’
getPval: no visible binding for global variable ‘normCut’
getPval: no visible global function definition for ‘lm’
getPval: no visible binding for global variable ‘distEqCut’
helperPval: no visible global function definition for ‘lm’
returnCutoff: no visible global function definition for ‘quantile’
testfun2: no visible global function definition for ‘runif’
testfun2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  distEqCut lm normCut quantile rnorm runif unifCut var
Consider adding
  importFrom("stats", "lm", "quantile", "rnorm", "runif", "var")
to your NAMESPACE file.
computePval: no visible global function definition for ‘lm’
computeQhat: no visible global function definition for ‘pnorm’
dbELnorm: no visible global function definition for ‘rnorm’
getCutoffTableThree: no visible global function definition for ‘lm’
getCutoffTableTwo: no visible global function definition for ‘lm’
getCutoffValue: no visible global function definition for ‘lm’
helperGetTstat: no visible global function definition for ‘rnorm’
returnCutoffValue: no visible global function definition for ‘rnorm’
returnCutoffValue: no visible global function definition for ‘quantile’
varianceEstimator: no visible global function definition for ‘density’
varianceEstimator: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf lm pnorm quantile rnorm
Consider adding
  importFrom("stats", "density", "ecdf", "lm", "pnorm", "quantile",
             "rnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘fdrtool’ which was already attached by Depends.
  Please remove these calls from your code.
avelinkdis: no visible global function definition for ‘sd’
avelinkdis: no visible global function definition for ‘dist’
centdis: no visible global function definition for ‘sd’
centdis: no visible global function definition for ‘dist’
distable: no visible global function definition for ‘write.table’
functionall: no visible global function definition for ‘read.table’
randdis: no visible global function definition for ‘write.table’
valuep: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  dist read.table sd write.csv write.table
Consider adding
  importFrom("stats", "dist", "sd")
  importFrom("utils", "read.table", "write.csv", "write.table")
to your NAMESPACE file.
Running examples in ‘dbmss-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot
> ### Title: ggplot methods to plot dbmss objects
> ### Aliases: autoplot.envelope
> 
> ### ** Examples
> 
> data(paracou16)
> # Keep only 20% of points to run this example
> X <- as.wmppp(rthin(paracou16, 0.2))
> 
> # Plot the envelope (should be 1000 simulations, reduced to 20 to save time)
> autoplot(KdEnvelope(X, ReferenceType="Q. Rosea", NumberOfSimulations=20))
Generating 20 simulations by evaluating expression  ...
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,  20.

Done.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dbparser.Rmd’ using rmarkdown
Quitting from lines 90-96 (dbparser.Rmd) 
Error: processing vignette 'dbparser.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dbparser.Rmd’

SUMMARY: processing the following file failed:
  ‘dbparser.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘dbplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dbplot_bar
> ### Title: Bar plot
> ### Aliases: dbplot_bar
> 
> ### ** Examples
> 
> 
> library(ggplot2)
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> 
> # Returns a plot of the row count per am
> mtcars %>%
+   dbplot_bar(am)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘DCEM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dcem_train
> ### Title: dcem_train: Part of DCEM package.
> ### Aliases: dcem_train
> 
> ### ** Examples
> 
> # Simulating a mixture of univariate samples from three distributions
> # with mean as 20, 70 and 100 and standard deviation as 10, 100 and 40 respectively.
> sample_uv_data = as.data.frame(c(rnorm(1000, 20, 10), rnorm(500, 70, 100),
+ rnorm(2000, 100, 40)), row=3500)
Warning in as.data.frame.numeric(c(rnorm(1000, 20, 10), rnorm(500, 70, 100),  :
  'row.names' is not a character vector of length 3500 -- omitting it. Will be an error!
> 
> # Randomly shuffle the samples.
> sample_uv_data = as.data.frame(sample_uv_data[sample(1:nrow(sample_uv_data)),],
+ row=nrow(sample_uv_data))
Warning in as.data.frame.numeric(sample_uv_data[sample(1:nrow(sample_uv_data)),  :
  'row.names' is not a character vector of length 3500 -- omitting it. Will be an error!
> 
> # Calling the dcem_train() function on the simulated data with threshold of
> # 0.000001 and iteration count of 1000 respectively.
> sample_uv_out = dcem_train(sample_uv_data, num_clusters = 3, iteration_count = 1000,
+ threshold = 0.000001)
Error in if (mean_diff < threshold) { : 
  missing value where TRUE/FALSE needed
Calls: dcem_train -> dcem_cluster_uv
Execution halted
.CA.fast2: no visible global function definition for ‘lsfit’
.T2.fast: no visible global function definition for ‘txtProgressBar’
.T2.fast: no visible global function definition for ‘setTxtProgressBar’
.dcemri.bayes: no visible global function definition for ‘median’
.dcemri.bayes: no visible global function definition for ‘sd’
.dcemri.map : posterior: no visible global function definition for
  ‘dnorm’
.dcemri.map : posterior: no visible global function definition for
  ‘dgamma’
.dcemri.map : posterior: no visible global function definition for
  ‘dbeta’
.dcemri.map.single: no visible global function definition for ‘optim’
.dcemri.spline: no visible binding for global variable ‘median’
.dcemri.spline: no visible global function definition for ‘median’
.dcemri.spline.single: no visible binding for global variable
  ‘quantile’
.dcemri.spline.single: no visible binding for global variable ‘median’
.dcemri.spline.single: no visible global function definition for
  ‘median’
.ftm: no visible global function definition for ‘fft’
.ftm: no visible global function definition for ‘matplot’
.ftm: no visible global function definition for ‘legend’
compartmentalModel : <anonymous>: no visible global function definition
  for ‘approx’
convFFT: no visible global function definition for ‘fft’
extractAIF : c.start: no visible global function definition for ‘sd’
extractAIF : c.start: no visible global function definition for ‘cor’
Undefined global functions or variables:
  approx cor dbeta dgamma dnorm fft legend lsfit matplot median optim
  quantile sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cor", "dbeta", "dgamma", "dnorm", "fft",
             "lsfit", "median", "optim", "quantile", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.LM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
getDelimiter: no visible global function definition for ‘read.csv’
setupfile: no visible global function definition for ‘read.csv’
treatPath: no visible global function definition for ‘file_test’
Undefined global functions or variables:
  file_test read.csv
Consider adding
  importFrom("utils", "file_test", "read.csv")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘algorithm.Rmd’ using rmarkdown
--- finished re-building ‘algorithm.Rmd’

--- re-building ‘extend.Rmd’ using rmarkdown
Quitting from lines 205-213 (extend.Rmd) 
Error: processing vignette 'extend.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘extend.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown

Attaching package: 'ddpcr'

The following object is masked from 'package:stats':

    step

Reading data files into plate... DONE (1 seconds)
Initializing plate of type `custom_thresholds`... DONE (0 seconds)
Identifying outlier droplets... DONE (0 seconds)
Classifying droplets... DONE (0 seconds)
Analysis complete
Quitting from lines 134-152 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘overview.Rmd’

--- re-building ‘technical_details.Rmd’ using rmarkdown
--- finished re-building ‘technical_details.Rmd’

SUMMARY: processing the following files failed:
  ‘extend.Rmd’ ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
ifft: no visible global function definition for ‘fft’
lines.deamer: no visible global function definition for ‘lines’
plot.deamer: no visible global function definition for ‘plot’
rlaplace: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fft lines plot runif
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
Running examples in ‘deaR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.dea
> ### Title: Plot for DEA models.
> ### Aliases: plot.dea
> 
> ### ** Examples
> 
> data_example <- read_data(datadea = Fortune500,
+                           dmus = 1,
+                           inputs = 2:4, 
+                           outputs = 5:6)
> result <- model_basic(data_example)
> plot(result)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
compare.relimp: no visible global function definition for ‘qchisq’
compare.relimp: no visible global function definition for ‘pchisq’
plot_transition: no visible global function definition for ‘dnorm’
plot_transition: no visible global function definition for ‘par’
plot_transition: no visible global function definition for ‘plot’
plot_transition: no visible global function definition for ‘lines’
plot_transition: no visible global function definition for ‘plogis’
plot_transition: no visible global function definition for ‘axis’
plot_transition: no visible global function definition for ‘mtext’
relative.importance: no visible global function definition for ‘glm’
relative.importance: no visible global function definition for ‘sd’
relative.importance : tr.pr: no visible global function definition for
  ‘pnorm’
relative.importance: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis plot pnorm qchisq sd
  vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MultiObjectiveDecisionAnalysisinR.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine

Quitting from lines 125-129 (MultiObjectiveDecisionAnalysisinR.Rmd) 
Error: processing vignette 'MultiObjectiveDecisionAnalysisinR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MultiObjectiveDecisionAnalysisinR.Rmd’

SUMMARY: processing the following file failed:
  ‘MultiObjectiveDecisionAnalysisinR.Rmd’

Error: Vignette re-building failed.
Execution halted
DeconCPdf: no visible global function definition for ‘bw.nrd0’
DeconCPdf: no visible global function definition for ‘bw.nrd’
DeconCPdf: no visible global function definition for ‘bw.ucv’
DeconCPdf: no visible global function definition for ‘bw.bcv’
DeconCPdf: no visible global function definition for ‘bw.SJ’
DeconCPdf: no visible global function definition for ‘density’
DeconCPdf: no visible global function definition for ‘dnorm’
bw.dboot2 : suppL2: no visible global function definition for ‘density’
bw.dboot2 : suppL2: no visible global function definition for ‘rnorm’
bw.dboot2 : gaussL2: no visible global function definition for
  ‘density’
bw.dboot2 : gaussL2: no visible global function definition for ‘rnorm’
bw.dmise: no visible global function definition for ‘var’
plot.Decon: no visible global function definition for ‘plot.default’
plot.Decon: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm plot.default
  rnorm var
Consider adding
  importFrom("graphics", "abline", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "rnorm", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Deducer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to ‘klaR’ which was already attached by Depends.
  Please remove these calls from your code.
.makeICCDialog: no visible global function definition for ‘J’
.makeICCDialog: no visible global function definition for ‘new’
.makeICCDialog: no visible global function definition for ‘.jnull’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘new’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘J’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘toJava’
.makeNewLDADialog: no visible global function definition for ‘new’
.makeNewLDADialog: no visible global function definition for ‘J’
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for ‘new’
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for ‘toJava’
.makeNewLDADialog: no visible global function definition for ‘toJava’
.makeNewReliabilityDialog: no visible global function definition for
  ‘new’
.makeNewReliabilityDialog: no visible global function definition for
  ‘toJava’
.onLoad: no visible global function definition for ‘.jnull’
.onLoad: no visible global function definition for ‘jgr.getMenuNames’
.onLoad: no visible global function definition for ‘jgr.insertMenu’
.onLoad: no visible global function definition for ‘jgr.addMenu’
.onLoad: no visible global function definition for ‘jgr.addMenuItem’
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘Deducer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggcorplot
> ### Title: Correlation matrix
> ### Aliases: ggcorplot
> 
> ### ** Examples
> 
> data(mtcars)
> corr.mat1<-cor.matrix(variables=d(mpg,carb,carb+rnorm(length(carb))),,
+ 	 data=mtcars,
+ 	 test=cor.test,
+ 	 method='spearman',
+ 	alternative="two.sided",exact=FALSE)
> 	
> p<-ggcorplot(corr.mat1,data = mtcars)
> print(p)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘UScensus2010’
A package should be listed in only one of these fields.
Non-standard file/directory found at top level:
  ‘org’
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.makeQuickWordcloud: no visible global function definition for ‘J’
.makeQuickWordcloud: no visible global function definition for ‘new’
.makeQuickWordcloud: no visible global function definition for ‘.jnull’
.makeTextPlot: no visible global function definition for ‘J’
.makeTextPlot: no visible global function definition for ‘new’
.makeTextPlot: no visible global function definition for ‘.jnull’
.onLoad: no visible global function definition for ‘.jpackage’
.onLoad: no visible global function definition for ‘.jnew’
.onLoad: no visible global function definition for ‘J’
make.color.scale: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  .jnew .jnull .jpackage J new rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
binary.state: no visible global function definition for ‘runif’
dbn.dnn.train: no visible global function definition for ‘runif’
dropout.mask: no visible global function definition for ‘runif’
nn.train: no visible global function definition for ‘runif’
rbm.train: no visible global function definition for ‘runif’
sae.dnn.train: no visible global function definition for ‘runif’
show.digit: no visible global function definition for ‘gray’
show.digit: no visible global function definition for ‘image’
Undefined global functions or variables:
  gray image runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
DEEPR : perm_function: no visible global function definition for ‘head’
DEEPR : perm_function: no visible global function definition for ‘tail’
simCophy: no visible global function definition for ‘rpois’
simCophy: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  head rmultinom rpois tail
Consider adding
  importFrom("stats", "rmultinom", "rpois")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
kern: no visible global function definition for ‘var’
kern: no visible global function definition for ‘dnorm’
pdeg: no visible global function definition for ‘var’
pdeg: no visible global function definition for ‘dnorm’
z.b: no visible binding for global variable ‘var’
z.s: no visible binding for global variable ‘var’
Undefined global functions or variables:
  dnorm var
Consider adding
  importFrom("stats", "dnorm", "var")
to your NAMESPACE file.
Running examples in ‘degenes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: deg
> ### Title: Detection of differentially expressed genes.
> ### Aliases: deg
> 
> ### ** Examples
> 
> X1 = matrix(rnorm(2000, 0, 1), 200, 10)
> X2 = matrix(rnorm(2000, 0, 1), 200, 10)
> index = sample(1:200, 5, replace=FALSE)
> X2[index,] = X2[index,] + 5
> D = deg(X1, X2)
Fri Mar 29 19:12:22 2019
Calculation of Z
Calculation of z
Calculation of the kernel estimator
Calculation of the kernel estimator
Determination of the rejection region
Error in if (integral > single.alpha) c1 <- c : 
  missing value where TRUE/FALSE needed
Calls: deg
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ODE_parameter_inference.Rmd’ using rmarkdown
Quitting from lines 115-125 (ODE_parameter_inference.Rmd) 
Error: processing vignette 'ODE_parameter_inference.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ODE_parameter_inference.Rmd’

SUMMARY: processing the following file failed:
  ‘ODE_parameter_inference.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/deisotoper.Rcheck/00install.out’ for details.
Found an obsolete/platform-specific call in the following function:
  ‘dr_df’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
bootbagg: no visible global function definition for ‘runif’
bootworpl: no visible global function definition for ‘runif’
des12: no visible global function definition for ‘rnorm’
des12: no visible global function definition for ‘runif’
eval.stage.gauss: no visible global function definition for ‘var’
plotparti: no visible global function definition for ‘plot’
plotparti: no visible global function definition for ‘lines’
plotpartilev: no visible global function definition for ‘plot’
plotpartilev: no visible global function definition for ‘polygon’
plotpartilev: no visible global function definition for ‘points’
simesi: no visible global function definition for ‘runif’
simesi3d: no visible global function definition for ‘runif’
simfssk: no visible global function definition for ‘rnorm’
simfssk: no visible global function definition for ‘runif’
simmix.delt: no visible global function definition for ‘rnorm’
simmix.delt: no visible global function definition for ‘runif’
simpp: no visible global function definition for ‘rnorm’
simpp: no visible global function definition for ‘runif’
simutree: no visible global function definition for ‘runif’
stage.gaussR: no visible global function definition for ‘var’
unidis: no visible global function definition for ‘runif’
Undefined global functions or variables:
  lines plot points polygon rnorm runif var
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Bootstrapping.CI: no visible global function definition for ‘quantile’
D.Jost: no visible global function definition for ‘read.table’
D.Jost: no visible global function definition for ‘write.table’
Dv.locis.corrected.calc: no visible global function definition for
  ‘p.adjust’
Gst.Nei: no visible global function definition for ‘read.table’
Gst.Nei: no visible global function definition for ‘write.table’
H.out: no visible global function definition for ‘write.table’
Hardy.calc: no visible global function definition for ‘chisq.test’
critical.ci.values: no visible global function definition for
  ‘quantile’
inputformat: no visible global function definition for ‘read.table’
inputformat: no visible global function definition for ‘write.table’
over.all.pops: no visible global function definition for ‘write.table’
p.value.correcture: no visible global function definition for
  ‘p.adjust’
pair.pops: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.

Found the following calls to attach():
File ‘DEMEtics/R/inputformat.r’:
  attach(y)
See section ‘Good practice’ in ‘?attach’.
DEMIPathway: no visible global function definition for ‘dhyper’
DEMIPathway: no visible global function definition for ‘p.adjust’
calcHypergeoExon: no visible global function definition for ‘dhyper’
calcHypergeoProb: no visible global function definition for ‘dhyper’
demi: no visible global function definition for ‘write.table’
demi.t.test: no visible global function definition for ‘t.test’
demi.wilcox.test: no visible global function definition for
  ‘wilcox.test’
demi.wilcox.test.fast: no visible global function definition for
  ‘wilcox.test’
demiequal: no visible global function definition for ‘wilcox.test’
wprob: no visible global function definition for ‘combn’
diffexp,DEMIDiff: no visible global function definition for ‘median’
diffexp,DEMIDiff: no visible global function definition for ‘p.adjust’
loadAnnotation,DEMIExperiment-environment: no visible global function
  definition for ‘data’
loadBlat,DEMIExperiment-environment: no visible global function
  definition for ‘data’
loadCytoband,DEMIExperiment-environment: no visible global function
  definition for ‘data’
loadPathway,DEMIExperiment-environment: no visible global function
  definition for ‘data’
Undefined global functions or variables:
  combn data dhyper median p.adjust t.test wilcox.test write.table
Consider adding
  importFrom("stats", "dhyper", "median", "p.adjust", "t.test",
             "wilcox.test")
  importFrom("utils", "combn", "data", "write.table")
to your NAMESPACE file.
Running examples in ‘DendroSync-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sync.plot
> ### Title: Plot within- and between-group synchrony
> ### Aliases: sync.plot
> 
> ### ** Examples
> 
> ## Plot homoscedastic narrow evaluation (mNE) and unstructured model (mUN)
>  # synchronies for conifersIP data:
>  data(conifersIP)
>      
>  ##Fit the homoscedastic set of varcov models (mBE, mNE, mCS, mUN)
>  # using geographic grouping criteria (ie. Region)
>  ModHm <- dendro.varcov(TRW ~ Code, varTime = "Year", varGroup = "Region", 
+                         data = conifersIP, homoscedastic = TRUE)
[1] "Please wait. I am fitting the models now :)"
>  
>  sync.plot(sync(ModHm, modname = "mNE"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: sync.plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘dendroTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glimpse_daily_data
> ### Title: glimpse_daily_data
> ### Aliases: glimpse_daily_data
> 
> ### ** Examples
> 
> data("LJ_daily_temperatures")
> glimpse_daily_data(env_data = LJ_daily_temperatures, tidy_env_data = FALSE, na.color = "white")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Examples_daily_response.Rmd’ using rmarkdown
Quitting from lines 36-43 (Examples_daily_response.Rmd) 
Error: processing vignette 'Examples_daily_response.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Examples_daily_response.Rmd’

--- re-building ‘compare_methods_vignette.Rmd’ using rmarkdown
Quitting from lines 53-55 (compare_methods_vignette.Rmd) 
Error: processing vignette 'compare_methods_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘compare_methods_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘Examples_daily_response.Rmd’ ‘compare_methods_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
DendSer: no visible global function definition for ‘getFromNamespace’
crit2cost : <anonymous>: no visible global function definition for
  ‘as.dist’
dser.dist: no visible global function definition for ‘hclust’
dser.matrix: no visible global function definition for ‘dist’
plotAsColor: no visible global function definition for ‘image’
plotAsColor: no visible global function definition for ‘box’
plotAsColor: no visible global function definition for ‘axis’
seriation_method_dist_dser: no visible global function definition for
  ‘hclust’
seriation_method_dist_dser: no visible global function definition for
  ‘modifyList’
seriation_method_leafsort: no visible global function definition for
  ‘modifyList’
Undefined global functions or variables:
  as.dist axis box dist getFromNamespace hclust image modifyList
Consider adding
  importFrom("graphics", "axis", "box", "image")
  importFrom("stats", "as.dist", "dist", "hclust")
  importFrom("utils", "getFromNamespace", "modifyList")
to your NAMESPACE file.
Running examples in ‘densityClust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDensityClust
> ### Title: Plot densityCluster results
> ### Aliases: plotDensityClust
> 
> ### ** Examples
> 
> data(iris)
> data.dist <- dist(iris[, 1:4])
> pca <- princomp(iris[, 1:4])
> 
> # Run initial density clustering
> dens.clust <- densityClust(data.dist)
Distance cutoff calculated to 0.2767655 
> op <- par(ask = TRUE)
> 
> # Show the decision graph
> plotDensityClust(dens.clust, type = "dg")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotDensityClust ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package suggested but not available for checking: ‘Rdonlp2’
Running examples in ‘DepthProc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DepthCurve-class
> ### Title: DepthCurve
> ### Aliases: DepthCurve-class
> 
> ### ** Examples
> 
> library(mvtnorm)
> x <- mvrnorm(n = 100, mu = c(0, 0), Sigma = 2 * diag(2))
> y <- rmvt(n = 100, sigma = diag(2), df = 4)
> s1 <- scaleCurve(x, depth_params = list(method = "Projection"))
> s2 <- scaleCurve(y, depth_params = list(method = "Projection"), name = "Set2")
> 
> sc_list <- combineDepthCurves(s1, s2) # Add one curve to another
> 
> plot(sc_list) # Draw plot with two curves
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
MBD: no visible global function definition for ‘par’
MBD: no visible global function definition for ‘gray’
MBD: no visible global function definition for ‘matplot’
MBD: no visible global function definition for ‘polygon’
MBD: no visible global function definition for ‘lines’
MBD: no visible global function definition for ‘legend’
MBD: no visible global function definition for ‘matlines’
R.test: no visible global function definition for ‘runif’
R.test: no visible global function definition for ‘wilcox.test’
centralPlot: no visible global function definition for ‘par’
centralPlot: no visible global function definition for
  ‘colorRampPalette’
centralPlot: no visible global function definition for ‘matplot’
centralPlot: no visible global function definition for ‘matlines’
centralPlot: no visible global function definition for ‘legend’
scalecurve: no visible global function definition for ‘plot’
scalecurve: no visible global function definition for ‘lines’
scalecurve: no visible global function definition for ‘legend’
tmean: no visible global function definition for ‘matplot’
tmean: no visible global function definition for ‘matlines’
tmean: no visible global function definition for ‘lines’
tmean: no visible global function definition for ‘legend’
tmean: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette gray legend lines matlines matplot par plot polygon
  runif wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "legend", "lines", "matlines", "matplot", "par",
             "plot", "polygon")
  importFrom("stats", "runif", "wilcox.test")
to your NAMESPACE file.
Running examples in ‘DescribeDisplay-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_axis
> ### Title: Geom Axis.
> ### Aliases: geom_axis
> ### Keywords: internal
> 
> ### ** Examples
> 
> library(ggplot2)
> print(ggplot(dd_example("tour2d")))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘descriptr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dist_binom_plot
> ### Title: Visualize binomial distribution
> ### Aliases: dist_binom_plot dist_binom_prob dist_binom_perc
> 
> ### ** Examples
> 
> # visualize binomial distribution
> dist_binom_plot(10, 0.3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: dist_binom_plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘categorical-data.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 57-59 (categorical-data.Rmd) 
Error: processing vignette 'categorical-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘categorical-data.Rmd’

--- re-building ‘continuous-data.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 84-86 (continuous-data.Rmd) 
Error: processing vignette 'continuous-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘continuous-data.Rmd’

--- re-building ‘visualization.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 46-47 (visualization.Rmd) 
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘visualization.Rmd’

SUMMARY: processing the following files failed:
  ‘categorical-data.Rmd’ ‘continuous-data.Rmd’ ‘visualization.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘RDCOMClient’
ds: no visible global function definition for ‘is.ts’
ds: no visible global function definition for ‘frequency’
getds: no visible global function definition for ‘resid’
getds: no visible global function definition for ‘lm.fit’
getds: no visible global function definition for ‘sd’
getds: no visible global function definition for ‘var’
getds: no visible global function definition for ‘fitted’
Undefined global functions or variables:
  fitted frequency is.ts lm.fit resid sd var
Consider adding
  importFrom("stats", "fitted", "frequency", "is.ts", "lm.fit", "resid",
             "sd", "var")
to your NAMESPACE file.
arrayUpdate : pairUpdate: no visible global function definition for
  ‘runif’
conditionUpdate: no visible global function definition for ‘runif’
designGG: no visible global function definition for ‘runif’
experimentDesignTable: no visible global function definition for
  ‘write.csv’
plotAllScores: no visible global function definition for ‘png’
plotAllScores: no visible global function definition for ‘par’
plotAllScores: no visible global function definition for ‘plot’
plotAllScores: no visible global function definition for ‘text’
plotAllScores: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par plot png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘gurobi’
fs.agreement.part: no visible global function definition for ‘as.dist’
fs.agreement.part: no visible global function definition for ‘cor’
fs.leave.k.out.combn: no visible global function definition for ‘sd’
fs.leave.k.out.sample: no visible global function definition for ‘sd’
fs.rd: no visible global function definition for ‘pchisq’
fs.selection: no visible global function definition for ‘p.adjust’
plot.FIT: no visible global function definition for ‘qchisq’
plot.FIT: no visible global function definition for ‘ppoints’
plot.FIT: no visible global function definition for ‘plot’
plot.FIT: no visible global function definition for ‘points’
plot.FIT: no visible global function definition for ‘abline’
plotJn: no visible global function definition for ‘plot’
plotJn: no visible global function definition for ‘points’
robust.distance.signed: no visible global function definition for
  ‘mahalanobis’
snowball: no visible global function definition for ‘is’
snowball: no visible global function definition for ‘median’
weight.sd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq plot points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘detectRUNS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_DistributionRuns
> ### Title: Plot Distribution of runs
> ### Aliases: plot_DistributionRuns
> 
> ### ** Examples
> 
> # getting map and ped paths
> genotypeFile <- system.file("extdata", "Kijas2016_Sheep_subset.ped", package = "detectRUNS")
> mapFile <- system.file("extdata", "Kijas2016_Sheep_subset.map", package = "detectRUNS")
> 
> # calculating runs of Homozygosity
> ## Not run: 
> ##D # skipping runs calculation
> ##D runs <- slidingRUNS.run(genotypeFile, mapFile, windowSize = 15, threshold = 0.1,  minSNP = 15,
> ##D ROHet = FALSE,  maxOppositeGenotype = 1, maxMiss = 1,  minLengthBps = 100000,  minDensity = 1/10000)
> ## End(Not run)
> # loading pre-calculated data
> runsFile <- system.file("extdata", "Kijas2016_Sheep_subset.sliding.csv", package="detectRUNS")
> runsDF <- readExternalRuns(inputFile = runsFile, program = 'detectRUNS')
Loading file from detectRUNS
> 
> plot_InbreedingChr(runs = runsDF, mapFile = mapFile, style='All')
Total genome length: 290826950
calculating Froh chromosome by chromosome
Total genome length: 290826950
calculating Froh on all genome
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_InbreedingChr ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Package in Depends field not imported from: ‘dplR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.get’ ‘InteractiveDetrending’ ‘RemoveTrend’
Error(s) in re-building vignettes:
  ...
--- re-building ‘batch-mode.Rmd’ using rmarkdown
--- finished re-building ‘batch-mode.Rmd’

--- re-building ‘single-images.Rmd’ using rmarkdown
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Quitting from lines 48-66 (single-images.Rmd) 
Error: processing vignette 'single-images.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘single-images.Rmd’

SUMMARY: processing the following file failed:
  ‘single-images.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  GetData.c:342:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
  GetData.c:355:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DetSel.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘ash’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running ‘test-that.R’ [79s/156s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  --- re-building ‘new.Rnw’ using Sweave
  --- finished re-building ‘new.Rnw’
  
  --- re-building ‘new.Rnw’ using Sweave
  --- finished re-building ‘new.Rnw’
  
  --- re-building ‘new.Rnw’ using Sweave
  --- finished re-building ‘new.Rnw’
  
  --- re-building ‘test.Rmd’ using knitr
  --- finished re-building ‘test.Rmd’
  
  --- re-building ‘test.Rmd’ using knitr
  --- finished re-building ‘test.Rmd’
  
  --- re-building ‘new.Rnw’ using Sweave
  --- finished re-building ‘new.Rnw’
  
  ── 1. Error: vignettes built on install (@test-vignettes.R#118)  ───────────────
  there is no package called 'testVignettesBuilt'
  1: vignette(package = "testVignettesBuilt") at testthat/test-vignettes.R:118
  2: tools::getVignetteInfo(package, lib.loc, all)
  3: find.package(package, lib.loc)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 41 SKIPPED: 11 FAILED: 1
  1. Error: vignettes built on install (@test-vignettes.R#118) 
  
  Error: testthat unit tests failed
  Execution halted
Unexported objects imported by ':::' calls:
  ‘dexter:::get_resp_data’ ‘dexter:::qcolors’
  See the note in ?`:::` about the use of this operator.
Error(s) in re-building vignettes:
  ...
--- re-building ‘multistage_fundamentals.Rmd’ using rmarkdown
Computing non-mst profile_tables over an mst design, did you mean to use profile_tables_mst?
Warning: Removed 33 rows containing missing values (geom_point).
Quitting from lines 282-313 (multistage_fundamentals.Rmd) 
Error: processing vignette 'multistage_fundamentals.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘multistage_fundamentals.Rmd’

SUMMARY: processing the following file failed:
  ‘multistage_fundamentals.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Equating.Rmd’ using rmarkdown
no column `person_id` provided, automatically generating unique person id's
Quitting from lines 116-130 (Equating.Rmd) 
Error: processing vignette 'Equating.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Equating.Rmd’

--- re-building ‘Plausible_Values.Rmd’ using rmarkdown
--- finished re-building ‘Plausible_Values.Rmd’

--- re-building ‘Test_Individual_differences.Rmd’ using rmarkdown
--- finished re-building ‘Test_Individual_differences.Rmd’

--- re-building ‘data_management.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: RSQLite
--- finished re-building ‘data_management.Rmd’

--- re-building ‘dexter.Rmd’ using rmarkdown
Loading required package: RSQLite
--- finished re-building ‘dexter.Rmd’

--- re-building ‘profile-plots.Rmd’ using rmarkdown
no column `person_id` provided, automatically generating unique person id's
--- finished re-building ‘profile-plots.Rmd’

SUMMARY: processing the following file failed:
  ‘Equating.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘dfConn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_generate_timeDependence
> ### Title: 95% Coverage time dependence plots for dFCM
> ### Aliases: plot_generate_timeDependence
> 
> ### ** Examples
> 
> data(DynModel_results) # Load sample model result object
> scan.length <- DynModel_results$params$ntp_per_scan
> plot_generate_timeDependence(DynModel_results$est_CI[1], scan.length, rois=c(114,134))
Loading required namespace: ggplot2
[[1]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for ‘rbinom’
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for ‘rnorm’
simulate_dataframe : generate_initial: no visible global function
  definition for ‘rbinom’
simulate_dataframe: no visible binding for global variable ‘randu’
simulate_dataframe: no visible global function definition for ‘rbinom’
simulate_dataframe: no visible global function definition for ‘rnorm’
simulate_dataframe: no visible global function definition for ‘rpois’
simulate_dataframe : add_NAs: no visible global function definition for
  ‘rbinom’
Undefined global functions or variables:
  randu rbinom rnorm rpois
Consider adding
  importFrom("datasets", "randu")
  importFrom("stats", "rbinom", "rnorm", "rpois")
to your NAMESPACE file.
Running examples in ‘dfexplore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dfexplore-package
> ### Title: Data-frame explorer
> ### Aliases: dfexplore-package dfexplore
> ### Keywords: package
> 
> ### ** Examples
> 
> dfplot(example_df)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘test_dfplot.R’ [1s/2s]
  Running ‘test_expand_dfmatrix.R’ [1s/1s]
  Running ‘test_simulate_dataframe.R’ [1s/2s]
Running the tests in ‘tests/test_dfplot.R’ failed.
Complete output:
  > library(dfexplore)
  Loading required package: ggplot2
  > #test_dfplot
  > data(example_df)
  > dfplot(example_df)
  Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
    VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
  Execution halted
Running examples in ‘DFIT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotNcdif
> ### Title: Plot the item characteristic (expected score) curve for focal
> ###   and reference groups for the iiItem along with a representation of
> ###   the focal group density.
> ### Aliases: PlotNcdif
> 
> ### ** Examples
> 
> 
> data(dichotomousItemParameters)
> # # Non Uniform - != guess DIF item close to focal distribution
> PlotNcdif(iiItem = 46, itemParameters = dichotomousItemParameters, irtModel = "3pl",
+           plotDensity = FALSE, main = "Item 46 Non uniform and different guessing DIF. 3PL")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Dforest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DF_easy
> ### Title: Simple pre-defined pipeline for Decision forest
> ### Aliases: DF_easy
> 
> ### ** Examples
> 
>   # data(demo_simple)
>   X = iris[,1:4]
>   Y = iris[,5]
>   names(Y)=rownames(X)
> 
>   random_seq=sample(nrow(X))
>   split_rate=3
>   split_sample = suppressWarnings(split(random_seq,1:split_rate))
>   Train_X = X[-random_seq[split_sample[[1]]],]
>   Train_Y = Y[-random_seq[split_sample[[1]]]]
>   Test_X = X[random_seq[split_sample[[1]]],]
>   Test_Y = Y[random_seq[split_sample[[1]]]]
> 
>   Result = DF_easy(Train_X, Train_Y, Test_X, Test_Y)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: DF_easy ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
makeAdjMatrix: no visible global function definition for ‘combn’
plotPosteriorN: no visible global function definition for ‘plot’
plotPosteriorN: no visible global function definition for ‘title’
plotPosteriorN: no visible global function definition for ‘lines’
plotPosteriorN: no visible global function definition for ‘legend’
venn3: no visible global function definition for ‘plot’
venn3: no visible global function definition for ‘runif’
venn3: no visible global function definition for ‘points’
venn3: no visible global function definition for ‘lines’
venn3: no visible global function definition for ‘text’
venn4: no visible global function definition for ‘plot’
venn4: no visible global function definition for ‘lines’
venn4: no visible global function definition for ‘runif’
venn4: no visible global function definition for ‘points’
Undefined global functions or variables:
  combn legend lines plot points runif text title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text",
             "title")
  importFrom("stats", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘DGCA_basic.Rmd’ using rmarkdown

Classifying the differential correlation calls.
Calculating permutation number 1.
Calculating permutation number 2.
Calculating permutation number 3.
Calculating permutation number 4.
Calculating permutation number 5.
Calculating empirical p-values using the permutation sample statistics.
Sorting the combination of the actual and permuted test statistics.
Finding the proportion of each actual test statistic greater than the permuted test statistics.
Calculating qvalues from the empirical p-values.
Classifying the differential correlation calls.
Quitting from lines 65-67 (DGCA_basic.Rmd) 
Error: processing vignette 'DGCA_basic.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DGCA_basic.Rmd’

SUMMARY: processing the following file failed:
  ‘DGCA_basic.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dggridR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘dggridR.Rmd’ using rmarkdown
Loading required package: rgdal
Loading required package: sp
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1 
Loading required package: ggplot2
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 16-44 (dggridR.Rmd) 
Error: processing vignette 'dggridR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dggridR.Rmd’

--- re-building ‘dggrid_v62_manual.pdf.asis’ using asis
--- finished re-building ‘dggrid_v62_manual.pdf.asis’

SUMMARY: processing the following file failed:
  ‘dggridR.Rmd’

Error: Vignette re-building failed.
Execution halted
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘integrate’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘dchisq’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘nlm’
cvm.test : cvm.stat.disc: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘runif’
cvm.test: no visible global function definition for ‘is.stepfun’
cvm.test: no visible global function definition for ‘knots’
ks.test : exact.pval : ts.pval: no visible global function definition
  for ‘ecdf’
ks.test : sim.pval: no visible global function definition for ‘runif’
ks.test : sim.pval : getks: no visible global function definition for
  ‘ecdf’
ks.test: no visible global function definition for ‘is.stepfun’
ks.test: no visible global function definition for ‘knots’
ks.test: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  dchisq ecdf integrate is.stepfun knots nlm runif
Consider adding
  importFrom("stats", "dchisq", "ecdf", "integrate", "is.stepfun",
             "knots", "nlm", "runif")
to your NAMESPACE file.
Running examples in ‘diagis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diagis
> ### Title: Auxiliary functions and diagnostic plots for importance sampling
> ### Aliases: diagis diagis-package
> 
> ### ** Examples
> 
> # simple importance sampling example
> # true distribution is a standard normal:
> p <- function(x) dnorm(x)
> # proposal distribution is normal with sd s
> q <- function(x, s) dnorm(x, 0, s)
> 
> # IS weights have finite variance only if s^2 > 1/2
> # variance is s/(2-1/s^2)^(3/2)
> 
> #optimal case
> set.seed(42)
> s_opt <- sqrt(2)
> x_opt <- rnorm(1000, sd = s_opt)
> w_opt <- p(x_opt) / q(x_opt, s_opt) 
> weighted_mean(x_opt, w_opt)
[1] -0.01223051
> weighted_var(x_opt, w_opt)
[1] 0.9954861
> s_inf <- 0.25
> x_inf <- rnorm(1000, sd = s_inf)
> w_inf <- p(x_inf) / q(x_inf, s_inf)
> weighted_mean(x_inf, w_inf) #!!
[1] 0.1281881
> weighted_var(x_inf, w_inf) #!!
[1] 0.2531165
> # diagnostic plots
> weight_plot(w_inf)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: weight_plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diagis.Rmd’ using rmarkdown
Quitting from lines 73-74 (diagis.Rmd) 
Error: processing vignette 'diagis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘diagis.Rmd’

SUMMARY: processing the following file failed:
  ‘diagis.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘diceR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: graphs
> ### Title: Graphical Displays
> ### Aliases: graphs graph_cdf graph_delta_area graph_heatmap graph_tracking
> ###   graph_all
> 
> ### ** Examples
> 
> # Consensus clustering for 3 algorithms
> library(ggplot2)
> suppressWarnings(RNGversion("3.5.0"))
> set.seed(911)
> x <- matrix(rnorm(80), ncol = 10)
> CC1 <- consensus_cluster(x, nk = 2:4, reps = 3,
+ algorithms = c("hc", "pam", "km"), progress = FALSE)
> 
> # Plot CDF
> p <- graph_cdf(CC1)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: graph_cdf ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
dichromat: no visible global function definition for ‘col2rgb’
dichromat: no visible global function definition for ‘predict’
dichromat: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  col2rgb predict rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("stats", "predict")
to your NAMESPACE file.
le.pesquisa: no visible global function definition for ‘txtProgressBar’
le.pesquisa: no visible global function definition for ‘type.convert’
le.pesquisa: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar type.convert
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "type.convert")
to your NAMESPACE file.
Running examples in ‘dief-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dief
> ### Title: Tools for Computing Diefficiency Metrics
> ### Aliases: dief
> ### Keywords: package
> 
> ### ** Examples
> 
> # This example uses the answer traces provided in the package.  
> # These traces record the answers produced by three approaches "Selective", 
> # "Not Adaptive", "Random"  when executing the test "Q9.sparql"
> data(traces)
> 	
> # Plot answer traces for test "Q9.sparql"
> plotAnswerTrace(traces, "Q9.sparql")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotAnswerTrace ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
L2eV: no visible binding for global variable ‘constants’
L2w: no visible binding for global variable ‘constants’
dielectric: no visible global function definition for ‘new’
dielectric2plot: no visible global function definition for ‘reshape’
eV2L: no visible binding for global variable ‘constants’
t2eV: no visible binding for global variable ‘constants’
Undefined global functions or variables:
  constants new reshape
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "reshape")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘dielectric-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AgPalik
> ### Title: AgPalik
> ### Aliases: AgPalik
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(AgPalik)
> str(AgPalik$raw())
'data.frame':	241 obs. of  4 variables:
 $ wavelength: num  0.155 0.207 0.248 0.275 0.31 ...
 $ epsilon   : cplx  1+0i 1+0i 1+0i ...
 $ real      : num  1 1 1 1 1.01 ...
 $ imag      : num  5.84e-06 1.68e-05 3.04e-05 4.42e-05 7.16e-05 ...
> AgPalik$comment
$source
[1] "Silver in the visible, Palik"

$units
[1] "nanometres"

> demo(AgPalik)


	demo(AgPalik)
	---- ~~~~~~~

> library(dielectric)

> library(ggplot2)

> data(AgPalik)

> AgPalik$set_span(200, 800)

> raw <- dielectric2plot(AgPalik$raw())

> silver <- AgPalik$predict(n=300, all.knots=TRUE, df=200)

> d <- dielectric2plot(silver)

> ggplot(d, aes(wavelength, value)) + geom_path() +
+   facet_grid(variable~., scales="free") +
+   geom_point(data=raw)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: demo ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Packages in Depends field not imported from:
  ‘PropCIs’ ‘gee’ ‘rootSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
diffpci: no visible global function definition for ‘diffpropci.Wald.mp’
diffpci: no visible global function definition for ‘diffpropci.mp’
diffpci: no visible global function definition for ‘scoreci.mp’
exact.cond : exactci: no visible global function definition for ‘qf’
exact.midp : binom.midp : f.low: no visible global function definition
  for ‘dbinom’
exact.midp : binom.midp : f.low: no visible global function definition
  for ‘pbinom’
exact.midp : binom.midp : f.up: no visible global function definition
  for ‘dbinom’
exact.midp : binom.midp : f.up: no visible global function definition
  for ‘pbinom’
exact.midp : binom.midp : one.ci: no visible global function definition
  for ‘uniroot’
np.nv: no visible global function definition for ‘qnorm’
np.t: no visible global function definition for ‘qt’
uncond: no visible global function definition for ‘qnorm’
wald.cc: no visible global function definition for ‘qnorm’
wilson: no visible global function definition for ‘qnorm’
wilson: no visible global function definition for ‘uniroot.all’
wilson.cc: no visible global function definition for ‘qnorm’
wilson.cc: no visible global function definition for ‘uniroot.all’
wilson.phi: no visible global function definition for ‘qnorm’
wilson.phi: no visible global function definition for ‘uniroot.all’
Undefined global functions or variables:
  dbinom diffpropci.Wald.mp diffpropci.mp pbinom qf qnorm qt scoreci.mp
  uniroot uniroot.all
Consider adding
  importFrom("stats", "dbinom", "pbinom", "qf", "qnorm", "qt", "uniroot")
to your NAMESPACE file.
rkMethodPlot: no visible global function definition for ‘par’
rkMethodPlot: no visible global function definition for ‘axis’
rkMethodPlot: no visible global function definition for ‘points’
rkMethodPlot: no visible global function definition for ‘text’
rkMethodPlot: no visible global function definition for ‘segments’
rkimp: no visible global function definition for ‘runif’
stability.bruteforce: no visible global function definition for ‘plot’
stability.bruteforce: no visible global function definition for
  ‘points’
stability.bruteforce: no visible global function definition for
  ‘abline’
stability.multistep: no visible global function definition for ‘plot’
stability.multistep: no visible global function definition for ‘lines’
stability.multistep: no visible global function definition for
  ‘polygon’
stability.multistep: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis lines par plot points polygon runif segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "polygon", "segments", "text")
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘diffeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MAD
> ### Title: Mean Absolute Deviation (MAD)
> ### Aliases: MAD
> ### Keywords: spatial
> 
> ### ** Examples
> 
> old.par <- par(no.readonly = TRUE)
> grid1 <- raster(system.file("external/GRID1_INT.rst", package="diffeR"))
> grid2 <- raster(system.file("external/GRID2_INT.rst", package="diffeR"))
> strata <- raster(system.file("external/strata_int.rst", package="diffeR"))
> MAD(grid1, grid2, strata, eval="original")
[1] "The mean of grid1 is less than the mean of grid2"
  Resolution Quantity Strata Element Total
1          1      2.5      0       1   3.5
> MAD(grid1, grid2, strata, eval="multiple")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: MAD ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘maptools’ ‘spatstat’ ‘spdep’
  Please remove these calls from your code.
fAssocmatrix : fAssocmatrix1: no visible global function definition for
  ‘coordinates<-’
fAssocplot: no visible global function definition for ‘plot’
fAssocplot: no visible global function definition for ‘coordinates’
fAssocplot: no visible global function definition for ‘text’
fAssocplot: no visible global function definition for ‘box’
fDrawfigure: no visible global function definition for ‘slot’
fDrawfigure : <anonymous>: no visible global function definition for
  ‘slot’
fDrawfigure: no visible global function definition for
  ‘SpatialPolygons’
fDrawfigure: no visible global function definition for ‘spsample’
fDrawfigure: no visible global function definition for ‘plot’
fDrawfigure: no visible global function definition for ‘image’
fDrawfigure: no visible global function definition for
  ‘colorRampPalette’
fDrawfigure: no visible global function definition for ‘points’
fRanXY : <anonymous>: no visible global function definition for ‘slot’
fRanXY : <anonymous>: no visible global function definition for
  ‘spsample’
Undefined global functions or variables:
  SpatialPolygons box colorRampPalette coordinates coordinates<- image
  plot points slot spsample text
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "box", "image", "plot", "points", "text")
  importFrom("methods", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  ‘Rcpp’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘dimRed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_R_NX
> ### Title: plot_R_NX
> ### Aliases: plot_R_NX
> 
> ### ** Examples
> 
> 
> ## define which methods to apply
> embed_methods <- c("Isomap", "PCA")
> ## load test data set
> data_set <- loadDataSet("3D S Curve", n = 200)
> ## apply dimensionality reduction
> data_emb <- lapply(embed_methods, function(x) embed(data_set, x))
2019-03-29 19:16:47: Isomap START
2019-03-29 19:16:47: constructing knn graph
2019-03-29 19:16:47: calculating geodesic distances
2019-03-29 19:16:47: Classical Scaling
> names(data_emb) <- embed_methods
> ## plot the R_NX curves:
> plot_R_NX(data_emb) +
+     ggplot2::theme(legend.title = ggplot2::element_blank(),
+                    legend.position = c(0.5, 0.1),
+                    legend.justification = c(0.5, 0.1))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘dint-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_date_xx
> ### Title: ggplot2 Scales For date_xx Objects
> ### Aliases: scale_date_xx scale_x_date_yq scale_y_date_yq scale_x_date_ym
> ###   scale_y_date_ym scale_x_date_yw scale_y_date_yw
> 
> ### ** Examples
> 
> if (require("ggplot2", quietly = TRUE)){
+ 
+ dd <- data.frame(date = seq(date_yq(2016, 1), date_yq(2018, 1)), V1 = 1:9)
+ p <- ggplot(dd, aes(x = date, y = V1)) +
+   geom_point()
+ 
+ p  # automatically uses the proper scale
+ p + scale_x_date_yq("quarters with default spacing")
+ p + scale_x_date_yq(breaks = date_yq_breaks(3))
+ 
+ 
+ # Different ways to specify breaks and labels
+ p <- ggplot(
+   data.frame(date = seq(date_yq(2012, 4), date_yq(2018, 4)), V1 = 1:25),
+   aes(x = date, y = V1)
+ ) +
+   geom_point()
+ 
+ p + scale_x_date_yq(labels = waiver()) + ggtitle("auto Labels")
+ p + scale_x_date_yq(labels = NULL) + ggtitle("no Labels")
+ p + scale_x_date_yq(labels = LETTERS[1:4]) + ggtitle("manual Labels")
+ p + scale_x_date_yq(labels = format_yq_iso) + ggtitle("function Labels")
+ 
+ p + scale_x_date_yq(breaks = waiver()) + ggtitle("auto breaks")
+ p + scale_x_date_yq(breaks = NULL) + ggtitle("no breaks")
+ p + scale_x_date_yq(breaks = date_yq(2013, 2:3) ) + ggtitle("manual breaks")
+ p + scale_x_date_yq(breaks = date_yq_breaks(1) ) + ggtitle("function breaks")
+ }
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dint)
  > 
  > test_check("dint")
  ── 1. Error: scale_date_xx works as expected (@test_scale_date_xx.R#17)  ───────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_silent(print(ggplot2::ggplot(tdf, ggplot2::aes(x = yq, y = vals)))) at testthat/test_scale_date_xx.R:17
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: print(ggplot2::ggplot(tdf, ggplot2::aes(x = yq, y = vals)))
  10: print.ggplot(ggplot2::ggplot(tdf, ggplot2::aes(x = yq, y = vals)))
  ...
  15: preDraw(x)
  16: preDraw.gTree(x)
  17: pushvpgp(x)
  18: pushgrobvp(x$vp)
  19: pushgrobvp.viewport(x$vp)
  20: pushViewport(vp, recording = FALSE)
  21: lapply(vps, push.vp, recording)
  22: FUN(X[[i]], ...)
  23: push.vp.viewport(X[[i]], ...)
  24: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1239 SKIPPED: 2 FAILED: 1
  1. Error: scale_date_xx works as expected (@test_scale_date_xx.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dint.Rmd’ using rmarkdown
Quitting from lines 254-287 (dint.Rmd) 
Error: processing vignette 'dint.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dint.Rmd’

SUMMARY: processing the following file failed:
  ‘dint.Rmd’

Error: Vignette re-building failed.
Execution halted
aLine: no visible global function definition for ‘lines’
aLine: no visible global function definition for ‘ecdf’
dip.test: no visible global function definition for ‘complete.cases’
dip.test: no visible global function definition for ‘runif’
dip.test: no visible global function definition for ‘approx’
plot.dip: no visible global function definition for ‘par’
plot.dip: no visible global function definition for ‘ecdf’
plot.dip: no visible global function definition for ‘plot’
plot.dip: no visible global function definition for ‘title’
plot.dip: no visible global function definition for ‘abline’
plot.dip: no visible global function definition for ‘axis’
plot.dip: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline approx axis complete.cases ecdf legend lines par plot runif
  title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "approx", "complete.cases", "ecdf", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘DirectEffects.Rmd’ using rmarkdown
Quitting from lines 150-165 (DirectEffects.Rmd) 
Error: processing vignette 'DirectEffects.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DirectEffects.Rmd’

SUMMARY: processing the following file failed:
  ‘DirectEffects.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘inlinedocs’
Running examples in ‘directlabels-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: direct.label
> ### Title: Direct labels for color decoding
> ### Aliases: direct.label directlabels
> 
> ### ** Examples
> 
> if(require(ggplot2)){
+   ## Add direct labels to a ggplot2 scatterplot, making sure that each
+   ## label is close to its point cloud, and doesn't overlap points or
+   ## other labels.
+   scatter <- qplot(jitter(hwy),jitter(cty),data=mpg,colour=class,
+                    main="Fuel efficiency depends on car size")
+   print(direct.label(scatter))
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Non-standard file/directory found at top level:
  ‘dirmult.pdf’
nullTest: no visible global function definition for ‘rmultinom’
rdirichlet: no visible global function definition for ‘rgamma’
simPop: no visible global function definition for ‘rnorm’
simPop: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  rgamma rmultinom rnorm
Consider adding
  importFrom("stats", "rgamma", "rmultinom", "rnorm")
to your NAMESPACE file.
Running examples in ‘disclapmix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.disclapmixfit
> ### Title: Plot a disclapmixfit
> ### Aliases: plot.disclapmixfit
> ### Keywords: plot
> 
> ### ** Examples
> 
> 
> data(danes)
> db <- as.matrix(danes[rep(1:nrow(danes), danes$n), 1:(ncol(danes)-1)])
> fit <- disclapmix(db, clusters = 4L)
> plot(fit)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 77-78 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘mixtures.Rmd’ using rmarkdown
--- finished re-building ‘mixtures.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
rdisclap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘disco-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDisco
> ### Title: plots log2FC of the corresponding genes against each other
> ### Aliases: plotDisco
> 
> ### ** Examples
> 
> library(tmod)
For tmod user guide, type `tmodUserGuide()'
> data(tmod)
> data(orthologs)
> ds <- disco.score(orthologs)
> plotDisco(orthologs, ds, tmod$MODULES2GENES[["LI.M1.0"]])
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
p.discrete.adjust : <anonymous>: no visible global function definition
  for ‘stepfun’
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
value: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘RUnit’ ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mix.distlist.facing.gamma : <anonymous>: no visible global function
  definition for ‘dgamma’
mix.distlist.norm: no visible binding for global variable ‘dnorm’
mix.mle: no visible global function definition for ‘sd’
mix.mle: no visible global function definition for ‘quantile’
mix.mle: no visible global function definition for ‘median’
mix.mle: no visible global function definition for ‘optim’
mix.synthetic.facing.gamma: no visible global function definition for
  ‘runif’
mix.synthetic.facing.gamma: no visible global function definition for
  ‘rgamma’
mix.synthetic.normal: no visible global function definition for ‘runif’
mix.synthetic.normal: no visible global function definition for ‘rnorm’
plot.discrimARTs: no visible global function definition for ‘hist’
plot.discrimARTs: no visible global function definition for ‘points’
plot.discrimARTs: no visible global function definition for ‘lines’
plot.discrimARTs: no visible global function definition for ‘grid.text’
plot.discrimARTs: no visible global function definition for ‘gpar’
Undefined global functions or variables:
  dgamma dnorm gpar grid.text hist lines median optim points quantile
  rgamma rnorm runif sd
Consider adding
  importFrom("graphics", "hist", "lines", "points")
  importFrom("stats", "dgamma", "dnorm", "median", "optim", "quantile",
             "rgamma", "rnorm", "runif", "sd")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘INLA’
densest: no visible global function definition for ‘weighted.mean’
diss: no visible global function definition for ‘cov’
neighbors: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov weighted.mean
Consider adding
  importFrom("stats", "cov", "weighted.mean")
to your NAMESPACE file.
Running examples in ‘disto-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.disto
> ### Title: Plot a disto object
> ### Aliases: plot.disto
> 
> ### ** Examples
> 
> temp <- stats::dist(iris[,1:4])
> dio  <- disto(objectname = "temp")
> plot(dio, type = "heatmap")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_disto.Rmd’ using rmarkdown
Quitting from lines 42-72 (vignette_disto.Rmd) 
Error: processing vignette 'vignette_disto.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette_disto.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette_disto.Rmd’

Error: Vignette re-building failed.
Execution halted
dist.multiPhylo: no visible global function definition for ‘as.dist’
gromov.hyperbolicity: no visible global function definition for
  ‘as.dist’
mcmc.target.seq: no visible global function definition for ‘runif’
phylo.diff: no visible global function definition for ‘par’
phylo.diff: no visible global function definition for ‘plot’
Undefined global functions or variables:
  as.dist par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.dist", "runif")
to your NAMESPACE file.
Running examples in ‘distreg.vis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_dist
> ### Title: Plot predicted bamlss distribution families with ggplot2
> ### Aliases: plot_dist
> 
> ### ** Examples
> 
> # Generating data
> data_fam <- model_fam_data(fam_name = "BE")
> # Fit model
> library("gamlss")
Loading required package: splines
Loading required package: gamlss.data

Attaching package: ‘gamlss.data’

The following object is masked from ‘package:datasets’:

    sleep

Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
 **********   GAMLSS Version 5.1-3  ********** 
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.

> beta_model <- gamlss(BE ~ norm2 + binomial1,
+   data = data_fam, family = BE())
GAMLSS-RS iteration 1: Global Deviance = -1003.068 
GAMLSS-RS iteration 2: Global Deviance = -1016.132 
GAMLSS-RS iteration 3: Global Deviance = -1016.132 
> # Get 3 predictions
> pred_df <- data_fam[sample(1:nrow(data_fam), 3), c("norm2", "binomial1")]
> param_preds <- preds(beta_model, pred_df)
> # Create pdf, cdf plots
> plot_dist(beta_model, param_preds, rug = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package required but not available: ‘glmulti’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' call to ‘glmnet’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘glmnet’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘asreml’
'library' or 'require' calls to packages already attached by Depends:
  ‘nlme’ ‘wgaim’
  Please remove these calls from your code.
'library' or 'require' call to ‘asreml’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘ibdreg’ ‘mgcv’ ‘nlme’ ‘qtl’ ‘wgaim’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘qtl:::adjust.rf.ri’
  See the note in ?`:::` about the use of this operator.
Foreign function call to a different package:
  .C(cfunc, ..., PACKAGE = "qtl")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘DLMtool-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: matlenlim
> ### Title: Size limit management procedures
> ### Aliases: matlenlim matlenlim2 minlenLopt1 slotlim
> 
> ### ** Examples
> 
> matlenlim(1, DLMtool::Atlantic_mackerel, plot=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: matlenlim ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dlstats.Rmd’ using rmarkdown
Quitting from lines 46-53 (dlstats.Rmd) 
Error: processing vignette 'dlstats.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dlstats.Rmd’

SUMMARY: processing the following file failed:
  ‘dlstats.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘dMod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Xd
> ### Title: Model prediction function from data.frame
> ### Aliases: Xd
> 
> ### ** Examples
> 
> # Generate a data.frame and corresponding prediction function
> timesD <- seq(0, 2*pi, 0.5)
> mydata <- data.frame(name = "A", time = timesD, value = sin(timesD), 
+                      row.names = paste0("par", 1:length(timesD)))
> x <- Xd(mydata)
> 
> # Evaluate the prediction function at different time points
> times <- seq(0, 2*pi, 0.01)
> pouter <- structure(mydata$value, names = rownames(mydata))
> prediction <- x(times, pouter)
> plot(prediction)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dMod.Rmd’ using rmarkdown
Loading required package: cOde

Attaching package: 'dMod'

The following object is masked from 'package:stats':

    profile


Attaching package: 'dplyr'

The following object is masked from 'package:dMod':

    combine

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

jakstat_8ccb23dc.c:6:15: warning: ISO C forbids zero-size array ‘forc’ [-Wpedantic]
 static double forc[0];
               ^~~~
jakstat_8ccb23dc.c:7:15: warning: ISO C forbids zero-size array ‘cons’ [-Wpedantic]
 static double cons[0];
               ^~~~
jakstat_8ccb23dc.c:8:15: warning: ‘range’ defined but not used [-Wunused-variable]
 static double range[2];
               ^~~~~
jakstat_8ccb23dc.c:7:15: warning: ‘cons’ defined but not used [-Wunused-variable]
 static double cons[0];
               ^~~~
jakstat_8ccb23dc_s.c:6:15: warning: ISO C forbids zero-size array ‘forc’ [-Wpedantic]
 static double forc[0];
               ^~~~
jakstat_8ccb23dc_s.c:7:15: warning: ISO C forbids zero-size array ‘cons’ [-Wpedantic]
 static double cons[0];
               ^~~~
jakstat_8ccb23dc_s.c:8:15: warning: ‘range’ defined but not used [-Wunused-variable]
 static double range[2];
               ^~~~~
jakstat_8ccb23dc_s.c:7:15: warning: ‘cons’ defined but not used [-Wunused-variable]
 static double cons[0];
               ^~~~
Quitting from lines 74-84 (dMod.Rmd) 
Error: processing vignette 'dMod.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dMod.Rmd’

SUMMARY: processing the following file failed:
  ‘dMod.Rmd’

Error: Vignette re-building failed.
Execution halted
Warning: no function found corresponding to methods exports from ‘DMwR’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing object imported by a ':::' call: ‘rpart:::rpconvert’
Unexported objects imported by ':::' calls:
  ‘rpart:::rpart.branch’ ‘rpart:::rpartco’
  ‘rpart:::string.bounding.box’
  See the note in ?`:::` about the use of this operator.
'library' or 'require' call to ‘igraph’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
network.modules: no visible global function definition for
  ‘graph.empty’
network.modules: no visible global function definition for
  ‘add.vertices’
network.modules: no visible global function definition for ‘add.edges’
network.modules: no visible global function definition for ‘tkplot’
network.modules: no visible global function definition for ‘V’
Undefined global functions or variables:
  V add.edges add.vertices graph.empty tkplot
DNMF: no visible global function definition for ‘runif’
NMFpval: no visible global function definition for ‘p.adjust’
ndNMF: no visible global function definition for ‘runif’
rnk: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust runif write.table
Consider adding
  importFrom("stats", "p.adjust", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘linest-lsmeans.Rnw’ using knitr
Quitting from lines 329-333 (linest-lsmeans.Rnw) 
Error: processing vignette 'linest-lsmeans.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘linest-lsmeans.Rnw’

--- re-building ‘doBy.Rnw’ using Sweave
Warning in dir.create("figures") : ‘figures’ already exists
--- finished re-building ‘doBy.Rnw’

SUMMARY: processing the following file failed:
  ‘linest-lsmeans.Rnw’

Error: Vignette re-building failed.
Execution halted
ppert: no visible global function definition for ‘pbeta’
prepare8pkg: no visible global function definition for ‘glob2rx’
qpert: no visible global function definition for ‘qbeta’
rpert: no visible global function definition for ‘rbeta’
Undefined global functions or variables:
  glob2rx pbeta qbeta rbeta
Consider adding
  importFrom("stats", "pbeta", "qbeta", "rbeta")
  importFrom("utils", "glob2rx")
to your NAMESPACE file.
Running examples in ‘docxtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: put_gap
> ### Title: Insert a gap or whitespace in a document.
> ### Aliases: put_gap
> 
> ### ** Examples
> 
> put_gap()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: put_gap ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(docxtools)
  > 
  > test_check("docxtools")
  ── 1. Error: put_gap() attributes match expectations (@test_put.R#40)  ─────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: put_gap() at testthat/test_put.R:40
  2: print(p)
  3: print.ggplot(p)
  4: grid.draw(gtable)
  5: grid.draw.gTree(gtable)
  6: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  7: drawGTree(x)
  8: preDraw(x)
  9: preDraw.gTree(x)
  10: pushvpgp(x)
  11: pushgrobvp(x$vp)
  12: pushgrobvp.viewport(x$vp)
  13: pushViewport(vp, recording = FALSE)
  14: lapply(vps, push.vp, recording)
  15: FUN(X[[i]], ...)
  16: push.vp.viewport(X[[i]], ...)
  17: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Error: put_gap() attributes match expectations (@test_put.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
.info: no visible global function definition for ‘packageDescription’
redisWorker: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  flush.console packageDescription
Consider adding
  importFrom("utils", "flush.console", "packageDescription")
to your NAMESPACE file.
Running examples in ‘doremi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.doremi
> ### Title: S3 method to plot DOREMI objects
> ### Aliases: plot.doremi
> 
> ### ** Examples
> 
> mydata <- generate.panel.remi(nind = 2,
+                            dampingtime = 10,
+                            amplitude = c(5,10),
+                            nexc = 2,
+                            duration = 20,
+                            deltatf = 2,
+                            tmax = 200,
+                            minspacing = 0,
+                            internoise = 0.2,
+                            intranoise = 0.1)
> myresult <- remi(data = mydata,
+                  id = "id",
+                  input = "excitation",
+                  time = "time",
+                  signal = "dampedsignal",
+                  embedding = 5)
> plot(myresult)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-doremi.Rmd’ using rmarkdown
Quitting from lines 41-68 (Introduction-to-doremi.Rmd) 
Error: processing vignette 'Introduction-to-doremi.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction-to-doremi.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-doremi.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
dostats: no visible binding for global variable ‘na.fail’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
pval.default: no visible global function definition for ‘.hasSlot’
pval.lm: no visible global function definition for ‘anova’
Undefined global functions or variables:
  .hasSlot anova head na.fail tail
Consider adding
  importFrom("methods", ".hasSlot")
  importFrom("stats", "anova", "na.fail")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘dotwhisker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_brackets
> ### Title: Add Labelled Brackets to Group Predictors in a Dot-and-Whisker
> ###   Plot
> ### Aliases: add_brackets
> 
> ### ** Examples
> 
> library(broom)
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> data(mtcars)
> m1 <- lm(mpg ~ wt + cyl + disp, data = mtcars)
> two_brackets <- list(c("Engine", "Cylinder", "Displacement"),
+                      c("Not Engine", "Intercept", "Weight"))
> 
> {dwplot(m1, show_intercept = TRUE) %>%
+        relabel_predictors("(Intercept)" = "Intercept",
+                           wt = "Weight",
+                           cyl = "Cylinder",
+                           disp = "Displacement") +
+        theme_bw() + xlab("Coefficient") + ylab("") +
+        theme(legend.position="none") +
+        geom_vline(xintercept = 0, colour = "grey50", linetype = 2)} %>%
+    add_brackets(two_brackets)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dotwhisker-vignette.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 23-33 (dotwhisker-vignette.Rmd) 
Error: processing vignette 'dotwhisker-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dotwhisker-vignette.Rmd’

--- re-building ‘kl2007_examples.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following object is masked from 'package:gridExtra':

    combine

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: ggplot2
Quitting from lines 73-92 (kl2007_examples.Rmd) 
Error: processing vignette 'kl2007_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘kl2007_examples.Rmd’

SUMMARY: processing the following files failed:
  ‘dotwhisker-vignette.Rmd’ ‘kl2007_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘dpcR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dpcr_density_table
> ### Title: Calculate Density of Multiple dPCR runs
> ### Aliases: dpcr_density_table
> ### Keywords: dplot hplot
> 
> ### ** Examples
> 
> dens <- dpcr_density_table(six_panels)
> 
> # create plot using ggplot2
> library(ggplot2)
> 
> ggplot(dens[["Experiment2.2"]], aes(x = x, y = y)) + 
+   geom_line() + 
+   geom_area(aes(fill = !(conf_up | conf_low))) +
+   scale_y_continuous("Density") +
+   scale_fill_discrete("0.95 CI")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 284-293 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘compatibility.Rmd’ using rmarkdown
--- finished re-building ‘compatibility.Rmd’

--- re-building ‘dplyr.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Warning: Removed 1 rows containing non-finite values (stat_smooth).
Warning: Removed 1 rows containing missing values (geom_point).
Quitting from lines 224-237 (dplyr.Rmd) 
Error: processing vignette 'dplyr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dplyr.Rmd’

--- re-building ‘programming.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘programming.Rmd’

--- re-building ‘two-table.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘two-table.Rmd’

--- re-building ‘window-functions.Rmd’ using rmarkdown
--- finished re-building ‘window-functions.Rmd’

SUMMARY: processing the following file failed:
  ‘dplyr.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘dr4pl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dr4pl
> ### Title: Fitting 4 Parameter Logistic (4PL) models to dose-response data.
> ### Aliases: dr4pl dr4pl-package dr4pl.formula dr4pl.data.frame
> ###   dr4pl.default
> 
> ### ** Examples
> 
>   ##Assign method.init = "logistic" to use logistic method of estimation.
>   ##default method
>   a <- dr4pl(dose = sample_data_1$Dose,
+              response = sample_data_1$Response,
+              method.init = "logistic")
>   plot(a)
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous x-axis
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘walk_through_in_R.Rmd’ using rmarkdown
Quitting from lines 33-38 (walk_through_in_R.Rmd) 
Error: processing vignette 'walk_through_in_R.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘walk_through_in_R.Rmd’

SUMMARY: processing the following file failed:
  ‘walk_through_in_R.Rmd’

Error: Vignette re-building failed.
Execution halted
DRaWR: no visible global function definition for ‘write.table’
DRaWR: no visible global function definition for ‘read.table’
DRaWR: no visible global function definition for ‘aggregate’
DRaWR: no visible global function definition for ‘slot’
Undefined global functions or variables:
  aggregate read.table slot write.table
Consider adding
  importFrom("methods", "slot")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘DrBats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: visW
> ### Title: Plot the estimates for the latent factors
> ### Aliases: visW
> 
> ### ** Examples
> 
> data("toydata")
> data("stanfit")
> codafit <- coda.obj(stanfit) ## convert to mcmc.list
> W.res <- visW(codafit, Y = toydata$Y.simul$Y, D = toydata$wlu$D,
+ chain = 1, factors = c(1, 2))
> 
> ## plot the results
> 
> data <- data.frame(time = rep(1:9, 2), W.res$res.W)
> ggplot2::ggplot() +
+   ggplot2::geom_step(data = data, ggplot2::aes(x = time, y = Estimation, colour = Factor)) +
+   ggplot2::geom_step(data = data, ggplot2::aes(x = time, y = Lower.est, colour = Factor),
+   linetype = "longdash") +
+   ggplot2::geom_step(data = data, ggplot2::aes(x = time, y = Upper.est, colour = Factor),
+   linetype = "longdash")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DataSimulationandProjection.Rmd’ using rmarkdown
--- finished re-building ‘DataSimulationandProjection.Rmd’

--- re-building ‘DimensionReduction.Rmd’ using rmarkdown
Quitting from lines 68-78 (DimensionReduction.Rmd) 
Error: processing vignette 'DimensionReduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DimensionReduction.Rmd’

--- re-building ‘DrBats.Rmd’ using rmarkdown
Quitting from lines 163-169 (DrBats.Rmd) 
Error: processing vignette 'DrBats.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DrBats.Rmd’

--- re-building ‘ModelEvaluation.Rmd’ using rmarkdown
Quitting from lines 57-62 (ModelEvaluation.Rmd) 
Error: processing vignette 'ModelEvaluation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ModelEvaluation.Rmd’

--- re-building ‘ModelFit.Rmd’ using rmarkdown
Quitting from lines 75-81 (ModelFit.Rmd) 
Error: processing vignette 'ModelFit.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ModelFit.Rmd’

SUMMARY: processing the following files failed:
  ‘DimensionReduction.Rmd’ ‘DrBats.Rmd’ ‘ModelEvaluation.Rmd’
  ‘ModelFit.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘drLumi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.scluminex
> ### Title: Plot method for the scluminex class
> ### Aliases: plot.scluminex
> 
> ### ** Examples
> 
> # Load data and estimate models
> data(ecdata)
> data(mfidata)
> 
> dat <- mfidata[mfidata$plate=="plate_1" & mfidata$analyte=="FGF",]
> 
> sdf <- data_selection(dat, ecdata)[[1]]
> sdf_luminex <- scluminex("plate_1",sdf$standard, sdf$background,
+ "SSl4", bkg="ignore", fmfi="mfi", verbose=FALSE)
> 
> # Plot standard curves
> plot(sdf_luminex, "sc")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘drLumi.rnw’ using knitr
Quitting from lines 405-410 (drLumi.rnw) 
Error: processing vignette 'drLumi.rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘drLumi.rnw’

SUMMARY: processing the following file failed:
  ‘drLumi.rnw’

Error: Vignette re-building failed.
Execution halted
cdfDRM: no visible global function definition for ‘tail’
densityDRM: no visible binding for global variable ‘density’
drmdel: no visible binding for global variable ‘optim’
drmdel: no visible global function definition for ‘pchisq’
quantEst: no visible global function definition for ‘tail’
quantileCompWald: no visible global function definition for ‘pchisq’
quantileCompWald: no visible global function definition for ‘p.adjust’
quantileDRM: no visible global function definition for ‘tail’
quantileDRM: no visible global function definition for ‘density’
Undefined global functions or variables:
  density optim p.adjust pchisq tail
Consider adding
  importFrom("stats", "density", "optim", "p.adjust", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
compute_xsq: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  chisq.test
Consider adding
  importFrom("stats", "chisq.test")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.Rmd’ using rmarkdown
Quitting from lines 159-163 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘userGuide.Rmd’

SUMMARY: processing the following file failed:
  ‘userGuide.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DSAIDE)
  Loading required package: shiny
  Welcome to the DSAIDE package. Type dsaidemenu() to get started.
  > 
  > test_check("DSAIDE")
  ── 1. Error: generate_plots returns a plot (@test-generate_plots.R#8)  ─────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_is(DSAIDE::generate_plots(result), "ggplot") at testthat/test-generate_plots.R:8
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: DSAIDE::generate_plots(result)
  5: graphics::plot(pfinal)
  6: plot.ggplot(pfinal)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 1
  1. Error: generate_plots returns a plot (@test-generate_plots.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DSAIRM)
  Loading required package: shiny
  Welcome to the DSAIRM package. Type dsairmmenu() to get started.
  > 
  > test_check("DSAIRM")
  ── 1. Error: generate_plots returns a plot (@test-generate_plots.R#8)  ─────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_is(DSAIRM::generate_plots(result), "ggplot") at testthat/test-generate_plots.R:8
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: DSAIRM::generate_plots(result)
  5: graphics::plot(pfinal)
  6: plot.ggplot(pfinal)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 15 SKIPPED: 0 FAILED: 1
  1. Error: generate_plots returns a plot (@test-generate_plots.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘dsa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: daily_sim
> ### Title: Create a simple, exemplary, seasonal, daily time series
> ### Aliases: daily_sim
> 
> ### ** Examples
> 
> time_series <- daily_sim(n=4, year_effect=3)
> xtsplot(time_series[,1], font="sans") # Plot of the time series
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
DSBayes: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘coef’
DSBayes: no visible global function definition for ‘vcov’
DSBayes : MLE: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘integrate’
DSBayes : qfunc.numer : <anonymous>: no visible global function
  definition for ‘dnorm’
DSBayes : ds.numer: no visible global function definition for
  ‘integrate’
DSBayes : lower: no visible global function definition for ‘qlogis’
DSBayes : lower: no visible global function definition for ‘integrate’
DSBayes : upper: no visible global function definition for ‘qlogis’
DSBayes : upper: no visible global function definition for ‘integrate’
DSBayes: no visible global function definition for ‘optimize’
DSBayes: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  coef dnorm integrate optimize qlogis qnorm uniroot vcov
Consider adding
  importFrom("stats", "coef", "dnorm", "integrate", "optimize", "qlogis",
             "qnorm", "uniroot", "vcov")
to your NAMESPACE file.
Running examples in ‘dslabs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ds_theme_set
> ### Title: dslabs theme set
> ### Aliases: ds_theme_set
> 
> ### ** Examples
> 
> library(ggplot2)
> ds_theme_set()
> qplot(hp, mpg, data=mtcars, color=am, facets=gear~cyl, 
+ main="Scatterplots of MPG vs. Horsepower", 
+ xlab="Horsepower", ylab="Miles per Gallon")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dslice.Rnw’ using Sweave
Loading required package: Rcpp
Loading required package: ggplot2
Loading required package: scales
Error: processing vignette 'dslice.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dslice.Rnw’

SUMMARY: processing the following file failed:
  ‘dslice.Rnw’

Error: Vignette re-building failed.
Execution halted
AIC.dspat: no visible global function definition for ‘coef’
LTDataFrame: no visible global function definition for ‘as.formula’
coef.dspat: no visible global function definition for ‘coef’
integrate.intensity: no visible global function definition for ‘coef’
integrate.intensity: no visible global function definition for
  ‘predict’
integrate.intensity: no visible global function definition for
  ‘model.matrix’
integrate.intensity: no visible global function definition for ‘vcov’
integrate.intensity: no visible global function definition for ‘fitted’
lgcp.correction: no visible global function definition for ‘predict’
lgcp.correction: no visible global function definition for
  ‘model.matrix’
lgcp.correction: no visible global function definition for ‘fitted’
lgcp.correction: no visible global function definition for ‘var’
lines_to_strips : line_to_strip: no visible global function definition
  for ‘as’
owin.gpc.poly: no visible global function definition for ‘as’
sample.points : sample.points.from.line: no visible global function
  definition for ‘runif’
sample.points: no visible global function definition for ‘model.matrix’
simCovariates: no visible global function definition for ‘quantile’
simPts: no visible global function definition for ‘model.matrix’
transect.intensity: no visible global function definition for ‘predict’
transect.intensity: no visible global function definition for ‘hist’
Undefined global functions or variables:
  as as.formula coef fitted hist model.matrix predict quantile runif
  var vcov
Consider adding
  importFrom("graphics", "hist")
  importFrom("methods", "as")
  importFrom("stats", "as.formula", "coef", "fitted", "model.matrix",
             "predict", "quantile", "runif", "var", "vcov")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
X: no visible global function definition for ‘read.table’
dplot: no visible global function definition for ‘matplot’
dplot: no visible global function definition for ‘legend’
dscor : <anonymous>: no visible global function definition for ‘combn’
dscor : <anonymous> : <anonymous>: no visible global function
  definition for ‘cor.test’
gds: no visible binding for global variable ‘na.omit’
gds : medi: no visible global function definition for ‘median’
gds : quant: no visible global function definition for ‘quantile’
gds: no visible binding for global variable ‘shapiro.test’
tables: no visible binding for global variable ‘chisq.test’
tables: no visible binding for global variable ‘fisher.test’
Undefined global functions or variables:
  chisq.test combn cor.test fisher.test legend matplot median na.omit
  quantile read.table shapiro.test
Consider adding
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "chisq.test", "cor.test", "fisher.test", "median",
             "na.omit", "quantile", "shapiro.test")
  importFrom("utils", "combn", "read.table")
to your NAMESPACE file.
Running examples in ‘DstarM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rtDescriptives
> ### Title: Descriptives of reaction time data
> ### Aliases: rtDescriptives
> 
> ### ** Examples
> 
> tt <- seq(0, 5, .01)
> pars <- matrix(.5, 5, 2)
> pars[1, ] <- 1
> pars[2, ] <- c(0, 2)
> dat <- simData(n = 3e3, pars = pars, tt = tt, pdfND = dbeta(tt, 10, 30))
> x <- rtDescriptives(data = dat)
  Condition Response Pairs 
  Prop                Counts
      lower     upper lower upper
1 0.4993333 0.5006667   749   751
2 0.1453333 0.8546667   218  1282
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: rtDescriptives ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DstarM)
  > 
  > test_check("DstarM")
  ── 1. Failure: rtDescriptives works (@test-simulate.R#113)  ────────────────────
  print(rtDescriptives) threw an error.
  Message: VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Class:   simpleError/error/condition
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 23 SKIPPED: 1 FAILED: 1
  1. Failure: rtDescriptives works (@test-simulate.R#113) 
  
  Error: testthat unit tests failed
  Execution halted
DStree: no visible global function definition for ‘model.frame’
DStree: no visible global function definition for ‘model.matrix’
DStree: no visible global function definition for ‘model.response’
DStree: no visible global function definition for ‘as.formula’
bag: no visible global function definition for ‘model.frame’
bag: no visible global function definition for ‘model.response’
plot.DStree: no visible global function definition for ‘par’
plot.DStree: no visible global function definition for ‘plot’
plot.DStree: no visible global function definition for ‘rainbow’
plot.DStree: no visible global function definition for ‘lines’
plot.DStree: no visible global function definition for ‘legend’
predict.DStree: no visible global function definition for ‘predict’
print.DStree: no visible global function definition for ‘naprint’
prune.DStree: no visible global function definition for ‘median’
prune.DStree: no visible global function definition for ‘predict’
prune.DStree: no visible binding for global variable ‘var’
summ.MAE: no visible global function definition for ‘predict’
summary.DStree: no visible global function definition for ‘naprint’
Undefined global functions or variables:
  as.formula legend lines median model.frame model.matrix
  model.response naprint par plot predict rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("stats", "as.formula", "median", "model.frame",
             "model.matrix", "model.response", "naprint", "predict",
             "var")
to your NAMESPACE file.
DCEA: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘pdf’
DS: no visible global function definition for ‘plot’
DS: no visible global function definition for ‘dev.off’
LFC: no visible global function definition for ‘glm’
LFC: no visible global function definition for ‘predict’
PartialCor: no visible global function definition for ‘na.omit’
comDCGLplot: no visible global function definition for ‘pdf’
comDCGLplot: no visible global function definition for ‘plot’
comDCGLplot: no visible global function definition for ‘dev.off’
percentLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘pt’
qLinkfilter: no visible global function definition for ‘p.adjust’
rLinkfilter: no visible global function definition for ‘cor’
varianceBasedfilter: no visible binding for global variable ‘var’
varianceBasedfilter: no visible global function definition for ‘median’
varianceBasedfilter: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor dev.off glm median na.omit p.adjust pchisq pdf plot predict pt
  var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "glm", "median", "na.omit", "p.adjust",
             "pchisq", "predict", "pt", "var")
to your NAMESPACE file.
DLR: no visible global function definition for ‘formula’
DLR: no visible global function definition for ‘terms’
DLR: no visible global function definition for ‘model.matrix’
DLR: no visible global function definition for ‘as.formula’
DLR: no visible binding for global variable ‘binomial’
DLR: no visible global function definition for ‘coef’
DLR: no visible global function definition for ‘pnorm’
DLR: no visible global function definition for ‘qnorm’
acc.1test: no visible global function definition for ‘qnorm’
pv.gs: no visible global function definition for ‘pchisq’
pv.rpv: no visible global function definition for ‘qnorm’
pv.rpv: no visible global function definition for ‘pnorm’
pv.wgs: no visible global function definition for ‘pchisq’
sesp.diff.ci: no visible global function definition for ‘qnorm’
sesp.mcnemar: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  as.formula binomial coef formula model.matrix pchisq pnorm qnorm
  terms
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "formula",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
efron.petrosian: no visible global function definition for ‘dev.new’
efron.petrosian: no visible global function definition for ‘par’
efron.petrosian: no visible global function definition for ‘plot’
efron.petrosian: no visible global function definition for ‘segments’
lynden: no visible global function definition for ‘dev.new’
lynden: no visible global function definition for ‘par’
lynden: no visible global function definition for ‘plot’
lynden: no visible global function definition for ‘segments’
shen: no visible global function definition for ‘image’
shen: no visible global function definition for ‘runif’
shen: no visible global function definition for ‘filled.contour’
shen: no visible binding for global variable ‘rainbow’
shen: no visible binding for global variable ‘topo.colors’
shen: no visible global function definition for ‘topo.colors’
shen: no visible global function definition for ‘persp’
shen: no visible global function definition for ‘dev.new’
shen: no visible global function definition for ‘par’
shen: no visible global function definition for ‘plot’
shen: no visible global function definition for ‘segments’
Undefined global functions or variables:
  dev.new filled.contour image par persp plot rainbow runif segments
  topo.colors
Consider adding
  importFrom("grDevices", "dev.new", "rainbow", "topo.colors")
  importFrom("graphics", "filled.contour", "image", "par", "persp",
             "plot", "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
DTK.plot: no visible global function definition for ‘plot’
DTK.plot: no visible global function definition for ‘axis’
DTK.plot: no visible global function definition for ‘title’
DTK.plot: no visible global function definition for ‘lines’
DTK.plot: no visible global function definition for ‘points’
DTK.test: no visible binding for global variable ‘sd’
DTK.test: no visible global function definition for ‘qtukey’
TK.test: no visible global function definition for ‘TukeyHSD’
TK.test: no visible global function definition for ‘aov’
Undefined global functions or variables:
  TukeyHSD aov axis lines plot points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "plot", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
DTMC: no visible global function definition for ‘runif’
DTMC: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘DTRlearn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Olearning_Single
> ### Title: Improved single stage O-learning with cross validation
> ### Aliases: Olearning_Single
> 
> ### ** Examples
> 
> n_cluster=5
> pinfo=10
> pnoise=10
> n_sample=50
> set.seed(3)
> example=make_classification(n_cluster,pinfo,pnoise,n_sample)
> pi=list()
> pi[[2]]=pi[[1]]=rep(1,n_sample)
> modelrbf=Olearning_Single(example$X,example$A,example$R,kernel='rbf',m=3,sigma=0.05)
[1] 0.5
[1] NA
Error in svd(rbind(rho, tau, matrix(alpha), nu)) : 
  infinite or missing values in 'x'
Calls: Olearning_Single -> wsvm -> ipop -> ipop -> svd
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘parallelization-considerations.Rmd’ using rmarkdown
--- finished re-building ‘parallelization-considerations.Rmd’

--- re-building ‘timing-experiments.Rmd’ using rmarkdown
Quitting from lines 160-173 (timing-experiments.Rmd) 
Error: processing vignette 'timing-experiments.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘timing-experiments.Rmd’

--- re-building ‘dtwclust.Rnw’ using knitr_notangle
Quitting from lines 1689-1691 (dtwclust.Rnw) 
Error: processing vignette 'dtwclust.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dtwclust.Rnw’

SUMMARY: processing the following files failed:
  ‘timing-experiments.Rmd’ ‘dtwclust.Rnw’

Error: Vignette re-building failed.
Execution halted
dummy: no visible global function definition for ‘model.matrix’
dummy: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  model.frame model.matrix
Consider adding
  importFrom("stats", "model.frame", "model.matrix")
to your NAMESPACE file.
cvSDDT: no visible global function definition for ‘qt’
cvSDDT : Cj_SD.fun: no visible global function definition for ‘combn’
cvSDDT: no visible global function definition for ‘uniroot’
cvSUDT: no visible global function definition for ‘rnorm’
cvSUDT: no visible global function definition for ‘rchisq’
cvSUDT : psi.fun: no visible global function definition for ‘pnorm’
cvSUDT: no visible global function definition for ‘qt’
cvSUDT: no visible global function definition for ‘uniroot’
cvSUDT: no visible global function definition for ‘combn’
nvDT : samplesize: no visible global function definition for ‘rnorm’
nvDT : samplesize: no visible global function definition for ‘rchisq’
nvDT : samplesize: no visible global function definition for ‘pnorm’
nvDT : ssBonf: no visible global function definition for ‘qnorm’
nvDT : ssBonf: no visible global function definition for ‘qt’
nvDT : ssBonf: no visible global function definition for ‘rnorm’
nvDT : ssBonf: no visible global function definition for ‘rchisq’
nvDT : ssBonf: no visible global function definition for ‘pnorm’
nvDT: no visible global function definition for ‘uniroot’
powDT: no visible global function definition for ‘rnorm’
powDT: no visible global function definition for ‘rchisq’
powDT: no visible global function definition for ‘pnorm’
qvSDDT: no visible global function definition for ‘pt’
qvSUDT: no visible global function definition for ‘rnorm’
qvSUDT: no visible global function definition for ‘rchisq’
qvSUDT : psi.fun: no visible global function definition for ‘pnorm’
qvSUDT: no visible global function definition for ‘pt’
qvSUDT : Pj.fun: no visible global function definition for ‘qt’
qvSUDT : Pj.fun: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn pnorm pt qnorm qt rchisq rnorm uniroot
Consider adding
  importFrom("stats", "pnorm", "pt", "qnorm", "qt", "rchisq", "rnorm",
             "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
Clough: no visible global function definition for ‘dgamma’
computePosterior,Counts: no visible global function definition for
  ‘dnbinom’
getPosteriorParam,Counts: no visible global function definition for
  ‘qgamma’
getPosteriorParam,Counts: no visible global function definition for
  ‘dgamma’
getPosteriorParam,Counts: no visible global function definition for
  ‘pgamma’
plotPosterior,Counts: no visible global function definition for ‘axis’
plotPosterior,Counts: no visible global function definition for
  ‘abline’
plotPosterior,Counts: no visible global function definition for ‘lines’
plotPosterior,Counts: no visible global function definition for ‘rect’
plotPosterior,Counts: no visible global function definition for ‘curve’
plotPosterior,Counts: no visible global function definition for
  ‘dgamma’
plotPosterior,Counts: no visible global function definition for
  ‘legend’
show,Counts: no visible global function definition for ‘head’
show,Counts: no visible global function definition for ‘tail’
Undefined global functions or variables:
  abline axis curve dgamma dnbinom head legend lines pgamma qgamma rect
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "curve", "legend", "lines",
             "rect")
  importFrom("stats", "dgamma", "dnbinom", "pgamma", "qgamma")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Running examples in ‘DVHmetrics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DVHmetrics-package
> ### Title: Analyze Dose-Volume Histograms and Check Constraints
> ### Aliases: DVHmetrics-package DVHmetrics
> ### Keywords: package
> 
> ### ** Examples
> 
> showDVH(dataMZ[[1]])
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: showDVH ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DVHmetrics.Rnw’ using knitr
Warning in getVolume(pm$valRefNum, type = "absolute", unitRef = pm$unitRef,  :
  max dose is less than requested dose
Warning in getVolume(pm$valRefNum, type = "absolute", unitRef = pm$unitRef,  :
  max dose is less than requested dose
Warning in getVolume(pm$valRefNum, type = "absolute", unitRef = pm$unitRef,  :
  max dose is less than requested dose
Warning in getVolume(pm$valRefNum, type = "absolute", unitRef = pm$unitRef,  :
  max dose is less than requested dose
Quitting from lines 411-412 (DVHmetrics.Rnw) 
Error: processing vignette 'DVHmetrics.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DVHmetrics.Rnw’

--- re-building ‘DVHshiny.Rnw’ using knitr
--- finished re-building ‘DVHshiny.Rnw’

SUMMARY: processing the following file failed:
  ‘DVHmetrics.Rnw’

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘HISTORY’
'library' or 'require' calls to packages already attached by Depends:
  ‘ggm’ ‘tcltk’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggm’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MultiTestH0 : MultiTestOneColumn: no visible global function definition
  for ‘pchisq’
RunClustering : CheckClusterNew: no visible global function definition
  for ‘qchisq’
RunClustering: no visible global function definition for ‘qchisq’
RunDenoising: no visible binding for global variable ‘var’
RunDenoising: no visible global function definition for ‘qchisq’
RunDenoising: no visible binding for global variable ‘median’
RunDenoising: no visible global function definition for ‘var’
RunDenoising : buildEstimate: no visible global function definition for
  ‘qchisq’
Undefined global functions or variables:
  median pchisq qchisq var
Consider adding
  importFrom("stats", "median", "pchisq", "qchisq", "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Loading required package: survival
Loading required package: optimx

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 110-117 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
GetIntMod: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘logLik’
GetPV: no visible global function definition for ‘optimize’
GetPV: no visible global function definition for ‘pchisq’
fitdi: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  arima logLik optimize pchisq
Consider adding
  importFrom("stats", "arima", "logLik", "optimize", "pchisq")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘TutorialdynRB.Rmd’ using rmarkdown
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
Quitting from lines 134-143 (TutorialdynRB.Rmd) 
Error: processing vignette 'TutorialdynRB.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TutorialdynRB.Rmd’

SUMMARY: processing the following file failed:
  ‘TutorialdynRB.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dynsim-overview.Rnw’ using knitr

Lagging invest by 1 time units.

Quitting from lines 263-267 (dynsim-overview.Rnw) 
Error: processing vignette 'dynsim-overview.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dynsim-overview.Rnw’

SUMMARY: processing the following file failed:
  ‘dynsim-overview.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘functionality.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 94-110 (functionality.Rmd) 
Error: processing vignette 'functionality.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘functionality.Rmd’

SUMMARY: processing the following file failed:
  ‘functionality.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘DZEXPM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dzexpm
> ### Title: The estimation and prediction function for the skewed spatial
> ###   processes
> ### Aliases: dzexpm
> 
> ### ** Examples
> 
>   real<- as.matrix(do.call(cbind, MaxTemp03))
>   n_ful<- nrow(real)
>   y_ful<- real[,2]
>   x_ful<- real[,7]
>   x_ful<- log(x_ful)
>   x_ful<- scale(x_ful)
>   u1<- real[,3]
>   u2<- real[,4]
>   theta<- 2/150000
>   n<- 56
>   p<- 0.1
>  dzexpm(y_ful, x_ful, n_ful, n, u1, u2, theta, p, 50, 20)
Error in chol.default(Cpred) : 
  the leading minor of order 19 is not positive definite
Calls: dzexpm -> t -> chol -> chol.default
Execution halted
Running examples in ‘earlywarnings-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotPotential
> ### Title: Description: Plot Potential
> ### Aliases: PlotPotential
> ### Keywords: early-warning
> 
> ### ** Examples
> 
> X = c(rnorm(1000, mean = 0), rnorm(1000, mean = -2), rnorm(1000, mean = 2)); 
> param = seq(0,5,length=3000); res <- movpotential_ews(X, param); 
> PlotPotential(res$res, title = '', xlab.text = '', ylab.text = '', 
+ cutoff = 0.5, plot.contours = TRUE, binwidth = 0.2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘easyalluvial-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alluvial_long
> ### Title: alluvial plot of data in long format
> ### Aliases: alluvial_long
> 
> ### ** Examples
> 
> 
> 
>  data = quarterly_flights
> 
>  alluvial_long( data, key = qu, value = mean_arr_delay, id = tailnum, fill_by = 'last_variable' )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Non-standard files/directories found at top level:
  ‘easy_html_report_tmp_1376284934.59207.tsv’
  ‘easy_html_report_tmp_1376284935.5951.tsv’
  ‘easy_html_report_tmp_1376284936.59848.tsv’
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.file_attachment: no visible global function definition for
  ‘base64encode’
.plot_attachment: no visible global function definition for ‘dev.off’
.update_list: no visible global function definition for ‘modifyList’
easyHtmlReport: no visible global function definition for ‘knit’
easyHtmlReport: no visible global function definition for
  ‘markdownToHTML’
mime_part.data.frame: no visible global function definition for
  ‘write.table’
mime_part.ggplot: no visible binding for global variable ‘pdf’
mime_part.matrix: no visible global function definition for
  ‘write.table’
mime_part.trellis: no visible binding for global variable ‘pdf’
simpleHtmlReport : <anonymous>: no visible global function definition
  for ‘write.table’
Undefined global functions or variables:
  base64encode dev.off knit markdownToHTML modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
MARK.MCMC : Model.Creator: no visible global function definition for
  ‘combn’
MARK.MCMC : formula.Maker: no visible global function definition for
  ‘combn’
Simulate.CH: no visible global function definition for ‘rnorm’
Simulate.CH: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  combn rbinom rnorm
Consider adding
  importFrom("stats", "rbinom", "rnorm")
  importFrom("utils", "combn")
to your NAMESPACE file.
eb: no visible global function definition for ‘optimize’
ebalance: no visible global function definition for ‘var’
Undefined global functions or variables:
  optimize var
Consider adding
  importFrom("stats", "optimize", "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ebayesthresh.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 49-60 (ebayesthresh.Rmd) 
Error: processing vignette 'ebayesthresh.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ebayesthresh.Rmd’

SUMMARY: processing the following file failed:
  ‘ebayesthresh.Rmd’

Error: Vignette re-building failed.
Execution halted
ebSNP: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ecb_sdw.Rmd’ using rmarkdown
Warning: Removed 28 rows containing non-finite values (stat_smooth).
Warning: Removed 28 rows containing missing values (geom_point).
Quitting from lines 163-178 (ecb_sdw.Rmd) 
Error: processing vignette 'ecb_sdw.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ecb_sdw.Rmd’

SUMMARY: processing the following file failed:
  ‘ecb_sdw.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘echo-vignette.Rmd’ using rmarkdown
Quitting from lines 49-98 (echo-vignette.Rmd) 
Error: processing vignette 'echo-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘echo-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘echo-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
ecipex: no visible binding for global variable ‘nistiso’
ecipex : <anonymous>: no visible global function definition for ‘nextn’
ecipex : <anonymous>: no visible global function definition for ‘fft’
ecipex : <anonymous> : <anonymous>: no visible global function
  definition for ‘fft’
Undefined global functions or variables:
  fft nextn nistiso
Consider adding
  importFrom("stats", "fft", "nextn")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘eclust.Rmd’ using rmarkdown
See example usage at http://sahirbhatnagar.com/eclust/
Quitting from lines 470-471 (eclust.Rmd) 
Error: processing vignette 'eclust.Rmd' failed with diagnostics:
`heatmap_width` and `width` should not all be the absolute units.
--- failed re-building ‘eclust.Rmd’

SUMMARY: processing the following file failed:
  ‘eclust.Rmd’

Error: Vignette re-building failed.
Execution halted
dilution: no visible global function definition for ‘grey’
dilution: no visible global function definition for ‘lines’
dilution: no visible global function definition for ‘rect’
dilution: no visible global function definition for ‘segments’
dilution: no visible global function definition for ‘text’
dilution: no visible global function definition for ‘arrows’
pricefit: no visible global function definition for ‘runif’
Undefined global functions or variables:
  arrows grey lines rect runif segments text
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "arrows", "lines", "rect", "segments", "text")
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘ecolottery-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coalesc
> ### Title: Coalescent-based simulation of ecological communities undergoing
> ###   both neutral and niche-base dynamics
> ### Aliases: coalesc
> ### Keywords: coalescent neutral dynamics niche-based dynamics
> 
> ### ** Examples
> 
> # Simulation of a neutral community including 100 individuals
> J <- 500; theta <- 50; m <- 0.1
> comm1 <- coalesc(J, m, theta) 
> # Regional and local trait distributions
> plot_comm(comm1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Barro_Colorado.Rmd’ using rmarkdown
--- finished re-building ‘Barro_Colorado.Rmd’

--- re-building ‘coalesc_vignette.Rmd’ using rmarkdown
Quitting from lines 112-121 (coalesc_vignette.Rmd) 
Error: processing vignette 'coalesc_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘coalesc_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘coalesc_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 36-42 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘EDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EDA
> ### Title: Energy consumption analysis for calculating carbon emission
> ###   changes
> ### Aliases: EDA print.EDA plot.EDA
> 
> ### ** Examples
> 
> library(EDA)
> data(carbon)
> data(factordata)
> ## set parameters
> cdata <- carbon[,-c(1,2)]
> Year <- 2001:2005
> Sector <- c("b1", "b2", "b3")
> Fuel <- colnames(cdata)
> Factor <- names(factordata)
> ## run EDA model
> eda1 <- EDA(cdata, factordata, Year = Year, Factor = Factor, 
+     Fuel = Fuel, Sector = Sector, method = "LMDI")
> eda1
Annual changes:
  Year    Change
1 2002  43054129
2 2003  99178362
3 2004 117880293
4 2005  94842144
Total change:  354954928> plot(eda1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EDA.Rmd’ using rmarkdown
Quitting from lines 116-129 (EDA.Rmd) 
Error: processing vignette 'EDA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘EDA.Rmd’

SUMMARY: processing the following file failed:
  ‘EDA.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘edarf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_imp
> ### Title: Plot variable importance from random forests
> ### Aliases: plot_imp
> 
> ### ** Examples
> 
> library(randomForest)
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
> data(iris)
> fit = randomForest(Species ~ ., iris)
> imp = variable_importance(fit, nperm = 2, data = iris)
> plot_imp(imp)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package in Depends field not imported from: ‘spc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error(s) in re-building vignettes:
  ...
--- re-building ‘filters.Rmd’ using rmarkdown
--- finished re-building ‘filters.Rmd’

--- re-building ‘metrics.Rmd’ using rmarkdown
Quitting from lines 41-44 (metrics.Rmd) 
Error: processing vignette 'metrics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘metrics.Rmd’

SUMMARY: processing the following file failed:
  ‘metrics.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘edfReaderVignette.Rmd’ using rmarkdown
Quitting from lines 434-470 (edfReaderVignette.Rmd) 
Error: processing vignette 'edfReaderVignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘edfReaderVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘edfReaderVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘edgarWebR.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 109-112 (edgarWebR.Rmd) 
Error: processing vignette 'edgarWebR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘edgarWebR.Rmd’

--- re-building ‘parsing.Rmd’ using rmarkdown
--- finished re-building ‘parsing.Rmd’

SUMMARY: processing the following file failed:
  ‘edgarWebR.Rmd’

Error: Vignette re-building failed.
Execution halted
UCexactTest: no visible global function definition for ‘is’
UCexactTest: no visible global function definition for ‘new’
pvalue: no visible global function definition for ‘dnbinom’
pvalue: no visible global function definition for ‘pnbinom’
sup.mu: no visible global function definition for ‘predict’
Undefined global functions or variables:
  dnbinom is new pnbinom predict
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "dnbinom", "pnbinom", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error(s) in re-building vignettes:
  ...
--- re-building ‘eechidna-intro.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 86-105 (eechidna-intro.Rmd) 
Error: processing vignette 'eechidna-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘eechidna-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘eechidna-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
geteegdata: no visible global function definition for ‘untar’
geteegdata: no visible global function definition for ‘read.table’
geteegdata: no visible global function definition for ‘write.csv’
geteegdata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table untar write.csv write.table
Consider adding
  importFrom("utils", "read.table", "untar", "write.csv", "write.table")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘file-io.Rmd’ using knitr
--- finished re-building ‘file-io.Rmd’

--- re-building ‘vignette.Rmd’ using knitr
Quitting from lines 103-111 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 81-114 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘eeptools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.lm
> ### Title: A function to replicate the basic plot function for linear
> ###   models in ggplot2
> ### Aliases: autoplot.lm
> 
> ### ** Examples
> 
> # Univariate
> a <- runif(1000)
> b <- 7 * a + rnorm(1)
> mymod <- lm(b~a)
> autoplot(mymod)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: autoplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘test-all.R’ [13s/16s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Error: Autoplot works as expected for linear models (@test-plots.R#12)  ──
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: autoplot(mymod) at testthat/test-plots.R:12
  2: autoplot.lm(mymod)
  3: print(plots[[i]], vp = grid::viewport(layout.pos.row = mypos[j, ][1], layout.pos.col = mypos[j, 
         ][2]))
  4: print.ggplot(plots[[i]], vp = grid::viewport(layout.pos.row = mypos[j, ][1], layout.pos.col = mypos[j, 
         ][2]))
  5: grid.draw(gtable)
  6: grid.draw.gTree(gtable)
  7: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  8: drawGTree(x)
  9: preDraw(x)
  10: preDraw.gTree(x)
  11: pushvpgp(x)
  12: pushgrobvp(x$vp)
  13: pushgrobvp.viewport(x$vp)
  14: pushViewport(vp, recording = FALSE)
  15: lapply(vps, push.vp, recording)
  16: FUN(X[[i]], ...)
  17: push.vp.viewport(X[[i]], ...)
  18: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 516 SKIPPED: 0 FAILED: 1
  1. Error: Autoplot works as expected for linear models (@test-plots.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 170-173 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘eesim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calendar_plot
> ### Title: Create calendar plot
> ### Aliases: calendar_plot
> 
> ### ** Examples
> 
> testdat <- sim_exposure(n = 1000, central = 0.1,
+            exposure_type = "binary")
> testdat$x[c(89,101,367,500,502,598,678,700,895)] <- 3
> calendar_plot(testdat, type = "discrete", labels = c("no", "yes", "maybe"))
Error in Summary.unit(c(0, 0), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘eesim.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine

This is dlnm 2.3.9. For details: help(dlnm) and vignette('dlnmOverview').
Quitting from lines 35-50 (eesim.Rmd) 
Error: processing vignette 'eesim.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘eesim.Rmd’

SUMMARY: processing the following file failed:
  ‘eesim.Rmd’

Error: Vignette re-building failed.
Execution halted
.gdf : find_loss: no visible global function definition for ‘rnorm’
.p.values : <anonymous>: no visible global function definition for
  ‘pnorm’
.relist.dwt: no visible global function definition for ‘relist’
.relist.dwt: no visible global function definition for ‘as’
.std.wav.coeff : <anonymous>: no visible global function definition for
  ‘mad’
regrid: no visible global function definition for ‘predict’
regrid: no visible global function definition for ‘var’
regrid: no visible global function definition for ‘medpolish’
Undefined global functions or variables:
  as mad medpolish pnorm predict relist rnorm var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "mad", "medpolish", "pnorm", "predict", "rnorm",
             "var")
  importFrom("utils", "relist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘EffectLiteR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: conditionalEffectsPlot
> ### Title: Plot conditional effects
> ### Aliases: conditionalEffectsPlot
> 
> ### ** Examples
> 
> m1 <- effectLite(y="dv", x="x", k="k1", z="z1", control="control", data=example01)
> conditionalEffectsPlot(m1, zsel="z1", gxsel="g1", colour="k1")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ega-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotClarkeGrid
> ### Title: Plot a Clarke Error Grid
> ### Aliases: plotClarkeGrid
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # default
> plotClarkeGrid(glucose_data$ref, glucose_data$test)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ega.Rmd’ using rmarkdown
Quitting from lines 26-30 (ega.Rmd) 
Error: processing vignette 'ega.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ega.Rmd’

SUMMARY: processing the following file failed:
  ‘ega.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘eggCountsExtra’
Running examples in ‘egg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: expose_layout
> ### Title: expose_layout
> ### Aliases: expose_layout
> 
> ### ** Examples
> 
> p1 <- qplot(mpg, wt, data=mtcars, colour=cyl)
> p2 <- qplot(mpg, data = mtcars) + ggtitle('title')
> p3 <- qplot(mpg, data = mtcars, geom = 'dotplot')
> p4 <- p1 + facet_wrap(~carb, nrow=1) + theme(legend.position='none') +
+   ggtitle('facetted plot')
> pl <- lapply(list(p1,p2, p3, p4), expose_layout, FALSE, FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: lapply ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Ecosystem.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 38-54 (Ecosystem.Rmd) 
Error: processing vignette 'Ecosystem.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Ecosystem.Rmd’

--- re-building ‘Overview.Rmd’ using rmarkdown
Loading required package: gridExtra
Loading required package: ggplot2
Quitting from lines 33-46 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following files failed:
  ‘Ecosystem.Rmd’ ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘egoTERGM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_ego_tergm
> ### Title: Function to plot role assignments.
> ### Aliases: plot_ego_tergm
> ### Keywords: assignments interpretation plot summary
> 
> ### ** Examples
> 
> plots <- plot_ego_tergm(ego_tergm_fit = ego_tergm_fit)
> plots[[1]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
eiginv: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
boot_pr_comp: no visible global function definition for ‘cov’
boot_pr_comp: no visible global function definition for ‘quantile’
boot_pr_comp: no visible global function definition for ‘segments’
boot_pr_comp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov quantile segments
Consider adding
  importFrom("graphics", "abline", "segments")
  importFrom("stats", "cov", "quantile")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘class’ ‘quantreg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cluster.segment: no visible global function definition for ‘kmeans’
cluster.segment: no visible global function definition for ‘knn’
comp.anc.dist: no visible global function definition for ‘wilcox.test’
eila: no visible global function definition for ‘hasArg’
get.prob.score: no visible global function definition for ‘glm’
get.prob.score: no visible global function definition for ‘binomial’
get.prob.score: no visible binding for global variable ‘logit’
get.prob.score: no visible global function definition for ‘predict’
quantreg.est: no visible global function definition for ‘rnorm’
quantreg.est: no visible global function definition for ‘rq.fit.fnb’
Undefined global functions or variables:
  binomial glm hasArg kmeans knn logit predict rnorm rq.fit.fnb
  wilcox.test
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "binomial", "glm", "kmeans", "predict", "rnorm",
             "wilcox.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
comPlot: no visible global function definition for ‘plot’
comPlot: no visible global function definition for ‘lines’
convertEiData: no visible global function definition for ‘model.frame’
plot.eiwild: no visible global function definition for ‘plot’
plot.eiwild: no visible global function definition for ‘par’
plotResult: no visible global function definition for ‘grey’
plotResult: no visible global function definition for
  ‘colorRampPalette’
plotResult: no visible global function definition for ‘plot.new’
plotResult: no visible global function definition for ‘plot.window’
prioriPlot: no visible global function definition for ‘par’
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for ‘rgamma’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rbeta’
prioriPlot: no visible global function definition for ‘hist’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rgamma’
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for ‘rexp’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rexp’
runMBayes: no visible global function definition for ‘runif’
runMBayes: no visible global function definition for ‘rgamma’
runMBayes: no visible global function definition for ‘rexp’
str0: no visible global function definition for ‘str’
tuneVars: no visible global function definition for ‘sd’
Undefined global functions or variables:
  colorRampPalette grey hist lines model.frame par plot plot.new
  plot.window rbeta rexp rgamma runif sd str
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey")
  importFrom("graphics", "hist", "lines", "par", "plot", "plot.new",
             "plot.window")
  importFrom("stats", "model.frame", "rbeta", "rexp", "rgamma", "runif",
             "sd")
  importFrom("utils", "str")
to your NAMESPACE file.
Running examples in ‘EleChemr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CV
> ### Title: Cyclic voltammetry digitial simulation
> ### Aliases: CV
> 
> ### ** Examples
> 
> CV(Co = 0.001, DerApprox = 2, errCheck = FALSE, Method = "Euler")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package in Depends field not imported from: ‘elec’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BaB: no visible binding for global variable ‘calc.pairwise.e_p’
BaB: no visible global function definition for ‘weight.function’
BaB: no visible global function definition for ‘compute.stark.t’
LKPBound: no visible binding for global variable ‘calc.pairwise.e_p’
LKPBound: no visible global function definition for ‘weight.function’
LKPBound: no visible global function definition for ‘compute.stark.t’
eqValBound: no visible binding for global variable ‘calc.pairwise.e_p’
eqValBound: no visible global function definition for ‘weight.function’
eqValBound: no visible global function definition for ‘compute.stark.t’
getEbsMargin: no visible global function definition for ‘is.elec.data’
getEbsMargin: no visible global function definition for
  ‘maximumMarginBound’
makeStratObj: no visible global function definition for ‘is.elec.data’
makeStratObj: no visible global function definition for
  ‘maximumMarginBound’
strat.elec.data: no visible global function definition for ‘elec.data’
takeOutZeroMMB: no visible global function definition for
  ‘maximumMarginBound’
withReplaceBound: no visible binding for global variable
  ‘calc.pairwise.e_p’
withReplaceBound: no visible global function definition for
  ‘weight.function’
withReplaceBound: no visible global function definition for
  ‘compute.stark.t’
Undefined global functions or variables:
  calc.pairwise.e_p compute.stark.t elec.data is.elec.data
  maximumMarginBound weight.function
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Likelihood: no visible global function definition for
  ‘makePSOCKcluster’
Likelihood: no visible global function definition for ‘clusterExport’
Likelihood: no visible global function definition for ‘makeForkCluster’
Likelihood.first.run: no visible global function definition for
  ‘clusterApply’
Likelihood.next.runs: no visible global function definition for
  ‘clusterApply’
es.stopCluster: no visible global function definition for ‘stopCluster’
plot.es.pedigree: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
  clusterApply clusterExport hasArg makeForkCluster makePSOCKcluster
  stopCluster
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘etc’
Packages in Depends field not imported from:
  ‘MASS’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘emil-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: learning_curve
> ### Title: Learning curve analysis
> ### Aliases: learning_curve
> 
> ### ** Examples
> 
> options(emil_max_indent=3)
> lc <- learning_curve(c(Linear="lda", Quadratic="qda"),
+                      iris[-5], iris$Species, test_fraction=c(.7, .5, .3))
29 Mar 19:26  Learning curve analysis
29 Mar 19:26    Test set test_fraction 1 of 3 (0.7)
29 Mar 19:26      Evaluating modeling performance...
29 Mar 19:26    Test set test_fraction 2 of 3 (0.5)
29 Mar 19:26      Evaluating modeling performance...
29 Mar 19:26    Test set test_fraction 3 of 3 (0.3)
29 Mar 19:26      Evaluating modeling performance...
> plot(lc)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running ‘testthat.R’ [11s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  ── 1. Failure: k-NN imputation (@test-preprocess.r#30)  ────────────────────────
  sets$test$x[na.ind] not equivalent to ifelse(na.ind[, 2] <= 3, 5, 4.5).
  3/10 mismatches (average diff: 0.5)
  [5]  5 - 4.5 == 0.5
  [7]  5 - 4.5 == 0.5
  [10] 5 - 4.5 == 0.5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 183 SKIPPED: 1 FAILED: 1
  1. Failure: k-NN imputation (@test-preprocess.r#30) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distance: no visible global function definition for
  ‘data.Normalization’
emmatn: no visible global function definition for ‘runif’
estimateModel: no visible global function definition for ‘as.formula’
estimateModel: no visible global function definition for ‘earth’
estimateModel: no visible global function definition for ‘plotmo’
estimateModel: no visible global function definition for ‘predict’
mutation: no visible global function definition for ‘runif’
plot.emma: no visible global function definition for ‘colorRampPalette’
plot.emma: no visible global function definition for ‘par’
plot.emma: no visible global function definition for ‘persp’
plot.emma: no visible global function definition for ‘points’
plot.emma: no visible global function definition for ‘trans3d’
Undefined global functions or variables:
  as.formula colorRampPalette data.Normalization earth par persp plotmo
  points predict runif trans3d
Consider adding
  importFrom("grDevices", "colorRampPalette", "trans3d")
  importFrom("graphics", "par", "persp", "points")
  importFrom("stats", "as.formula", "predict", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘reshape’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MFFetch: no visible global function definition for ‘melt’
Undefined global functions or variables:
  melt
Running examples in ‘emmeans-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: auto.noise
> ### Title: Auto Pollution Filter Noise
> ### Aliases: auto.noise
> ### Keywords: datasets
> 
> ### ** Examples
> 
> noise.lm <- lm(noise ~ size * type * side, data = auto.noise)
> 
> # Interaction plot of predictions
> emmip(noise.lm, type ~ size | side)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘EMMIXmfa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: factor_scores
> ### Title: Computes Factor Scores
> ### Aliases: factor_scores factor_scores.mcfa factor_scores.mctfa
> ###   plot.emmix
> ### Keywords: cluster multivariate models
> 
> ### ** Examples
> 
> # Fit a MCFA model to a subset
> set.seed(1)
> samp_size <- dim(iris)[1]
> sel_subset <- sample(1 : samp_size, 50)
> model <- mcfa(iris[sel_subset, -5], g = 3, q = 2, 
+                           nkmeans = 1, nrandom = 0, itmax = 100)

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |......................................................................| 100%
> 
> # plot the data points in the factor space
> plot(model)
> 
> # Allocating new samples to the clusters
> Y <- iris[-c(sel_subset), -5]
> Y <- as.matrix(Y)
> clust <- predict(model, Y)
> 
> fa_scores <- factor_scores(model, Y)
> # Visualizing new data in factor space
> plot_factors(fa_scores, type = "Umean", clust = clust)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_factors ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
nondominated_ordering: no visible binding for global variable ‘par’
rsbxbeta: no visible global function definition for ‘runif’
Undefined global functions or variables:
  par runif
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘emojifont.Rmd’ using rmarkdown
Quitting from lines 102-109 (emojifont.Rmd) 
Error: processing vignette 'emojifont.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘emojifont.Rmd’

SUMMARY: processing the following file failed:
  ‘emojifont.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘EmpiricalCalibration-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCalibration
> ### Title: Create a calibration plot
> ### Aliases: plotCalibration
> 
> ### ** Examples
> 
> data(sccs)
> negatives <- sccs[sccs$groundTruth == 0, ]
> plotCalibration(negatives$logRr, negatives$seLogRr)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EmpiricalCiCalibrationVignette.Rmd’ using rmarkdown
Quitting from lines 68-70 (EmpiricalCiCalibrationVignette.Rmd) 
Error: processing vignette 'EmpiricalCiCalibrationVignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘EmpiricalCiCalibrationVignette.Rmd’

--- re-building ‘EmpiricalPCalibrationVignette.Rmd’ using rmarkdown
Quitting from lines 52-53 (EmpiricalPCalibrationVignette.Rmd) 
Error: processing vignette 'EmpiricalPCalibrationVignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘EmpiricalPCalibrationVignette.Rmd’

SUMMARY: processing the following files failed:
  ‘EmpiricalCiCalibrationVignette.Rmd’
  ‘EmpiricalPCalibrationVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
empiricalFDR: no visible global function definition for ‘axis’
empiricalFDR: no visible global function definition for ‘loess’
empiricalFDR: no visible global function definition for ‘predict’
empiricalFDR: no visible global function definition for ‘lines’
empiricalFDR: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘plot’
fdrBiCurve: no visible global function definition for ‘axis’
fdrBiCurve: no visible global function definition for ‘lines’
fdrBiCurve: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘legend’
simulateCounts: no visible global function definition for
  ‘txtProgressBar’
simulateCounts: no visible global function definition for
  ‘setTxtProgressBar’
simulateCounts: no visible global function definition for ‘rnorm’
simulateCounts: no visible global function definition for ‘hist’
simulateCounts: no visible global function definition for ‘colData’
Undefined global functions or variables:
  abline axis colData hist legend lines loess plot predict rnorm
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "plot")
  importFrom("stats", "loess", "predict", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running examples in ‘emstreeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_MST
> ### Title: Euclidean Minimum Spanning Tree Stat Function
> ### Aliases: stat_MST
> 
> ### ** Examples
> 
> 
> ## 2D artificial data:
> set.seed(1984)
> n <- 15
> c1 <- data.frame(x = rnorm(n, -0.2, sd = 0.2), y = rnorm(n, -2, sd = 0.2))
> c2 <- data.frame(x = rnorm(n, -1.1, sd = 0.15), y = rnorm(n, -2, sd = 0.3)) 
> d <- rbind(c1, c2)
> d <- as.data.frame(d)
> 
> ## MST:
> out <- ComputeMST(d)
18 edges found so far.
482 cumulative base cases.
4 cumulative node combinations scored.
25 edges found so far.
891 cumulative base cases.
8 cumulative node combinations scored.
29 edges found so far.
1224 cumulative base cases.
12 cumulative node combinations scored.
Total spanning tree length: 11.6963
> 
> #1) simple plot
> library(ggplot2)
> ggplot(data = out, 
+     aes(x = x, y = y, 
+     from = from, to = to))+ 
+     geom_point()+
+     stat_MST(colour = "red", linetype = 2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
ExactMultinomialTest: no visible global function definition for
  ‘dmultinom’
ExactMultinomialTest : <anonymous>: no visible global function
  definition for ‘dmultinom’
ExactMultinomialTestChisquare : <anonymous>: no visible global function
  definition for ‘dmultinom’
MonteCarloMultinomialTest: no visible global function definition for
  ‘rmultinom’
MonteCarloMultinomialTest: no visible global function definition for
  ‘flush.console’
MonteCarloMultinomialTestChisquare: no visible global function
  definition for ‘rmultinom’
MonteCarloMultinomialTestChisquare: no visible global function
  definition for ‘flush.console’
multinomial.test: no visible global function definition for
  ‘flush.console’
plotMultinom: no visible global function definition for ‘barplot’
plotMultinom: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  barplot dmultinom flush.console mtext rmultinom
Consider adding
  importFrom("graphics", "barplot", "mtext")
  importFrom("stats", "dmultinom", "rmultinom")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘EQL.Rmd’ using rmarkdown

Attaching package: 'emuR'

The following object is masked from 'package:base':

    norm

--- finished re-building ‘EQL.Rmd’

--- re-building ‘emuDB.Rmd’ using rmarkdown

Attaching package: 'emuR'

The following object is masked from 'package:base':

    norm

Warning: call dbDisconnect() when finished working with a connection
--- finished re-building ‘emuDB.Rmd’

--- re-building ‘emuR_intro.Rmd’ using rmarkdown

Attaching package: 'emuR'

The following object is masked from 'package:base':

    norm

Quitting from lines 262-275 (emuR_intro.Rmd) 
Error: processing vignette 'emuR_intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘emuR_intro.Rmd’

SUMMARY: processing the following file failed:
  ‘emuR_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘CHANGES.txt’
'library' or 'require' call to ‘RColorBrewer’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Rcmdr’ ‘gWidgets’ ‘gWidgetstcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘RColorBrewer’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘enpls-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv.enpls
> ### Title: Cross Validation for Ensemble Partial Least Squares Regression
> ### Aliases: cv.enpls
> 
> ### ** Examples
> 
> data("alkanes")
> x = alkanes$x
> y = alkanes$y
> 
> set.seed(42)
> cvfit = cv.enpls(x, y, reptimes = 10)
Beginning fold 1 
Beginning fold 2 
Beginning fold 3 
Beginning fold 4 
Beginning fold 5 
> print(cvfit)
Cross Validation Result for Ensemble Partial Least Squares
---
RMSE = 3.6481
MAE = 2.515792
Rsquare = 0.999961
> plot(cvfit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘enpls.Rmd’ using rmarkdown
Quitting from lines 62-73 (enpls.Rmd) 
Error: processing vignette 'enpls.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘enpls.Rmd’

SUMMARY: processing the following file failed:
  ‘enpls.Rmd’

Error: Vignette re-building failed.
Execution halted
Deprecated license: BSD
Checking should be performed on sources prepared by ‘R CMD build’.
matplot_enrichment_curve: no visible global function definition for
  ‘plot’
matplot_enrichment_curve: no visible global function definition for
  ‘lines’
matplot_enrichment_curve: no visible global function definition for
  ‘legend’
plot_enrichment_curve: no visible global function definition for ‘plot’
plot_enrichment_curve: no visible global function definition for
  ‘lines’
plot_enrichment_curve: no visible global function definition for
  ‘plot.xy’
plot_enrichment_curve: no visible global function definition for
  ‘xy.coords’
plot_enrichment_curve: no visible global function definition for
  ‘rainbow’
plot_enrichment_curve: no visible global function definition for
  ‘axTicks’
plot_enrichment_curve: no visible global function definition for ‘rect’
plot_enrichment_curve: no visible global function definition for ‘axis’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘plot’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘lines’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘plot.xy’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘xy.coords’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘rainbow’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘axTicks’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘rect’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘axis’
Undefined global functions or variables:
  axTicks axis legend lines plot plot.xy rainbow rect xy.coords
Consider adding
  importFrom("grDevices", "rainbow", "xy.coords")
  importFrom("graphics", "axTicks", "axis", "legend", "lines", "plot",
             "plot.xy", "rect")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘GLMs.Rmd’ using rmarkdown
Quitting from lines 50-69 (GLMs.Rmd) 
Error: processing vignette 'GLMs.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GLMs.Rmd’

--- re-building ‘bias.Rmd’ using rmarkdown
--- finished re-building ‘bias.Rmd’

--- re-building ‘exponential_family.Rmd’ using rmarkdown
--- finished re-building ‘exponential_family.Rmd’

SUMMARY: processing the following file failed:
  ‘GLMs.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ensr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lambda_alpha_grid
> ### Title: Lambda Alpha Grid
> ### Aliases: lambda_alpha_grid
> 
> ### ** Examples
> 
> 
> data(tbi)
> Xmat <- model.matrix( ~ . - injury1 - injury2 - injury3 - 1, data = tbi)
> Yvec <- matrix(tbi$injury1, ncol = 1)
> alphas <- seq(0, 1, length = 20)
> 
> lga <- lambda_alpha_grid(alphas = alphas, lambdas = lambda_max(Yvec, Xmat, alpha = alphas))
> 
> ggplot2::ggplot() +
+   ggplot2::theme_bw() +
+   ggplot2::aes_string(x = "a", y = "log10(l)") +
+   ggplot2::geom_path(data = lga$top) +
+   ggplot2::geom_point(data = lga$lgrid,
+                       mapping = ggplot2::aes(color = cos(a) + sin(log10(l)))) +
+   ggplot2::geom_contour(data = lga$lgrid,
+                         mapping = ggplot2::aes(z = cos(a) + sin(log10(l)))) +
+   ggplot2::scale_color_gradient2(low = "blue", high = "red", mid = "grey")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
diffcv: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘fligner.test’
diffcvall: no visible global function definition for ‘p.adjust’
diffcvpFK: no visible global function definition for ‘fligner.test’
diffcvpFK: no visible global function definition for ‘p.adjust’
diffexp: no visible global function definition for ‘var’
diffexp: no visible global function definition for ‘t.test’
diffexp: no visible global function definition for ‘p.adjust’
diffexp2: no visible global function definition for ‘var’
diffexp2: no visible global function definition for ‘t.test’
diffexp2: no visible global function definition for ‘p.adjust’
diffnsepperm: no visible global function definition for ‘p.adjust’
diffseall: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  fligner.test p.adjust sd t.test var
Consider adding
  importFrom("stats", "fligner.test", "p.adjust", "sd", "t.test", "var")
to your NAMESPACE file.
Running examples in ‘envalysis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme_publish
> ### Title: ggplot2 theme for scientific publications
> ### Aliases: theme_publish
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
> p <- ggplot(mtcars) + geom_point(aes(x = wt, y = mpg,
+      colour=factor(gear))) + facet_wrap( ~ am)
> p
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘texture.Rmd’ using rmarkdown
--- finished re-building ‘texture.Rmd’

--- re-building ‘theme_publish.Rmd’ using rmarkdown
Loading required package: envalysis
Loading required package: ggplot2
Quitting from lines 29-35 (theme_publish.Rmd) 
Error: processing vignette 'theme_publish.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘theme_publish.Rmd’

SUMMARY: processing the following file failed:
  ‘theme_publish.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  main.c:334:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:575:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:518:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:805:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:755:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1034:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:983:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1377:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1279:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1678:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1962:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1912:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2316:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2212:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/enviPat.Rcheck/00install.out’ for details.
Running examples in ‘EnvStats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_stripchart
> ### Title: 1-D Scatter Plots with Confidence Intervals Using ggplot2
> ### Aliases: geom_stripchart
> ### Keywords: hplot htest
> 
> ### ** Examples
> 
> 
>   # First, load and attach the ggplot2 package.
>   #--------------------------------------------
> 
>   library(ggplot2)
> 
>   #==========
> 
>   #---------------------
>   # 3 Independent Groups
>   #---------------------
> 
>   # Example 1:
> 
>   # Using the built-in data frame mtcars, 
>   # create a stipchart of miles per gallon vs. number of cylinders
>   # using different colors for each level of the number of cylinders.
>   #------------------------------------------------------------------
> 
>   p <- ggplot(mtcars, aes(x = factor(cyl), y = mpg, color = factor(cyl))) 
> 
>   p + geom_stripchart() + 
+     labs(x = "Number of Cylinders", y = "Miles per Gallon")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' call to ‘plotrix’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Hmisc’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘plotrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘a.alpha.ade’ ‘a.coladd.ade’ ‘a.getcol.ade’ ‘a.glc’
Found the following significant warnings:
  epanet.c:999:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1000:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1492:3: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2308:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2309:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:454:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:455:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input3.c:604:2: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/epanet2toolkit.Rcheck/00install.out’ for details.
Running examples in ‘EpiCurve-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EpiCurve
> ### Title: Plot an Epidemic Curve
> ### Aliases: EpiCurve
> 
> ### ** Examples
> 
> # library(Epicurve)
> date <- seq(as.timeDate("2017-05-10 21:35:22"), as.timeDate("2017-05-12 06:15:12"), by="12 min")
> val <- rep(1, length(date))
> tri <- rep(c("Alive", "Died","Unknown"), length.out=length(date))
> DF <- data.frame(date, val, tri)
> names(DF) <- c("date","value", "tri")
> 
> 
> EpiCurve(DF,
+          date = "date",
+          freq = "value",
+          period = "hour",
+          split = 4,
+          cutvar = "tri",
+          ylabel="Number of cases",
+          xlabel= "From 2017-05-10 21:35:22 To 2017-05-12 06:15:12",
+          title = "Epidemic Curve")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EpiCurve.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: ISOweek
Loading required package: scales
Quitting from lines 132-137 (EpiCurve.Rmd) 
Error: processing vignette 'EpiCurve.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘EpiCurve.Rmd’

SUMMARY: processing the following file failed:
  ‘EpiCurve.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘EpiDynamics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MultiStrainPartialImmunity
> ### Title: Partial immunity model that cycles (P 4.2).
> ### Aliases: MultiStrainPartialImmunity
> 
> ### ** Examples
> 
> # Parameters and initial conditions.
> parameters <- c(beta = rep(40, 4), gamma = rep(9.98, 4),
+                        mu = 0.02, a = 0.4 )
> 
> initials <- c(S = c(0.08, 0.1, 0.1, 0.11),
+                        P = c(0.4, 0.3, 0.3, 0.29),
+                        L = c(0.15, 0.02, 0.1, 0.01))
> 
> # Solve and plot.
> mlti.strain.pi <- MultiStrainPartialImmunity(pars = parameters, 
+                                              init = initials, 
+                                              time = 0:200)
> PlotMods(mlti.strain.pi, variables = c('L1', 'L2', 'L3', 'L4'), grid = FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: PlotMods ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Non-standard file/directory found at top level:
  ‘sync.x64.ffs_db’
DiscrSI : CDFGamma: no visible global function definition for ‘pgamma’
EstimateR : SampleFromPosterior : <anonymous>: no visible global
  function definition for ‘rgamma’
EstimateR: no visible global function definition for ‘rnorm’
EstimateR: no visible binding for global variable ‘sd’
EstimateR: no visible binding for global variable ‘quantile’
EstimateR: no visible binding for global variable ‘median’
EstimateR: no visible global function definition for ‘qgamma’
EstimateR: no visible global function definition for ‘par’
EstimateR: no visible global function definition for ‘title’
EstimateR: no visible global function definition for ‘polygon’
EstimateR: no visible global function definition for ‘lines’
EstimateR: no visible global function definition for ‘legend’
EstimateR: no visible global function definition for ‘hist’
WT : DrawOneSetOfAncestries: no visible global function definition for
  ‘rmultinom’
WT: no visible binding for global variable ‘quantile’
WT: no visible binding for global variable ‘sd’
WT: no visible global function definition for ‘par’
WT: no visible global function definition for ‘segments’
WT: no visible global function definition for ‘points’
WT: no visible global function definition for ‘lines’
WT: no visible global function definition for ‘legend’
Undefined global functions or variables:
  hist legend lines median par pgamma points polygon qgamma quantile
  rgamma rmultinom rnorm sd segments title
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "par", "points",
             "polygon", "segments", "title")
  importFrom("stats", "median", "pgamma", "qgamma", "quantile", "rgamma",
             "rmultinom", "rnorm", "sd")
to your NAMESPACE file.
Running examples in ‘epiflows-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.epiflows
> ### Title: Various plots for epiflows objects
> ### Aliases: plot.epiflows
> 
> ### ** Examples
> 
> data("Brazil_epiflows")
> 
> # no coordinates, defaults to network
> plot(Brazil_epiflows) 
type 'map' requested but 'x' has no spatial coordinates
using 'network' instead
> 
> # grid bubbleplot
> plot(Brazil_epiflows, "grid")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
Quitting from lines 108-117 (epiflows-class.Rmd) 
Error: processing vignette 'epiflows-class.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 50-70 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘epiflows-class.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘EpiModel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_bands
> ### Title: ggplot2 geom for Quantile Bands
> ### Aliases: geom_bands
> ### Keywords: plot
> 
> ### ** Examples
> 
> param <- param.icm(inf.prob = 0.2, act.rate = 0.25)
> init <- init.icm(s.num = 500, i.num = 1)
> control <- control.icm(type = "SI", nsteps = 250, nsims = 5)
> mod1 <- icm(param, init, control)
> df <- as.data.frame(mod1)
> df.mean <- as.data.frame(mod1, out = "mean")
> 
> library(ggplot2)
> ggplot() +
+    geom_line(data = df, mapping = aes(time, i.num, group = sim), alpha = 0.25,
+              lwd = 0.25, color = "firebrick") +
+    geom_bands(data = df, mapping = aes(time, i.num),
+               lower = 0.1, upper = 0.9, fill = "firebrick") +
+    geom_line(data = df.mean, mapping = aes(time, i.num)) +
+    theme_minimal()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘epiphy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clump
> ### Title: Regroup observational data into even clumps of individuals.
> ### Aliases: clump clump.intensity
> 
> ### ** Examples
> 
> my_incidence <- incidence(tomato_tswv$field_1929)
> plot(my_incidence, type = "all")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘defs-and-eqns.Rmd’ using rmarkdown
--- finished re-building ‘defs-and-eqns.Rmd’

--- re-building ‘epiphy.Rmd’ using rmarkdown
Quitting from lines 84-85 (epiphy.Rmd) 
Error: processing vignette 'epiphy.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘epiphy.Rmd’

SUMMARY: processing the following file failed:
  ‘epiphy.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘EpiReport-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getAER
> ### Title: Get full disease-specific epidemiological report
> ### Aliases: getAER
> 
> ### ** Examples
> 
> # --- Generating the AER report using the default Salmonellosis dataset
> getAER()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: getAER ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EpiReport_Vignette.Rmd’ using rmarkdown
Quitting from lines 273-291 (EpiReport_Vignette.Rmd) 
Error: processing vignette 'EpiReport_Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘EpiReport_Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘EpiReport_Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘episensr.Rmd’ using rmarkdown
Warning: Removed 438 rows containing non-finite values (stat_bin).
Warning: Removed 438 rows containing non-finite values (stat_density).
Quitting from lines 296-297 (episensr.Rmd) 
Error: processing vignette 'episensr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘episensr.Rmd’

SUMMARY: processing the following file failed:
  ‘episensr.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘episheet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pvalueplot
> ### Title: Plot the p-value function
> ### Aliases: pvalueplot
> ### Keywords: R Rothman episheet pvalues
> 
> ### ** Examples
> 
> pvalueplot(
+   est1.ll = 0.9,
+   est1.ul = 12,
+   xlabel = "Relative Risk"
+ )
Confidence interval type is  95%CI
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pvalueplot.Rmd’ using rmarkdown
Confidence interval type is  95%CI
Quitting from lines 21-26 (pvalueplot.Rmd) 
Error: processing vignette 'pvalueplot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pvalueplot.Rmd’

SUMMARY: processing the following file failed:
  ‘pvalueplot.Rmd’

Error: Vignette re-building failed.
Execution halted
plot.episplineDensity: no visible global function definition for ‘plot’
plot.episplineDensity: no visible global function definition for
  ‘points’
postproc: no visible global function definition for ‘plot’
postproc: no visible global function definition for ‘points’
preprocess.data: no visible global function definition for ‘sd’
Undefined global functions or variables:
  plot points sd
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘epitrix.Rmd’ using rmarkdown
Quitting from lines 122-133 (epitrix.Rmd) 
Error: processing vignette 'epitrix.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘epitrix.Rmd’

SUMMARY: processing the following file failed:
  ‘epitrix.Rmd’

Error: Vignette re-building failed.
Execution halted
FCIplot: no visible global function definition for ‘na.omit’
FCIplot: no visible global function definition for ‘plot’
FCIplot: no visible global function definition for ‘tail’
FCIplot: no visible global function definition for ‘grid’
FCIplot: no visible global function definition for ‘polygon’
FCIplot: no visible global function definition for ‘rgb’
linpred: no visible global function definition for ‘lm’
mplott: no visible global function definition for ‘par’
mplott: no visible global function definition for ‘plot’
mplott: no visible global function definition for ‘na.omit’
mplott: no visible global function definition for ‘lines’
mplott: no visible global function definition for ‘legend’
mplott: no visible global function definition for ‘grid’
plott: no visible global function definition for ‘lines’
plott: no visible global function definition for ‘par’
plott: no visible global function definition for ‘plot’
plott: no visible global function definition for ‘grid’
tsideplot: no visible global function definition for ‘par’
tsideplot: no visible global function definition for ‘plot’
tsideplot: no visible global function definition for ‘axis’
tsideplot: no visible global function definition for ‘grid’
Undefined global functions or variables:
  axis grid legend lines lm na.omit par plot polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
.getFactor: no visible global function definition for ‘integrate’
check.cumulants: no visible global function definition for ‘runif’
edgeworth: no visible global function definition for ‘dnorm’
eql : getEQL: no visible binding for global variable ‘glm’
eql: no visible global function definition for ‘splinefun’
eql: no visible binding for global variable ‘glm’
eql : <anonymous>: no visible global function definition for ‘glm’
plot.approximation: no visible global function definition for ‘mtext’
plot.eql: no visible global function definition for ‘points’
plot.eql: no visible global function definition for ‘par’
plot.eql: no visible global function definition for ‘segments’
plot.eql: no visible global function definition for ‘qchisq’
plot.eql: no visible global function definition for ‘text’
plot.eql: no visible global function definition for ‘abline’
plot.eql : eql.panel: no visible global function definition for
  ‘qchisq’
plot.eql: no visible global function definition for ‘colorRampPalette’
plot.eql: no visible global function definition for ‘heat.colors’
varianceFamily : devf : <anonymous>: no visible global function
  definition for ‘integrate’
varianceFamily: no visible global function definition for ‘make.link’
Undefined global functions or variables:
  abline colorRampPalette dnorm glm heat.colors integrate make.link
  mtext par points qchisq runif segments splinefun text
Consider adding
  importFrom("grDevices", "colorRampPalette", "heat.colors")
  importFrom("graphics", "abline", "mtext", "par", "points", "segments",
             "text")
  importFrom("stats", "dnorm", "glm", "integrate", "make.link", "qchisq",
             "runif", "splinefun")
to your NAMESPACE file.
eqs2lavaan: no visible global function definition for ‘ignore.case’
eqs2lavaan: no visible global function definition for ‘str_join’
eqs2lavaan: no visible binding for global variable ‘r’
eqsCorr: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘par’
plotCov: no visible global function definition for ‘image’
plotCov: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis cov2cor ignore.case image par r str_join
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "cov2cor")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘docs’ ‘license.txt’ ‘status.txt’
'library' or 'require' call to ‘qtl’ which was already attached by Depends.
  Please remove these calls from your code.
Unexported objects imported by ':::' calls:
  ‘qtl:::c.scanone’ ‘qtl:::plot.scanone’
  See the note in ?`:::` about the use of this operator.
The following files contain a license that requires
distribution of original sources:
  ‘upgreek.sty’
Please ensure that you have complied with it.
Found the following apparent S3 methods exported but not registered:
  mixingmatrix.egodata
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'mixingmatrix.egodata':
  ‘mixingmatrix.egodata’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  coef.length.model plot.mcmc.list.ergm plot.network.ergm
  summary.statistics
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ERSA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pcpPlot
> ### Title: A PCP plot of the data, residuals or hat values from regression
> ###   fits
> ### Aliases: pcpPlot
> 
> ### ** Examples
> 
> f <- lm(mpg ~ wt+hp+disp, data=mtcars)
> pcpPlot(mtcars, f, type="Residuals")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ERSA.Rmd’ using rmarkdown
Quitting from lines 101-104 (ERSA.Rmd) 
Error: processing vignette 'ERSA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ERSA.Rmd’

SUMMARY: processing the following file failed:
  ‘ERSA.Rmd’

Error: Vignette re-building failed.
Execution halted
ESA: no visible binding for global variable ‘var’
plot.esabcv: no visible global function definition for ‘plot’
plot.esabcv: no visible global function definition for ‘points’
plot.esabcv: no visible global function definition for ‘axis’
plot.esabcv: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis plot points title var
Consider adding
  importFrom("graphics", "axis", "plot", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
ESEA.Main: no visible global function definition for ‘rnorm’
ESEA.Main: no visible global function definition for ‘sd’
ESEA.Main: no visible global function definition for ‘p.adjust’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘plot’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘lines’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘colors’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘points’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘legend’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘text’
PlotPathwayGraph: no visible global function definition for ‘par’
PlotPathwayGraph: no visible global function definition for ‘plot’
PlotRunEnrichment: no visible global function definition for ‘plot’
PlotRunEnrichment: no visible global function definition for ‘lines’
PlotRunEnrichment: no visible global function definition for ‘colors’
PlotRunEnrichment: no visible global function definition for ‘text’
SavePathway2File: no visible global function definition for ‘is’
calEdgeCorScore: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colors is legend lines na.omit p.adjust par plot points rnorm sd text
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "text")
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "p.adjust", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘ESG-Ex.R’
rAllRisksFactors: no visible global function definition for ‘new’
rAssetDistribution: no visible global function definition for ‘new’
rDefaultSpread: no visible global function definition for ‘new’
rLiquiditySpread: no visible global function definition for ‘new’
rRealEstate: no visible global function definition for ‘new’
rShortRate: no visible global function definition for ‘new’
rStock: no visible global function definition for ‘new’
EuroCall_Stock_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroCall_ZC_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroPut_Stock_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroPut_ZC_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
MartingaleTest,Scenarios: no visible global function definition for
  ‘plot’
MartingaleTest,Scenarios: no visible global function definition for
  ‘lines’
MartingaleTest,Scenarios: no visible global function definition for
  ‘title’
customPathsGeneration,Scenarios: no visible global function definition
  for ‘rnorm’
Undefined global functions or variables:
  lines new plot pnorm rnorm title
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘ESGtoolkit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: esgplotts
> ### Title: Plot time series objects
> ### Aliases: esgplotts
> 
> ### ** Examples
> 
> kappa <- 1.5
> V0 <- theta <- 0.04
> sigma <- 0.2
> theta1 <- kappa*theta
> theta2 <- kappa
> theta3 <- sigma
> x <- simdiff(n = 10, horizon = 5, frequency = "quart",
+ model = "OU",
+ x0 = V0, theta1 = theta1, theta2 = theta2, theta3 = theta3)
> 
> esgplotts(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ESG2toolkit_Intro_062014.Rnw’ using knitr
Loading required package: CDVine
The CDVine package is no longer developed actively.
Please consider using the more general VineCopula package
(see https://CRAN.R-project.org/package=VineCopula),
which extends and improves the functionality of CDVine.

Loading required package: ggplot2
Loading required package: gridExtra
Loading required package: reshape2
Loading required package: ycinterextra
Loading required package: compiler

Attaching package: 'ycinterextra'

The following objects are masked from 'package:stats':

    deviance, fitted, residuals

The following object is masked from 'package:base':

    as.list

Quitting from lines 369-370 (ESG2toolkit_Intro_062014.Rnw) 
Error: processing vignette 'ESG2toolkit_Intro_062014.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ESG2toolkit_Intro_062014.Rnw’

SUMMARY: processing the following file failed:
  ‘ESG2toolkit_Intro_062014.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘esmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme_edi
> ### Title: Custom ggplot2 theme
> ### Aliases: theme_edi
> 
> ### ** Examples
> 
> library(ggplot2)
> p <- ggplot(mtcars) + 
+  geom_point(aes(x = wt, y = mpg, 
+ colour=factor(gear))) + facet_wrap(~am)
> p
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
cv.ES: no visible binding for global variable ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ESTER.Rmd’ using rmarkdown
Quitting from lines 95-102 (ESTER.Rmd) 
Error: processing vignette 'ESTER.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ESTER.Rmd’

SUMMARY: processing the following file failed:
  ‘ESTER.Rmd’

Error: Vignette re-building failed.
Execution halted
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘estoutstorage’
descsto: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.Transition: no visible global function definition for ‘rnorm’
.Transition.DC: no visible global function definition for ‘runif’
CondPdf.CC.interval: no visible global function definition for ‘plot’
CondPdf.DC.interval: no visible global function definition for ‘plot’
Simu.Cond.HR: no visible global function definition for ‘rpois’
Simu.Cond.HR: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘hist’
Simu.Cond.HR: no visible global function definition for ‘var’
Simu.HR: no visible global function definition for ‘rpois’
Simu.HR: no visible global function definition for ‘runif’
Simu.HR: no visible global function definition for ‘hist’
Simu.HR: no visible global function definition for ‘var’
Simu.PDMP: no visible global function definition for ‘plot’
Simu.PDMP.DC: no visible global function definition for ‘plot’
plotCHR: no visible global function definition for ‘plot’
plotHR: no visible global function definition for ‘plot’
Undefined global functions or variables:
  hist plot rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
corr_p_cell: no visible global function definition for ‘cov.wt’
iqr_cell: no visible global function definition for ‘quantile’
iqr_cell: no visible global function definition for ‘wtd.quantile’
mean_sd_cell: no visible global function definition for ‘wtd.mean’
mean_sd_cell: no visible global function definition for ‘wtd.var’
mode_cell: no visible global function definition for ‘wtd.table’
quantile_cell: no visible global function definition for ‘wtd.quantile’
quantile_cell: no visible global function definition for ‘quantile’
stat_cell: no visible global function definition for ‘quantile’
stat_cell: no visible global function definition for ‘wtd.quantile’
stat_cell: no visible global function definition for ‘wtd.mean’
stat_cell: no visible global function definition for ‘wtd.var’
stat_cell: no visible global function definition for ‘mad’
stat_cell: no visible global function definition for ‘wtd.table’
Undefined global functions or variables:
  cov.wt mad quantile wtd.mean wtd.quantile wtd.table wtd.var
Consider adding
  importFrom("stats", "cov.wt", "mad", "quantile")
to your NAMESPACE file.
etc.diff: no visible global function definition for ‘model.frame’
etc.diff: no visible binding for global variable ‘sd’
etc.diff: no visible global function definition for ‘qt’
etc.diff: no visible global function definition for ‘pt’
etc.diff: no visible global function definition for ‘wilcox.test’
etc.rat: no visible global function definition for ‘model.frame’
etc.rat: no visible binding for global variable ‘sd’
etc.rat: no visible global function definition for ‘qt’
etc.rat: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.frame pt qt sd wilcox.test
Consider adding
  importFrom("stats", "model.frame", "pt", "qt", "sd", "wilcox.test")
to your NAMESPACE file.
Running examples in ‘ethnobotanyR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Radial_plot
> ### Title: Radial bar plot of use reports (UR) per species
> ### Aliases: Radial_plot
> ### Keywords: cultural ethnobotany, report use value,
> 
> ### ** Examples
> 
> 
> #Use built-in ethnobotany data example and Frequency of Citation function FCs()
> Radial_plot(ethnobotanydata, analysis = FCs)
  sp_name FCs
1    sp_c  17
2    sp_a  15
3    sp_b  12
4    sp_d  12
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Radial_plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ethnobotanyr_vignette.Rmd’ using rmarkdown
Quitting from lines 47-48 (ethnobotanyr_vignette.Rmd) 
Error: processing vignette 'ethnobotanyr_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ethnobotanyr_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘ethnobotanyr_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘evergreenreviewgraphs.Rmd’ using rmarkdown
Quitting from lines 59-68 (evergreenreviewgraphs.Rmd) 
Error: processing vignette 'evergreenreviewgraphs.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘evergreenreviewgraphs.Rmd’

--- re-building ‘introducing-europepmc.Rmd’ using rmarkdown
171349 records found, returning 100
168667 records found, returning 100
1456 records found, returning 100
1456 records found, returning 10
1 records found, returning 1
1 records found, returning 1
1 records found, returning 1
1 records found, returning 1
10 records found, returning 10
564 records found, returning 564
135 records found, returning 135
73452 records found, returning 100
3521 records found, returning 100
231 records found. Returning 231
169 records found. Returning 169
--- finished re-building ‘introducing-europepmc.Rmd’

SUMMARY: processing the following file failed:
  ‘evergreenreviewgraphs.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘blogposts.Rmd’ using rmarkdown
--- finished re-building ‘blogposts.Rmd’

--- re-building ‘cheatsheet.Rmd’ using rmarkdown
--- finished re-building ‘cheatsheet.Rmd’

--- re-building ‘eurostat_tutorial.Rmd’ using rmarkdown
Loading required package: xml2
trying URL ‘https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ft2020_rk310.tsv.gz’
Content type 'application/octet-stream;charset=UTF-8' length 4476 bytes
==================================================
downloaded 4476 bytes

Table t2020_rk310 cached at /home/hornik/tmp/scratch/RtmpDiB81M/eurostat/t2020_rk310_num_code_TF.rds
Quitting from lines 219-223 (eurostat_tutorial.Rmd) 
Error: processing vignette 'eurostat_tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘eurostat_tutorial.Rmd’

--- re-building ‘publications.Rmd’ using rmarkdown
--- finished re-building ‘publications.Rmd’

SUMMARY: processing the following file failed:
  ‘eurostat_tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [2s/3s]
  Running ‘test-parse.R’ [0s/1s]
  Running ‘test-replay.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(evaluate)
  > 
  > if (require("testthat", quietly = TRUE)) test_check("evaluate")
  ── 1. Failure: ggplot is captured (@test-graphics.r#13)  ───────────────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 4 - 3 == 1
  
  ── 2. Failure: ggplot is captured (@test-graphics.r#15)  ───────────────────────
  `x` not equal to `expected`.
  Lengths differ: 4 is not 3
  
  ── 3. Failure: ggplot2 plots in a single expression are captured (@test-graphics
  `x` not equal to `expected`.
  1/4 mismatches
  x[3]: "simpleError"
  y[3]: "recordedplot"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 50 SKIPPED: 1 FAILED: 3
  1. Failure: ggplot is captured (@test-graphics.r#13) 
  2. Failure: ggplot is captured (@test-graphics.r#15) 
  3. Failure: ggplot2 plots in a single expression are captured (@test-graphics.r#49) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘evaluator-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_event_outcomes_plot
> ### Title: Display the distribution of threat events contained vs. realized
> ###   across all domains
> ### Aliases: generate_event_outcomes_plot
> 
> ### ** Examples
> 
> data(domain_summary)
> generate_event_outcomes_plot(domain_summary)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘EValue-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sens_plot
> ### Title: Plots for sensitivity analyses
> ### Aliases: sens_plot
> ### Keywords: confounding, meta-analysis, sensitivity
> 
> ### ** Examples
> 
> # with variable bias and with confidence band
> sens_plot( type="line", q=log(1.1), Bmin=log(1), Bmax=log(4), sigB=0.1,
+            yr=log(1.3), vyr=0.005, t2=0.4, vt2=0.03 )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
powerSet : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
mposterior: no visible global function definition for ‘optim’
rl.pred: no visible global function definition for ‘matplot’
rl.pst: no visible binding for global variable ‘quantile’
rl.pst: no visible global function definition for ‘matplot’
Undefined global functions or variables:
  matplot optim quantile
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘TODO.md’
make_dyads : ff: no visible global function definition for ‘aggregate’
make_scale: no visible global function definition for ‘read.csv’
plot_dyad: no visible global function definition for ‘is’
read_eventdata : read_ed_file: no visible global function definition
  for ‘read.csv’
Undefined global functions or variables:
  aggregate is read.csv
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘evolqg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CalcR2CvCorrected
> ### Title: Corrected integration value
> ### Aliases: CalcR2CvCorrected CalcR2CvCorrected.default
> ###   CalcR2CvCorrected.lm
> ### Keywords: correlation integration
> 
> ### ** Examples
> 
> integration.dist = CalcR2CvCorrected(iris[,1:4])
> 
> #adjusted values
> integration.dist[[1]]
       r2  eVals_cv 
0.3122038 1.6792943 
> 
> #ploting models
> library(ggplot2)
> ggplot(integration.dist$dist, aes(r2, mean_cv)) + geom_point() + 
+        geom_smooth(method = 'lm', color= 'black') + theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘EvolutionaryGames-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ILogit
> ### Title: ILogit dynamic
> ### Aliases: ILogit
> 
> ### ** Examples
> 
> dynamic <- ILogit
> A <- matrix(c(-1, 0, 0, 0, -1, 0, 0, 0, -1), 3, byrow=TRUE)
> state <- matrix(c(0.1, 0.2, 0.7, 0.2, 0.7, 0.1, 0.9, 0.05, 0.05), 3, 3, byrow=TRUE)
> eta <- 0.7
> phaseDiagram3S(A, dynamic, eta, state, TRUE, FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: phaseDiagram3S ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingEvolutionaryGames.Rmd’ using rmarkdown
Quitting from lines 204-207 (UsingEvolutionaryGames.Rmd) 
Error: processing vignette 'UsingEvolutionaryGames.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘UsingEvolutionaryGames.Rmd’

SUMMARY: processing the following file failed:
  ‘UsingEvolutionaryGames.Rmd’

Error: Vignette re-building failed.
Execution halted
evolvabilityBetaMCMC : <anonymous>: no visible binding for global
  variable ‘median’
evolvabilityBetaMCMC: no visible binding for global variable ‘median’
evolvabilityBetaMCMC2: no visible binding for global variable ‘median’
evolvabilityMeans: no visible global function definition for ‘var’
evolvabilityMeansMCMC : <anonymous>: no visible global function
  definition for ‘var’
evolvabilityMeansMCMC: no visible binding for global variable ‘median’
randomBeta: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  median rnorm var
Consider adding
  importFrom("stats", "median", "rnorm", "var")
to your NAMESPACE file.
Running examples in ‘Evomorph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DistancesPlot
> ### Title: Plot the Procrustes distances between a set of shapes and a
> ###   reference
> ### Aliases: DistancesPlot
> 
> ### ** Examples
> 
> 
> data("simulated_shape_distances")
> 
> #Plot distances between a set of simulated shapes a reference.
> 
> DistancesPlot(simulated_shape_distances)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
DPOT: no visible global function definition for ‘optim’
mop.rho: no visible global function definition for ‘median’
Undefined global functions or variables:
  median optim
Consider adding
  importFrom("stats", "median", "optim")
to your NAMESPACE file.
Errors in running code in vignettes:
when running code in ‘evtree.Rnw’
  ...

> options(prompt = "R> ", continue = "+  ", width = 70, 
+     useFancyQuotes = FALSE)

> library("rpart")

> library("evtree")
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm

> library("lattice")

> data("BBBClub", package = "evtree")

> cache <- FALSE

> X1 <- rep(seq(0.25, 1.75, 0.5), each = 4)

> X2 <- rep(seq(0.25, 1.75, 0.5), 4)

> Y <- rep(1, 16)

> Y[(X1 < 1 & X2 < 1) | (X1 > 1 & X2 > 1)] <- 2

> Y <- factor(Y, labels = c("O", "X"))

> chess22 <- data.frame(Y, X1, X2)

> set.seed(1090)

> print(evtree(Y ~ ., data = chess22, minbucket = 1, 
+     minsplit = 2))

Model formula:
Y ~ X1 + X2

Fitted party:
[1] root
|   [2] X1 < 1.25
|   |   [3] X2 < 1.25: X (n = 4, err = 0.0%)
|   |   [4] X2 >= 1.25: O (n = 4, err = 0.0%)
|   [5] X1 >= 1.25
|   |   [6] X2 < 1.25: O (n = 4, err = 0.0%)
|   |   [7] X2 >= 1.25: X (n = 4, err = 0.0%)

Number of inner nodes:    3
Number of terminal nodes: 4

> par(mar = c(4, 4, 1, 1))

> plot(X2 ~ X1, data = chess22, xlim = c(0, 2), ylim = c(0, 
+     2), pch = c(1, 4)[Y], col = c("black", "slategray")[Y])

> if (cache & file.exists("BBBClub-trees.rda")) {
+     load("BBBClub-trees.rda")
+ } else {
+     data("BBBClub", package = "evtree")
+     library(" ..." ... [TRUNCATED] 

  When sourcing 'evtree.R':
Error: no string supplied for 'strwidth/height' unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘evtree.Rnw’ using Sweave
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm

Error: processing vignette 'evtree.Rnw' failed with diagnostics:
 chunk 6 (label = BBBClub-cache) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building 'evtree.Rnw'

SUMMARY: processing the following file failed:
  'evtree.Rnw'

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ewoc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ewoc_d1classic
> ### Title: Escalation With Overdose Control
> ### Aliases: ewoc_d1classic
> 
> ### ** Examples
> 
> DLT <- 0
> dose <- 20
> test <- ewoc_d1classic(DLT ~ dose, type = 'discrete',
+                       theta = 0.33, alpha = 0.25,
+                       min_dose = 0, max_dose = 100,
+                       dose_set = seq(0, 100, 20),
+                       rho_prior = matrix(1, ncol = 2, nrow = 1),
+                       mtd_prior = matrix(1, ncol = 2, nrow = 1),
+                       rounding = "nearest")
Warning in limits_d1nocov(first_dose = first_dose, last_dose = last_dose,  :
  'first_dose' and  'last_dose' were defined as the first and last elements of 'dose_set', respectively.
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 1
   Unobserved stochastic nodes: 2
   Total graph size: 27

Initializing model

> summary(test)
Conditions
  Minimum Dose Maximum Dose Theta Alpha Number of patients
1            0          100  0.33  0.25                  1

Next Dose
  Estimate        95% HPD
1       20 (10.7 ; 99.92)

P(DLT| next dose)
  Estimate       95% HPD
1     0.25 (0.01 ; 0.46)
> plot(test)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
EW : PhiP : Phi: no visible global function definition for ‘pnorm’
EWplot: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot pnorm
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
BinomialCIone: no visible global function definition for ‘na.omit’
PairedCIone: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
build.mcx.obj: no visible global function definition for ‘glm’
build.mcx.obj: no visible binding for global variable ‘poisson’
build.mcx.obj: no visible global function definition for ‘fitted’
cab: no visible global function definition for ‘rbinom’
cab: no visible global function definition for ‘runif’
mcexact: no visible global function definition for ‘update’
rounded.tprob: no visible global function definition for ‘pt’
simtable.cab: no visible global function definition for ‘rbinom’
simtable.cab: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fitted glm poisson pt rbinom runif update
Consider adding
  importFrom("stats", "fitted", "glm", "poisson", "pt", "rbinom",
             "runif", "update")
to your NAMESPACE file.
Found the following assignments to the global environment:
File ‘exams/R/xexams.R’:
  assign(".xweave_svg_grdevice", .xweave_svg_grdevice, envir = .GlobalEnv)
plot.pgrid: no visible global function definition for ‘image’
statistic.cv: no visible global function definition for ‘quantile’
statistic.sim: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines image quantile
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "image")
  importFrom("stats", "quantile")
to your NAMESPACE file.
countBamInGRanges.exomeDepth: no visible global function definition for
  ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘ExPanDaR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: prepare_by_group_bar_graph
> ### Title: Prepares a by Group Bar Graph
> ### Aliases: prepare_by_group_bar_graph
> 
> ### ** Examples
> 
> data(russell_3000)
> graph <- prepare_by_group_bar_graph(russell_3000, "sector", "ni_sales", median)
> graph$plot
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ExPanDaR-functions.Rmd’ using rmarkdown
Quitting from lines 77-78 (ExPanDaR-functions.Rmd) 
Error: processing vignette 'ExPanDaR-functions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ExPanDaR-functions.Rmd’

--- re-building ‘use_ExPanD.Rmd’ using rmarkdown
--- finished re-building ‘use_ExPanD.Rmd’

SUMMARY: processing the following file failed:
  ‘ExPanDaR-functions.Rmd’

Error: Vignette re-building failed.
Execution halted
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of ‘dig’ to ‘digits’
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of ‘env’ to ‘envir’
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of ‘env’ to ‘envir’
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of ‘dig’ to ‘digits’
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of ‘env’ to ‘envir’
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of ‘env’ to ‘envir’
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  ‘wid’ to ‘width’
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in ‘exploreR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: massregplot
> ### Title: Mass Regression Plot
> ### Aliases: massregplot
> 
> ### ** Examples
> 
> exam.df <- iris
> massregplot(exam.df, "Sepal.Length", ignore = "Species")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: massregplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘exploreR.Rmd’ using rmarkdown
Quitting from lines 69-71 (exploreR.Rmd) 
Error: processing vignette 'exploreR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘exploreR.Rmd’

SUMMARY: processing the following file failed:
  ‘exploreR.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘export-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: graph2bitmap
> ### Title: Save currently active R graph to bitmap format
> ### Aliases: graph2bitmap graph2png graph2tif graph2jpg graph2png graph2tif
> ###   graph2jpg
> 
> ### ** Examples
> 
> # Create a file name
> filen <- tempfile(pattern = "ggplot") # or 
> # filen <- paste("YOUR_DIR/ggplot")
> 
> # Generate graphical output
> library(ggplot2)
> library(datasets)
> x=qplot(Sepal.Length, Petal.Length, data = iris, 
+         color = Species, size = Petal.Width, alpha = I(0.7))
> plot.fun <- function(){
+   print(qplot(Sepal.Length, Petal.Length, data = iris, 
+               color = Species, size = Petal.Width, alpha = 0.7))
+ }
> 
> # There are 3 ways to use graph2bitmap():
> ### 1. Pass the plot as an object
> graph2png(x=x, file=filen, dpi=400, height = 5, aspectr=4)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: graph2png ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘labels-support.Rmd’ using rmarkdown
Quitting from lines 111-119 (labels-support.Rmd) 
Error: processing vignette 'labels-support.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘labels-support.Rmd’

--- re-building ‘tables-with-labels.Rmd’ using rmarkdown
Quitting from lines 79-138 (tables-with-labels.Rmd) 
Error: processing vignette 'tables-with-labels.Rmd' failed with diagnostics:
<text>:1:12: unexpected symbol
1: Miles/(US) gallon
               ^
--- failed re-building ‘tables-with-labels.Rmd’

--- re-building ‘xlsx-export.Rmd’ using rmarkdown
--- finished re-building ‘xlsx-export.Rmd’

SUMMARY: processing the following files failed:
  ‘labels-support.Rmd’ ‘tables-with-labels.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘exreport-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCumulativeRank
> ### Title: Area plot for the rank distribution from a multiple test
> ### Aliases: plotCumulativeRank
> 
> ### ** Examples
> 
> # First we create an experiment from the wekaExperiment problem and prepare
> # it to apply the test:
> experiment <- expCreate(wekaExperiment, name="test", parameter="fold")
> experiment <- expReduce(experiment, "fold", mean)
> experiment <- expSubset(experiment, list(featureSelection = "no"))
> experiment <- expInstantiate(experiment, removeUnary=TRUE)
> 
> # Then we perform a Friedman test included ina a testMultipleControl
> # test procedure
> test <- testMultipleControl(experiment, "accuracy")
> 
> # Finally we obtain the plot
> plotCumulativeRank(test)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
index.citations: no visible global function definition for
  ‘txtProgressBar’
read.exsic: no visible global function definition for ‘read.csv’
update.pb: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  read.csv setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package in Depends field not imported from: ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
extfunnel: no visible global function definition for ‘qnorm’
extfunnel: no visible global function definition for ‘meta.summaries’
extfunnel: no visible global function definition for ‘flush.console’
extfunnel: no visible global function definition for ‘qt’
extfunnel: no visible global function definition for ‘dev.new’
extfunnel: no visible global function definition for ‘par’
extfunnel: no visible global function definition for ‘plot’
extfunnel: no visible global function definition for ‘polygon’
extfunnel: no visible global function definition for ‘segments’
extfunnel: no visible global function definition for ‘abline’
extfunnel: no visible global function definition for ‘axis’
extfunnel: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par plot polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "plot",
             "polygon", "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
bars: no visible global function definition for ‘segments’
cv.binomial: no visible binding for global variable ‘var’
cv.binomial: no visible global function definition for ‘abline’
cv.normal: no visible binding for global variable ‘var’
cv.normal: no visible global function definition for ‘abline’
cv.poisson: no visible binding for global variable ‘var’
cv.poisson: no visible global function definition for ‘abline’
plot.extlasso: no visible global function definition for ‘matplot’
plot.extlasso: no visible global function definition for ‘axis’
Undefined global functions or variables:
  abline axis matplot segments var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments")
  importFrom("stats", "var")
to your NAMESPACE file.
exbio: no visible global function definition for ‘as.formula’
exbio: no visible global function definition for ‘glm’
exbio: no visible binding for global variable ‘gaussian’
exbio: no visible global function definition for ‘Gamma’
exbio: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  Gamma as.formula gaussian glm pchisq
Consider adding
  importFrom("stats", "Gamma", "as.formula", "gaussian", "glm", "pchisq")
to your NAMESPACE file.
font_install: no visible global function definition for
  ‘installed.packages’
font_install: no visible global function definition for
  ‘install.packages’
fonttable_add: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  install.packages installed.packages write.csv
Consider adding
  importFrom("utils", "install.packages", "installed.packages",
             "write.csv")
to your NAMESPACE file.
toJavaMatrix2D: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
bootstrapCMLE: no visible global function definition for ‘qweibull’
bootstrapCMLE: no visible binding for global variable ‘sd’
bootstrapCMLE: no visible global function definition for ‘quantile’
bootstrapCenWbMix: no visible binding for global variable ‘sd’
bootstrapCenWbMix: no visible global function definition for ‘quantile’
cenWeibullMLE: no visible global function definition for ‘sd’
expmx.p2.censor: no visible global function definition for ‘dweibull’
expmx.p2.censor: no visible global function definition for ‘pweibull’
genWbMixIni: no visible global function definition for ‘runif’
log.llh.p2.censor: no visible global function definition for ‘dweibull’
log.llh.p2.censor: no visible global function definition for ‘pweibull’
quanWbMix : t.fun: no visible global function definition for ‘pweibull’
quanWbMix: no visible global function definition for ‘uniroot’
quanWbMix.int : t.fun: no visible global function definition for
  ‘pweibull’
quanWbMix.int: no visible global function definition for ‘uniroot’
simWbMix: no visible global function definition for ‘rbinom’
simWbMix: no visible global function definition for ‘rweibull’
Undefined global functions or variables:
  dweibull pweibull quantile qweibull rbinom runif rweibull sd uniroot
Consider adding
  importFrom("stats", "dweibull", "pweibull", "quantile", "qweibull",
             "rbinom", "runif", "rweibull", "sd", "uniroot")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
Loading required package: eyelinker
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 110-113 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘basics.Rmd’

SUMMARY: processing the following file failed:
  ‘basics.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ezplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bar_plot
> ### Title: bar_plot
> ### Aliases: bar_plot
> 
> ### ** Examples
> 
> df = ez_data()
> bar_plot(df, "year", "units")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ez-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ezCor
> ### Title: Compute and plot an information-dense correlation matrix
> ### Aliases: ezCor
> 
> ### ** Examples
> 
> ########
> # Set up some fake data
> ########
> library(MASS)
> N=100
> 
> #first pair of variables
> variance1=1
> variance2=2
> mean1=10
> mean2=20
> rho = .8
> Sigma=matrix(
+     c(
+         variance1
+         , sqrt(variance1*variance2)*rho
+         , sqrt(variance1*variance2)*rho
+         , variance2
+     )
+     , 2
+     , 2
+ )
> pair1=mvrnorm(N,c(mean1,mean2),Sigma,empirical=TRUE)
> 
> #second pair of variables
> variance1=10
> variance2=20
> mean1=100
> mean2=200
> rho = -.4
> Sigma=matrix(
+     c(
+         variance1
+         , sqrt(variance1*variance2)*rho
+         , sqrt(variance1*variance2)*rho
+         , variance2
+     )
+     , 2
+     , 2
+ )
> pair2=mvrnorm(N,c(mean1,mean2),Sigma,empirical=TRUE)
> 
> my_data=data.frame(cbind(pair1,pair2))
> 
> ########
> # Now plot
> ########
> p = ezCor(
+     data = my_data
+ )
> print(p)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
createFormula: no visible global function definition for ‘tail’
createFormula: no visible global function definition for ‘head’
createFormula: no visible global function definition for ‘as.formula’
ezsim: no visible global function definition for ‘runif’
plot.ezsim: no visible global function definition for ‘quantile’
plot.ezsim: no visible global function definition for ‘head’
plot.ezsim: no visible global function definition for ‘tail’
plot.ezsim: no visible global function definition for ‘plot’
plot.ezsim: no visible binding for global variable ‘dnorm’
plot.ezsim: no visible binding for global variable ‘pdf’
plot.ezsim: no visible global function definition for ‘dev.off’
plot.ezsim : <anonymous>: no visible global function definition for
  ‘dev.new’
plot.summary.ezsim: no visible global function definition for ‘head’
plot.summary.ezsim: no visible global function definition for ‘tail’
plot.summary.ezsim: no visible binding for global variable ‘pdf’
plot.summary.ezsim: no visible global function definition for ‘dev.off’
plot.summary.ezsim : <anonymous>: no visible global function definition
  for ‘dev.new’
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf plot quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rnw’ using Sweave
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.

Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 4 
Error in Summary.unit(structure(c(4.4, 4.4), unit = 8L, class = c("margin",  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
gibbs2: no visible global function definition for ‘rnorm’
gibbs_sampling: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
fma: no visible global function definition for ‘factanal’
fma: no visible global function definition for ‘runif’
fma: no visible global function definition for ‘kmeans’
fma: no visible global function definition for ‘var’
fma.em.alg: no visible global function definition for ‘var’
misc : q: no visible global function definition for ‘name’
Undefined global functions or variables:
  factanal kmeans name runif var
Consider adding
  importFrom("stats", "factanal", "kmeans", "runif", "var")
to your NAMESPACE file.
Running examples in ‘FactoClass-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.dudi
> ### Title: Factorial Planes from Objects of Class dudi
> ### Aliases: plot.dudi sutil.grid
> ### Keywords: multivariate hplot
> 
> ### ** Examples
> 
> data(Bogota)
> ca <- dudi.coa(Bogota[,2:7],scannf=FALSE,nf=4)
> # with ggplot2 and ggrepel
> plot(ca,gg=TRUE)
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘factoextra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dist
> ### Title: Enhanced Distance Matrix Computation and Visualization
> ### Aliases: dist get_dist fviz_dist
> 
> ### ** Examples
> 
> data(USArrests)
> res.dist <- get_dist(USArrests, stand = TRUE, method = "pearson")
> 
> fviz_dist(res.dist, 
+    gradient = list(low = "#00AFBB", mid = "white", high = "#FC4E07"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘brca.Rmd’ using rmarkdown
Welcome to factorMerger 0.3.6!

Loading required package: forcats
Quitting from lines 51-56 (brca.Rmd) 
Error: processing vignette 'brca.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘brca.Rmd’

--- re-building ‘factorMerger.Rmd’ using rmarkdown
Welcome to factorMerger 0.3.6!


Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 125-126 (factorMerger.Rmd) 
Error: processing vignette 'factorMerger.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘factorMerger.Rmd’

--- re-building ‘pisa2012.Rmd’ using rmarkdown
Welcome to factorMerger 0.3.6!


Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 35-37 (pisa2012.Rmd) 
Error: processing vignette 'pisa2012.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pisa2012.Rmd’

SUMMARY: processing the following files failed:
  ‘brca.Rmd’ ‘factorMerger.Rmd’ ‘pisa2012.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createFactualConnection: no visible global function definition for
  ‘new’
factualGetSchema: no visible global function definition for ‘fromJSON’
factualRead: no visible global function definition for ‘curlEscape’
factualRead: no visible global function definition for ‘fromJSON’
processFactualReadJSON: no visible global function definition for ‘new’
processFactualSchemaJSON: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  curlEscape fromJSON new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
faisalconjoint: no visible global function definition for ‘barplot’
faisalconjoint: no visible global function definition for ‘text’
faisalconjoint: no visible global function definition for ‘jpeg’
faisalconjoint: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  barplot dev.off jpeg text
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "barplot", "text")
to your NAMESPACE file.
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in '?.onAttach'.
coef.FAMILY: no visible global function definition for ‘glm’
coef.FAMILY: no visible global function definition for ‘lm’
fm2v: no visible global function definition for ‘na.omit’
l_inf_prox: no visible global function definition for ‘tail’
predict.FAMILY: no visible global function definition for ‘coef’
predict.FAMILY: no visible global function definition for ‘lm’
predict.FAMILY: no visible global function definition for ‘predict’
predict.FAMILY: no visible global function definition for ‘glm’
predict.FAMILY: no visible global function definition for ‘predict.glm’
v2fm: no visible global function definition for ‘tail’
Undefined global functions or variables:
  coef glm lm na.omit predict predict.glm tail
Consider adding
  importFrom("stats", "coef", "glm", "lm", "na.omit", "predict",
             "predict.glm")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘impute’ ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
S3 methods shown with full name in documentation object 'plot.fANCOVA':
  ‘plot.fANCOVA’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘tsbugs’
Aggregation : foo: no visible global function definition for
  ‘weighted.mean’
Aggregation: no visible global function definition for ‘txtProgressBar’
Aggregation: no visible global function definition for
  ‘setTxtProgressBar’
constructSYB: no visible global function definition for ‘str’
fillCountryCode: no visible global function definition for ‘na.omit’
getFAO: no visible global function definition for ‘read.csv’
getWDImetaData: no visible global function definition for ‘write.csv’
getWDItoSYB: no visible global function definition for ‘na.omit’
lsgr: no visible global function definition for ‘na.omit’
lsgr: no visible global function definition for ‘coef’
lsgr: no visible global function definition for ‘lm’
Undefined global functions or variables:
  coef lm na.omit read.csv setTxtProgressBar str txtProgressBar
  weighted.mean write.csv
Consider adding
  importFrom("stats", "coef", "lm", "na.omit", "weighted.mean")
  importFrom("utils", "read.csv", "setTxtProgressBar", "str",
             "txtProgressBar", "write.csv")
to your NAMESPACE file.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
basis_hica: no visible global function definition for ‘princomp’
energy_hica: no visible global function definition for ‘dev.new’
energy_hica: no visible global function definition for ‘points’
energy_hica: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dev.new legend points princomp
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "princomp")
to your NAMESPACE file.
Package suggested but not available for checking: ‘coxKM’
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘fastqcr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qc_plot
> ### Title: Plot FastQC Results
> ### Aliases: qc_plot print.qctable
> 
> ### ** Examples
> 
> # Demo file
> qc.file <- system.file("fastqc_results", "S1_fastqc.zip",  package = "fastqcr")
> qc.file
[1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/fastqcr/fastqc_results/S1_fastqc.zip"
> # Read all modules
> qc <- qc_read(qc.file)
Reading: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/fastqcr/fastqc_results/S1_fastqc.zip
> 
> # Plot per sequence GC content
> qc_plot(qc, "Per sequence GC content")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘fastR2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ACTgpa
> ### Title: ACT scores and GPA
> ### Aliases: ACTgpa
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> gf_point(GPA ~ ACT, data = ACTgpa)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
FBN.histogramMaxima: no visible global function definition for ‘hist’
FBN.kmeans: no visible global function definition for ‘median’
FBN.kmeans: no visible global function definition for ‘kmeans’
FBNormalization: no visible global function definition for ‘read.table’
FBNormalization: no visible global function definition for ‘median’
FBNormalization: no visible global function definition for ‘hist’
FBNormalization: no visible global function definition for ‘par’
FBNormalization: no visible global function definition for ‘dev.print’
FBNormalization: no visible binding for global variable ‘bmp’
FBNormalization: no visible global function definition for ‘sd’
FBNormalization: no visible global function definition for
  ‘write.table’
medianFilter: no visible global function definition for ‘median’
Undefined global functions or variables:
  bmp dev.print hist kmeans median par read.table sd write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.print")
  importFrom("graphics", "hist", "par")
  importFrom("stats", "kmeans", "median", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RCurl’ ‘RJSONIO’ ‘XML’ ‘glmnet’ ‘httr’ ‘speedglm’ ‘tcltk’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘fbroc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: boot.paired.roc
> ### Title: Bootstrap paired ROC curves
> ### Aliases: boot.paired.roc
> 
> ### ** Examples
> 
> data(roc.examples)
> # Do not use cache
> example <- boot.paired.roc(roc.examples$Cont.Pred, roc.examples$Cont.Pred.Outlier,
+                           roc.examples$True.Class, n.boot = 500)
> perf(example, "auc") # estimate difference in auc


                Bootstrapped ROC performance metric

Metric: AUC
Bootstrap replicates: 500

Classifier 1: 
Observed:0.929
Std. Error: 0.019
95% confidence interval:
0.89 0.962

Classifier 2: 
Observed:0.895
Std. Error: 0.028
95% confidence interval:
0.833 0.943

Delta: 
Observed:0.034
Std. Error: 0.021
95% confidence interval:
0 0.081

Correlation: 0.67

> perf(example, "tpr", fpr = 0.5) # estimate difference in TPR at a FPR of 50%


                Bootstrapped ROC performance metric

Metric: TPR at a fixed FPR of 0.5
Bootstrap replicates: 500

Classifier 1: 
Observed:0.988
Std. Error: 0.011
95% confidence interval:
0.962 1

Classifier 2: 
Observed:0.988
Std. Error: 0.012
95% confidence interval:
0.962 1

Delta: 
Observed:0
Std. Error: 0.006
95% confidence interval:
0 0.025

Correlation: 0.86

> plot(example) # show plot
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘glmnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fcd.cluster: no visible global function definition for ‘kmeans’
fcd.start: no visible global function definition for ‘ginv’
fcd.start: no visible global function definition for ‘glmnet’
gen.dcbm: no visible global function definition for ‘rbinom’
gen.sbm: no visible global function definition for ‘rbinom’
mis.cluster: no visible global function definition for ‘permn’
spectral.clustering: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  ginv glmnet kmeans permn rbinom
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
PTSingleAssetBarrierOption2: no visible global function definition for
  ‘new’
newton: no visible global function definition for ‘plot’
newton: no visible global function definition for ‘abline’
probInRange: no visible global function definition for ‘pnorm’
shortfall_risk: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline new plot pnorm
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignettes.Rmd’ using rmarkdown
Quitting from lines 178-185 (vignettes.Rmd) 
Error: processing vignette 'vignettes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignettes.Rmd’

SUMMARY: processing the following file failed:
  ‘vignettes.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘fdANOVA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.fanovatests
> ### Title: Plot P-values of Tests Based on Random Projections for FANOVA
> ###   Problem
> ### Aliases: plot.fanovatests
> ### Keywords: Plot
> 
> ### ** Examples
> 
> # Some of the examples may run some time.
> 
> # gait data (the first feature)
> library(fda)
Loading required package: splines
Loading required package: Matrix

Attaching package: ‘fda’

The following object is masked from ‘package:graphics’:

    matplot

> gait.data.frame <- as.data.frame(gait)
> x.gait <- as.matrix(gait.data.frame[, 1:39])
> 
> # vector of group labels
> group.label.gait <- rep(1:3, each = 13)
> ## Don't show: 
> fanova4 <- fanova.tests(x.gait, group.label.gait, test = "TRP",
+                         params = list(paramTRP = list(k = c(1, 3), B.TRP = 3)))
> fanova5 <- fanova.tests(x.gait, group.label.gait, test = "TRP",
+                         params = list(paramTRP = list(k = c(1, 3),
+                                                       permutation = TRUE, B.TRP = 3)))
> plot(x = fanova4)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following significant warnings:
  gropt/src/SmartSpace.cpp:142:24: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fdasrvf.Rcheck/00install.out’ for details.
asymp.vcov: no visible global function definition for ‘cov’
corFDG: no visible global function definition for ‘cor’
g.exponential: no visible global function definition for ‘integrate’
rho.exponential: no visible global function definition for ‘integrate’
rho.sinus: no visible global function definition for ‘integrate’
tau.exponential: no visible global function definition for ‘integrate’
tau.sinus: no visible global function definition for ‘integrate’
tfun.sinus.rho: no visible global function definition for ‘integrate’
wlsdc: no visible global function definition for ‘optim’
Undefined global functions or variables:
  cor cov integrate optim
Consider adding
  importFrom("stats", "cor", "cov", "integrate", "optim")
to your NAMESPACE file.
FDRreg: no visible global function definition for ‘dnorm’
colnormalize: no visible global function definition for ‘sd’
efron: no visible global function definition for ‘median’
efron: no visible global function definition for ‘hist’
efron: no visible global function definition for ‘glm’
efron: no visible binding for global variable ‘poisson’
efron: no visible global function definition for ‘qchisq’
efron: no visible global function definition for ‘predict’
efron: no visible global function definition for ‘quantile’
efron: no visible global function definition for ‘lm’
efron: no visible global function definition for ‘coef’
make.bspline.matrix: no visible global function definition for
  ‘quantile’
plotFDR: no visible global function definition for ‘hist’
plotFDR: no visible global function definition for ‘par’
plotFDR: no visible global function definition for ‘plot’
plotFDR: no visible global function definition for ‘axis’
plotFDR: no visible global function definition for ‘lines’
plotFDR: no visible global function definition for ‘legend’
plotFDR: no visible global function definition for ‘rug’
plotFDR: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par plot poisson
  predict qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par",
             "plot", "rug", "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
Running examples in ‘fergm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coef_plot
> ### Title: Plots the coefficients of FERGM and ERGM objects.
> ### Aliases: coef_plot
> ### Keywords: FERGM interpret summary
> 
> ### ** Examples
> 
> # load example data
> data("ergm.fit")
> data("fergm.fit")
> data("mesa")
> # Compare substantive implications via coef plot, these are with 95% credible intervals
> coef_plot(fergm.fit = fergm.fit, ergm.fit = ergm.fit,
+ custom_var_names =  c("Edges", "Sex Homophily", "Grade Homophily",
+ "Race Homophily", "GWESP", "Alternating K-Stars"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘fermicatsR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fermicatsR
> ### Title: fermicatsR (v 1.4): A package containing catalogs from the Fermi
> ###   Large Area Telescope.
> ### Aliases: fermicatsR fermicatsR-package
> 
> ### ** Examples
> 
> # Variability index vs Curvature significance of 2FGL sources, color-coded by source class
> data(FGL2)
> if (require("ggplot2")) {
+ qplot(log(Signif_Curve), log(Variability_Index), data = FGL2, color = CLASS1)
+ }
Loading required package: ggplot2
Warning in log(Variability_Index) : NaNs produced
Warning in log(Variability_Index) : NaNs produced
Warning: Removed 2 rows containing missing values (geom_point).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘gridExtra’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FFieldPtRepDemo: no visible global function definition for ‘ggplot’
FFieldPtRepDemo: no visible binding for global variable ‘mtcars’
FFieldPtRepDemo: no visible global function definition for ‘aes’
FFieldPtRepDemo: no visible binding for global variable ‘mpg’
FFieldPtRepDemo: no visible global function definition for ‘geom_point’
FFieldPtRepDemo: no visible global function definition for ‘geom_text’
FFieldPtRepDemo: no visible global function definition for ‘ggtitle’
FFieldPtRepDemo: no visible global function definition for
  ‘geom_segment’
FFieldPtRepDemo: no visible global function definition for
  ‘grid.arrange’
Undefined global functions or variables:
  aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg
  mtcars
Consider adding
  importFrom("datasets", "mtcars")
to your NAMESPACE file.
Running examples in ‘FField-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FField-package
> ### Title: Force field simulation for a set of points
> ### Aliases: FField FField-package
> ### Keywords: package
> 
> ### ** Examples
> 
> # Repel points
> coords <-
+   FFieldPtRep(coords = cbind(mtcars$wt * 100 / max(mtcars$wt), 
+                              mtcars$mpg * 100 / max(mtcars$mpg)),
+               rep.fact = 40)
> head(mtcars)
                   mpg cyl disp  hp drat    wt  qsec vs am gear carb
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1
> head(coords)
         x        y
1 45.11259 58.47014
2 54.19136 61.20140
3 40.34714 69.42976
4 62.48920 65.94822
5 59.81417 56.33633
6 66.54832 53.33343
>   
> # Demo
> FFieldPtRepDemo()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: FFieldPtRepDemo ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
ftest: no visible global function definition for ‘wilcox.test’
ftest: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  t.test wilcox.test
Consider adding
  importFrom("stats", "t.test", "wilcox.test")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘mvtnorm’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dmymvnorm: no visible global function definition for ‘dmvnorm’
dmymvt: no visible global function definition for ‘dmvt’
gof.test: no visible global function definition for ‘quantile’
gof.test : ecdf: no visible global function definition for ‘mecdf’
gof.test: no visible global function definition for ‘jacobian’
gof.test: no visible global function definition for ‘var’
gradCdfT: no visible global function definition for ‘dt’
gradCdfT: no visible global function definition for ‘pt’
gradCdfT: no visible global function definition for ‘pmvt’
influFun: no visible global function definition for ‘jacobian’
mult.sim: no visible global function definition for ‘rnorm’
plackettFormula: no visible global function definition for ‘pt’
plackettFormula: no visible global function definition for ‘pmvt’
pmymvnorm: no visible global function definition for ‘GenzBretz’
pmymvnorm: no visible global function definition for ‘TVPACK’
pmymvnorm : <anonymous>: no visible global function definition for
  ‘pmvnorm’
pmymvt: no visible global function definition for ‘GenzBretz’
pmymvt: no visible global function definition for ‘TVPACK’
pmymvt : <anonymous>: no visible global function definition for ‘pmvt’
rmymvnorm: no visible global function definition for ‘rmvnorm’
rmymvt: no visible global function definition for ‘rmvt’
Undefined global functions or variables:
  GenzBretz TVPACK dmvnorm dmvt dt jacobian mecdf pmvnorm pmvt pt
  quantile rmvnorm rmvt rnorm var
Consider adding
  importFrom("stats", "dt", "pt", "quantile", "rnorm", "var")
to your NAMESPACE file.
fgeasy: no visible global function definition for ‘dist’
fgeasy : cor.est: no visible global function definition for ‘cor.test’
fgeasy: no visible binding for global variable ‘var’
fgperm : runrand: no visible global function definition for ‘runif’
fgperm : runrand: no visible global function definition for ‘ave’
fgploc : runrand: no visible global function definition for ‘runif’
fgploc : runrand: no visible global function definition for ‘ave’
fyshuffle: no visible global function definition for ‘runif’
plot.fg: no visible global function definition for ‘par’
plot.fg: no visible global function definition for ‘plot’
plot.fg: no visible global function definition for ‘segments’
plot.fg: no visible binding for global variable ‘quantile’
plot.fg: no visible global function definition for ‘abline’
plot.fg: no visible global function definition for ‘axis’
summary.fg: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  abline ave axis cor.test dist par plot quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
Running examples in ‘fieldRS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rankPlots
> ### Title: rankPlots
> ### Aliases: rankPlots
> 
> ### ** Examples
> 
> {
+ 
+ require(raster)
+ require(RStoolbox)
+ require(ggplot2)
+ 
+ # read raster data
+ r <- brick(system.file("extdata", "ndvi.tif", package="fieldRS"))
+ 
+ # read road information
+ data(roads)
+ 
+ # unsupervised classification with kmeans
+ uc <- unsuperClass(r, nSamples=5000, nClasses=5)$map
+ 
+ # derive potential sampling plots
+ pp <- derivePlots(uc, 1000)
+ 
+ # plot ranking
+ pp@data <- rankPlots(uc, pp, roads)
+ 
+ # plot output
+ gp <- fortify(pp, region="ranking")
+ ggplot(gp, aes(x=long, y=lat, group=group, fill=as.numeric(gp$id))) + 
+ geom_polygon() + scale_fill_continuous(name="Ranking")
+ 
+ }
Loading required package: raster
Loading required package: sp
Loading required package: RStoolbox
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fieldRS.Rmd’ using rmarkdown
Loading required package: sp
Quitting from lines 124-129 (fieldRS.Rmd) 
Error: processing vignette 'fieldRS.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘fieldRS.Rmd’

SUMMARY: processing the following file failed:
  ‘fieldRS.Rmd’

Error: Vignette re-building failed.
Execution halted
fieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘filehash’ ‘DBI’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createSQLite: no visible global function definition for ‘dbDriver’
createSQLite: no visible global function definition for ‘dbConnect’
createSQLite: no visible global function definition for
  ‘dbUnloadDriver’
createSQLite: no visible global function definition for ‘dbGetQuery’
initializeSQLite: no visible global function definition for ‘dbDriver’
initializeSQLite: no visible global function definition for ‘dbConnect’
initializeSQLite: no visible global function definition for ‘new’
dbDelete,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbDisconnect,filehashSQLite: no visible global function definition for
  ‘dbUnloadDriver’
dbFetch,filehashSQLite-character: no visible global function definition
  for ‘dbGetQuery’
dbInsert,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbList,filehashSQLite: no visible global function definition for
  ‘dbGetQuery’
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘fingerPro-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fingerPro-package
> ### Title: Sediment Source Fingerprinting
> ### Aliases: fingerPro-package fingerPro
> ### Keywords: Sediment source fingerprinting package
> 
> ### ** Examples
> 
> #Created on 22/08/2018
> 
> #If you want to use your own data
> #setwd("the directory that contains your dataset")
> #data <- read.table('your dataset', header = T, sep = '\t')
> #install.packages("fingerPro")
> #library(fingerPro)
> #Example of the data included in the fingerPro package
> #Load the dataset called "catchment" 
> 
> # "Catchment": this dataset has been selected from a Mediterranean catchment for 
> #this purpose and contains high-quality radionuclides and geochemistry data.
> #AG (cropland)
> #PI and PI1 (Pine forest, at first looks different but when you display de LDA plot 
> #you will see that the wisher decision in join both pines as the same source)
> #SS (subsoil)
> data <- catchment
> #boxPlot(data, columns = 1:6, ncol = 3)
> #correlationPlot(data, columns = 1:5, mixtures = TRUE)
> LDAPlot(data, P3D=FALSE)
Warning in lda.default(x, grouping, ...) : variables are collinear
Too few points to calculate an ellipse
Too few points to calculate an ellipse
Warning: Removed 1 rows containing missing values (geom_path).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: LDAPlot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘fingertipscharts-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare_areas
> ### Title: Plot compare areas chart
> ### Aliases: compare_areas
> 
> ### ** Examples
> 
> library(fingertipsR)
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> region <- "South East region"
> top_names <- c("England", region)
> ordered_levels <- c("Better",
+                     "Similar",
+                     "Worse",
+                     "Not compared")
> df <- fingertips_data(90316) %>%
+         filter(is.na(CategoryType) &
+                        Timeperiod == "2016/17" &
+                        (AreaName %in% top_names |
+                                 ParentName == region) &
+                        Sex == "Persons") %>%
+         mutate(ComparedtoEnglandvalueorpercentiles =
+                        factor(ComparedtoEnglandvalueorpercentiles,
+                               levels = ordered_levels))
> p <- compare_areas(df, AreaName, Value,
+                    fill = ComparedtoEnglandvalueorpercentiles,
+                    lowerci = LowerCI95.0limit,
+                    upperci = UpperCI95.0limit,
+                    order = "desc",
+                    top_areas = top_names,
+                    title = unique(df$IndicatorName))
> p
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_charts.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 47-56 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quick_charts.Rmd’

SUMMARY: processing the following file failed:
  ‘quick_charts.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lifeExpectancy.Rmd’ using rmarkdown
Quitting from lines 140-156 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lifeExpectancy.Rmd’

--- re-building ‘selectIndicatorsRedRed.Rmd’ using rmarkdown
Quitting from lines 49-62 (selectIndicatorsRedRed.Rmd) 
Error: processing vignette 'selectIndicatorsRedRed.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘selectIndicatorsRedRed.Rmd’

SUMMARY: processing the following files failed:
  ‘lifeExpectancy.Rmd’ ‘selectIndicatorsRedRed.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘firebehavioR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fireChart
> ### Title: Fire Characteristics Chart
> ### Aliases: fireChart
> 
> ### ** Examples
> 
> fc = fireChart('fire',hpua = 15000, ros = 50)
> print(fc)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘firebehavioR.Rmd’ using rmarkdown
Quitting from lines 97-103 (firebehavioR.Rmd) 
Error: processing vignette 'firebehavioR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘firebehavioR.Rmd’

SUMMARY: processing the following file failed:
  ‘firebehavioR.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘tkrplot’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
lsmacof: no visible global function definition for ‘cmdscale’
plotInc: no visible global function definition for ‘rainbow’
plotInc: no visible global function definition for ‘plot’
prepareCalib: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmdscale lm plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "plot")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
fishmove : coefs: no visible global function definition for ‘coef’
fishmove : coefs: no visible global function definition for ‘pf’
fishmove: no visible global function definition for ‘lm’
fishmove: no visible global function definition for ‘predict.lm’
fishmove.estimate: no visible global function definition for ‘quantile’
fishmove.estimate : ddoublenorm: no visible global function definition
  for ‘dnorm’
fishmove.query: no visible global function definition for ‘hasArg’
fishmove.query : f: no visible global function definition for ‘pnorm’
fishmove.query: no visible global function definition for ‘uniroot’
pdk: no visible global function definition for ‘hasArg’
pdk : eq: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  coef dnorm hasArg lm pf pnorm predict.lm quantile uniroot
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "coef", "dnorm", "lm", "pf", "pnorm", "predict.lm",
             "quantile", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘fishmove-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fishmove-package
> ### Title: Prediction of Fish Movement Parameters based on Multiple
> ###   Regression
> ### Aliases: fishmove-package
> ### Keywords: package
> 
> ### ** Examples
> 
> 	# Prediction for a selected fish species with time=365 days
> 	trout <- fishmove(species="Salmo trutta fario",T=365)
> 
> 	# Plot of a leptokurtic dispersal kernel 
> 	# (density plot for fitted mean, lower and upper limit)
> 	pdk(trout)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Non-standard file/directory found at top level:
  ‘NAMESPACE.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘RGtk2’ ‘cairoDevice’ ‘gWidgets’ ‘gWidgetsRGtk2’ ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘FitAR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
FitARMA: no visible global function definition for ‘PacfDL’
FitARMA: no visible global function definition for ‘GetARMeanMLE’
FitARMA: no visible global function definition for
  ‘BackcastResidualsAR’
FitARMA: no visible global function definition for ‘LjungBoxTest’
GetFitARMA: no visible global function definition for ‘LoglikelihoodAR’
GetFitARMA: no visible global function definition for ‘ChampernowneD’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘PacfToAR’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘PacfDL’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘FastLoglikelihoodAR’
GetFitARMA: no visible global function definition for ‘PacfToAR’
InformationMatrixARMA: no visible global function definition for
  ‘InvertibleQ’
TacvfARMA: no visible global function definition for ‘InvertibleQ’
Undefined global functions or variables:
  BackcastResidualsAR ChampernowneD FastLoglikelihoodAR GetARMeanMLE
  InvertibleQ LjungBoxTest LoglikelihoodAR PacfDL PacfToAR
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘leaps’ ‘ltsa’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘bestglm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘ExtDist’
'library' or 'require' calls in package code:
  ‘devEMF’ ‘doMC’ ‘foreach’ ‘grDevices’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘fitur-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_density
> ### Title: Density Comparison Plot
> ### Aliases: plot_density
> 
> ### ** Examples
> 
> library(ggplot2)
> set.seed(37)
> x <- rgamma(10000, 5)
> dists <- c('gamma', 'lnorm', 'weibull')
> fits <- lapply(dists, fit_univariate, x = x)
> plot_density(x, fits, 30) +
+ theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diagnostic_plots.Rmd’ using rmarkdown
Quitting from lines 35-43 (diagnostic_plots.Rmd) 
Error: processing vignette 'diagnostic_plots.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘diagnostic_plots.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘univariate_distributions.Rmd’ using rmarkdown
--- finished re-building ‘univariate_distributions.Rmd’

SUMMARY: processing the following file failed:
  ‘diagnostic_plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bechdel.Rmd’ using rmarkdown
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Attaching package: 'magrittr'

The following object is masked from 'package:purrr':

    set_names

The following object is masked from 'package:tidyr':

    extract


Attaching package: 'scales'

The following object is masked from 'package:purrr':

    discard

The following object is masked from 'package:readr':

    col_factor

Quitting from lines 88-91 (bechdel.Rmd) 
Error: processing vignette 'bechdel.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bechdel.Rmd’

--- re-building ‘fivethirtyeight.Rmd’ using rmarkdown
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Parsed with column specification:
cols(
  .default = col_character(),
  ARTICLE_DATE = col_date(format = ""),
  DATAFRAME_NROWS = col_number(),
  DATAFRAME_NCOLS = col_double()
)
See spec(...) for full column specifications.
--- finished re-building ‘fivethirtyeight.Rmd’

--- re-building ‘user_contributed_vignettes.Rmd’ using rmarkdown
--- finished re-building ‘user_contributed_vignettes.Rmd’

SUMMARY: processing the following file failed:
  ‘bechdel.Rmd’

Error: Vignette re-building failed.
Execution halted
opc : <anonymous>: no visible global function definition for
  ‘parseWorkspace’
opc : <anonymous>: no visible global function definition for
  ‘closeWorkspace’
Undefined global functions or variables:
  closeWorkspace parseWorkspace
RIind: no visible global function definition for ‘aggregate’
RIind: no visible binding for global variable ‘sd’
RIpop: no visible global function definition for ‘aggregate’
RIpop: no visible binding for global variable ‘sd’
SI: no visible global function definition for ‘sd’
SI2: no visible global function definition for ‘sd’
SI3: no visible global function definition for ‘aggregate’
SI3: no visible global function definition for ‘pairs’
SI3: no visible global function definition for ‘cor’
SI4: no visible global function definition for ‘aggregate’
SI4: no visible global function definition for ‘sd’
fCV: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate cor pairs sd
Consider adding
  importFrom("graphics", "pairs")
  importFrom("stats", "aggregate", "cor", "sd")
to your NAMESPACE file.
GCV: no visible global function definition for ‘lm’
GCV: no visible global function definition for ‘resid’
ffplot: no visible global function definition for ‘par’
ffplot: no visible global function definition for ‘plot’
ffplot: no visible global function definition for ‘points’
ffplot: no visible global function definition for ‘legend’
flowfield: no visible global function definition for ‘write.table’
gpr: no visible global function definition for ‘quantile’
gpr: no visible global function definition for ‘var’
smoothp: no visible global function definition for ‘lm’
smoothp: no visible global function definition for ‘predict’
smoothp: no visible global function definition for ‘resid’
smoothp: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  legend lm optimize par plot points predict quantile resid var
  write.table
Consider adding
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
export: no visible global function definition for ‘write.table’
flux.odae : <anonymous>: no visible global function definition for
  ‘combn’
mf.flux: no visible global function definition for ‘runsd’
plot.fluss: no visible global function definition for ‘dev.new’
plot.fluss: no visible global function definition for ‘pdf’
plot.fluss: no visible global function definition for ‘dev.off’
plot.fluxes: no visible global function definition for ‘dev.new’
plot.fluxes: no visible global function definition for ‘devAskNewPage’
plot.fluxes: no visible global function definition for ‘pdf’
plot.fluxes: no visible global function definition for ‘dev.off’
plot.fluxxes: no visible global function definition for ‘dev.new’
plot.fluxxes: no visible global function definition for ‘devAskNewPage’
plot.fluxxes: no visible global function definition for ‘pdf’
plot.fluxxes: no visible global function definition for ‘dev.off’
reco.bulk : get.out: no visible global function definition for
  ‘boxplot.stats’
Undefined global functions or variables:
  boxplot.stats combn dev.new dev.off devAskNewPage pdf runsd
  write.table
Consider adding
  importFrom("grDevices", "boxplot.stats", "dev.new", "dev.off",
             "devAskNewPage", "pdf")
  importFrom("utils", "combn", "write.table")
to your NAMESPACE file.
BSOptionValue: no visible global function definition for ‘pnorm’
ImpliedVol: no visible global function definition for ‘uniroot’
callFMstable: no visible global function definition for ‘integrate’
fitGivenQuantile: no visible global function definition for ‘uniroot’
matchQuartiles: no visible global function definition for ‘optim’
putFMstable: no visible global function definition for ‘integrate’
standardStableQuantile: no visible global function definition for
  ‘qnorm’
tailsGstable: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate optim pnorm qnorm uniroot
Consider adding
  importFrom("stats", "integrate", "optim", "pnorm", "qnorm", "uniroot")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'predict.foba':
  ‘predict.foba’

S3 methods shown with full name in documentation object 'print.foba':
  ‘print.foba’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_fontHind.Rmd’ using rmarkdown
Quitting from lines 38-49 (Using_fontHind.Rmd) 
Error: processing vignette 'Using_fontHind.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Using_fontHind.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_fontHind.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_fontMPlus.Rmd’ using rmarkdown
Quitting from lines 56-67 (Using_fontMPlus.Rmd) 
Error: processing vignette 'Using_fontMPlus.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Using_fontMPlus.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_fontMPlus.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Running examples in ‘forcats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fct_reorder
> ### Title: Reorder factor levels by sorting along another variable
> ### Aliases: fct_reorder fct_reorder2 last2
> 
> ### ** Examples
> 
> boxplot(Sepal.Width ~ Species, data = iris)
> boxplot(Sepal.Width ~ fct_reorder(Species, Sepal.Width), data = iris)
> boxplot(Sepal.Width ~ fct_reorder(Species, Sepal.Width, .desc = TRUE), data = iris)
> 
> chks <- subset(ChickWeight, as.integer(Chick) < 10)
> chks <- transform(chks, Chick = fct_shuffle(Chick))
> 
> if (require("ggplot2")) {
+ ggplot(chks, aes(Time, weight, colour = Chick)) +
+   geom_point() +
+   geom_line()
+ 
+ # Note that lines match order in legend
+ ggplot(chks, aes(Time, weight, colour = fct_reorder2(Chick, Time, weight))) +
+   geom_point() +
+   geom_line() +
+   labs(colour = "Chick")
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘forcats.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 31-34 (forcats.Rmd) 
Error: processing vignette 'forcats.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘forcats.Rmd’

SUMMARY: processing the following file failed:
  ‘forcats.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ForecastComb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.foreccomb_res
> ### Title: Plot results from forecast combination model
> ### Aliases: plot.foreccomb_res
> 
> ### ** Examples
> 
> obs <- rnorm(100)
> preds <- matrix(rnorm(1000, 1), 100, 10)
> train_o<-obs[1:80]
> train_p<-preds[1:80,]
> test_o<-obs[81:100]
> test_p<-preds[81:100,]
> 
> data<-foreccomb(train_o, train_p, test_o, test_p)
> fit <- comb_EIG1(data)
> plot(fit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘forecastHybrid.Rmd’ using rmarkdown
Loading required package: forecast
Loading required package: thief
Quitting from lines 88-90 (forecastHybrid.Rmd) 
Error: processing vignette 'forecastHybrid.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘forecastHybrid.Rmd’

SUMMARY: processing the following file failed:
  ‘forecastHybrid.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘forecast-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Arima
> ### Title: Fit ARIMA model to univariate time series
> ### Aliases: Arima print.ARIMA summary.Arima as.character.Arima
> ### Keywords: ts
> 
> ### ** Examples
> 
> library(ggplot2)
> WWWusage %>%
+   Arima(order=c(3,1,0)) %>%
+   forecast(h=20) %>%
+   autoplot
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘combinat’ ‘genetics’
  Please remove these calls from your code.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘forensic/R/zzz.R’:
  .First.lib calls:
    cat("## Statistical Methods in Forensic Genetics \n")
    cat("## The work was supported by the project 1M06014 of the Ministry of \n        Education, Youth and Sports of the Czech Republic. \n")
    require(genetics, quietly = TRUE)
    require(combinat, quietly = TRUE)

Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette.Rmd’ using rmarkdown
Quitting from lines 187-227 (Vignette.Rmd) 
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘forestinventory-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.esttable
> ### Title: Plotting Estimation Results
> ### Aliases: plot.esttable
> 
> ### ** Examples
> 
> 
> ## run onephase estimation:
> op.a <- onephase(formula = tvol~1,
+                  data = grisons,
+                  phase_id = list(phase.col = "phase_id_2p", terrgrid.id = 2),
+                  area = list(sa.col = "smallarea", areas = c("A", "B", "C", "D")))
> 
> ## run small area twophase estimation:
> sae.2p.est <- twophase(formula = tvol ~ mean + stddev + max + q75,
+                        data = grisons,
+                        phase_id = list(phase.col = "phase_id_2p", terrgrid.id = 2),
+                        small_area = list(sa.col = "smallarea", areas = c("A", "B","C", "D"),
+                                          unbiased = TRUE))
> 
> ## run small area threephase estimation:
> sae.3p.est <- threephase(formula.s0 =  tvol ~ mean,
+                          formula.s1 = tvol ~ mean + stddev + max + q75,
+                          data = grisons,
+                          phase_id = list(phase.col = "phase_id_3p", s1.id = 1, terrgrid.id = 2),
+                          small_area=list(sa.col = "smallarea", areas = c("A", "B", "C", "D"),
+                                          unbiased = TRUE))
> 
> ## create estimation table:
> sae.table<- estTable(est.list = list(op.a, sae.2p.est, sae.3p.est), add.ci=TRUE,
+                      sae = TRUE, vartypes = c("variance", "g_variance",  "ext_variance"))
> 
> ## plot estimation errors:
> plot(sae.table)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘forestmodel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: forest_model
> ### Title: Produce a forest plot based on a regression model
> ### Aliases: forest_model
> 
> ### ** Examples
> 
> 
> library("survival")
> library("dplyr")

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> pretty_lung <- lung %>%
+   transmute(time,
+             status,
+             Age = age,
+             Sex = factor(sex, labels = c("Male", "Female")),
+             ECOG = factor(lung$ph.ecog),
+             `Meal Cal` = meal.cal)
> 
> print(forest_model(coxph(Surv(time, status) ~ ., pretty_lung)))
Warning: Ignoring unknown aesthetics: x
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pcl-vignette.Rmd’ using rmarkdown
Quitting from lines 43-49 (pcl-vignette.Rmd) 
Error: processing vignette 'pcl-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pcl-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘pcl-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
ForImp: no visible global function definition for ‘head’
ForImp: no visible global function definition for ‘tail’
ForImp: no visible global function definition for ‘dist’
medianimp: no visible global function definition for ‘quantile’
rancatmat: no visible global function definition for ‘runif’
transfmatcat: no visible global function definition for ‘qnorm’
transfmatcat: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dist head qnorm quantile runif sd tail
Consider adding
  importFrom("stats", "dist", "qnorm", "quantile", "runif", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
INFCvpe: no visible binding for global variable ‘INFCstats’
INFCvpe: no visible binding for global variable ‘INFCdomain’
Undefined global functions or variables:
  INFCdomain INFCstats
Warning: no function found corresponding to methods exports from ‘FormalSeries’ for: ‘initialize’, ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
&,fseries-numeric: no visible global function definition for ‘new’
*,fseries-fseries: no visible global function definition for ‘new’
*,fseries-numeric: no visible global function definition for ‘new’
*,numeric-fseries: no visible global function definition for ‘new’
+,fseries-fseries: no visible global function definition for ‘new’
+,fseries-numeric: no visible global function definition for ‘new’
+,numeric-fseries: no visible global function definition for ‘new’
-,fseries-ANY: no visible global function definition for ‘new’
-,fseries-numeric: no visible global function definition for ‘new’
-,numeric-fseries: no visible global function definition for ‘new’
/,fseries-numeric: no visible global function definition for ‘new’
[<-,fseries-matrix-missing-matrix: no visible global function
  definition for ‘new’
[<-,fseries-numeric-missing-numeric: no visible global function
  definition for ‘new’
initialize,fseries: no visible global function definition for
  ‘validObject’
rfseries,numeric-numeric-numeric: no visible global function definition
  for ‘runif’
rfseries,numeric-numeric-numeric: no visible global function definition
  for ‘rbinom’
rfseries,numeric-numeric-numeric: no visible global function definition
  for ‘new’
Undefined global functions or variables:
  new rbinom runif validObject
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "rbinom", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
ForwardSearch.fit: no visible global function definition for ‘glm.fit’
ForwardSearch.plot: no visible global function definition for ‘lines’
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for ‘qnorm’
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  dnorm glm.fit lines qnorm
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "dnorm", "glm.fit", "qnorm")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: xtable

Attaching package: 'likert'

The following object is masked from 'package:dplyr':

    recode

Scale for 'x' is already present. Adding another scale for 'x', which
will replace the existing scale.
Quitting from lines 55-61 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following file failed:
  ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘shapefiles’ which was already attached by Depends.
  Please remove these calls from your code.
dino.dist: no visible global function definition for ‘as.dist’
earth.dist: no visible global function definition for ‘as.dist’
ecol.dist: no visible global function definition for ‘as.dist’
loc.map: no visible global function definition for ‘points’
msn.map: no visible global function definition for ‘points’
msn.map: no visible global function definition for ‘lines’
mstlines: no visible global function definition for ‘lines’
nmds.mst: no visible global function definition for ‘lines’
rclust.null: no visible global function definition for ‘sd’
sim.occ: no visible global function definition for ‘rlnorm’
spp.est: no visible global function definition for ‘sd’
Undefined global functions or variables:
  as.dist lines points rlnorm sd
Consider adding
  importFrom("graphics", "lines", "points")
  importFrom("stats", "as.dist", "rlnorm", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘fourierin_details.Rmd’ using rmarkdown
Quitting from lines 50-83 (fourierin_details.Rmd) 
Error: processing vignette 'fourierin_details.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘fourierin_details.Rmd’

SUMMARY: processing the following file failed:
  ‘fourierin_details.Rmd’

Error: Vignette re-building failed.
Execution halted
GenObs: no visible global function definition for ‘rnorm’
GenObs.T: no visible global function definition for ‘rt’
MeasL: no visible global function definition for ‘rbeta’
OutDet: no visible global function definition for ‘median’
RanCur: no visible global function definition for ‘rnorm’
init: no visible global function definition for ‘prcomp’
Undefined global functions or variables:
  median prcomp rbeta rnorm rt
Consider adding
  importFrom("stats", "median", "prcomp", "rbeta", "rnorm", "rt")
to your NAMESPACE file.
Running examples in ‘fpp2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: a10
> ### Title: Monthly anti-diabetic drug sales in Australia from 1991 to 2008.
> ### Aliases: a10
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> autoplot(a10)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Non-standard files/directories found at top level:
  ‘Calling’ ‘Done’ ‘filters.R’
confint.fracdiff: no visible global function definition for ‘coef’
confint.fracdiff: no visible global function definition for ‘qnorm’
fdGPH: no visible global function definition for ‘na.fail’
fdGPH: no visible global function definition for ‘as.ts’
fdGPH: no visible global function definition for ‘lm’
fdGPH: no visible global function definition for ‘coef’
fdGPH: no visible global function definition for ‘resid’
fdSperio: no visible global function definition for ‘na.fail’
fdSperio: no visible global function definition for ‘as.ts’
fdSperio: no visible global function definition for ‘lm’
fdSperio: no visible global function definition for ‘coef’
fdSperio: no visible global function definition for ‘resid’
fracdiff.sim: no visible binding for global variable ‘rnorm’
logLik.fracdiff: no visible global function definition for ‘coef’
print.fracdiff: no visible global function definition for ‘coef’
print.summary.fracdiff: no visible global function definition for
  ‘printCoefmat’
print.summary.fracdiff: no visible global function definition for
  ‘symnum’
summary.fracdiff: no visible global function definition for ‘coef’
summary.fracdiff: no visible global function definition for ‘pnorm’
summary.fracdiff: no visible global function definition for ‘logLik’
summary.fracdiff: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC as.ts coef lm logLik na.fail pnorm printCoefmat qnorm resid rnorm
  symnum
Consider adding
  importFrom("stats", "AIC", "as.ts", "coef", "lm", "logLik", "na.fail",
             "pnorm", "printCoefmat", "qnorm", "resid", "rnorm",
             "symnum")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘pcaPP’ ‘snowFT’ ‘wavelets’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ComputeDCT2FFT: no visible global function definition for ‘fft’
ComputeSemipgramFFT: no visible global function definition for ‘fft’
WaveVarFD: no visible global function definition for ‘modwt’
do.fd.estimate: no visible global function definition for
  ‘performParallel’
do.fd.estimate2d.simple: no visible global function definition for
  ‘median’
fd.Genton: no visible global function definition for ‘qn’
fd.estimate.matrix: no visible global function definition for
  ‘performParallel’
fd.plot.legend: no visible global function definition for ‘legend’
fd.plot.loglog: no visible global function definition for ‘plot’
fd.plot.loglog: no visible global function definition for ‘points’
fd.plot.loglog: no visible global function definition for ‘abline’
summary.FractalDim: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline fft legend median modwt performParallel plot points qn sd
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points")
  importFrom("stats", "fft", "median", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘futile.any’ ‘futile.logger’ ‘quantmod’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Theory.Rmd’ using rmarkdown
Quitting from lines 264-277 (Theory.Rmd) 
Error: processing vignette 'Theory.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Theory.Rmd’

--- re-building ‘Vulgar_Fractions_in_R.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 190-200 (Vulgar_Fractions_in_R.Rmd) 
Error: processing vignette 'Vulgar_Fractions_in_R.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Vulgar_Fractions_in_R.Rmd’

SUMMARY: processing the following files failed:
  ‘Theory.Rmd’ ‘Vulgar_Fractions_in_R.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘frailtyEM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.emfrail
> ### Title: Plots for emfrail objects using 'ggplot2'
> ### Aliases: autoplot.emfrail
> 
> ### ** Examples
> 
> mod_rec <- emfrail(Surv(start, stop, status) ~ treatment + number + cluster(id), bladder1,
+ control = emfrail_control(ca_test = FALSE, lik_ci = FALSE))
Warning in Surv(start, stop, status) :
  Stop time must be > start time, NA created
Warning in Surv(start, stop, status) :
  Invalid status value, converted to NA
Warning in Surv(start, stop, status) :
  Stop time must be > start time, NA created
Warning in Surv(start, stop, status) :
  Invalid status value, converted to NA
> 
> # Histogram of the estimated frailties
> autoplot(mod_rec, type = "hist")
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘frailtyEM_manual.Rnw’ using Sweave
Loading required package: survival
Loading required package: gridExtra
Warning: Removed 2 rows containing missing values (geom_path).

Error: processing vignette 'frailtyEM_manual.Rnw' failed with diagnostics:
 chunk 8 (label = cgd_pred_plots) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘frailtyEM_manual.Rnw’

SUMMARY: processing the following file failed:
  ‘frailtyEM_manual.Rnw’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘CCP’ ‘MASS’ ‘calibrate’ ‘corpcor’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘CCP’ ‘MASS’ ‘calibrate’ ‘corpcor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
custom.draw.circle: no visible global function definition for ‘lines’
frcc: no visible binding for global variable ‘sd’
frcc: no visible global function definition for ‘cor.shrink’
frcc: no visible global function definition for ‘cor’
frcc: no visible global function definition for ‘p.asym’
generate_multivariate_normal_sample: no visible global function
  definition for ‘mvrnorm’
plot_units: no visible binding for global variable ‘sd’
plot_units: no visible global function definition for ‘plot’
plot_units: no visible global function definition for ‘points’
plot_units: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘plot’
plot_variables: no visible global function definition for ‘points’
plot_variables: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘segments’
Undefined global functions or variables:
  cor cor.shrink lines mvrnorm p.asym plot points sd segments textxy
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/freeknotsplines.Rcheck/00install.out’ for details.
cv.work: no visible global function definition for ‘predict’
fakedata: no visible global function definition for ‘runif’
Undefined global functions or variables:
  predict runif
Consider adding
  importFrom("stats", "predict", "runif")
to your NAMESPACE file.
Running examples in ‘freqparcoord-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: freqparcoord
> ### Title: Frequency-based parallel coordinates.
> ### Aliases: freqparcoord
> 
> ### ** Examples
> 
> # baseball player data courtesy of UCLA Stat. Dept., www.socr.ucla.edu
> data(mlb)
> 
> # plot baseball data, broken down by position category (infield,
> # outfield, etc.); plot the 5 higest-density values in each group
> freqparcoord(mlb,5,4:6,7,method="maxdens")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS without any C files
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS without any C files
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Non-standard file/directory found at top level:
  ‘FrF2.catlg128-Ex.R’
Package in Depends field not imported from: ‘FrF2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error(s) in re-building vignettes:
  ...
--- re-building ‘FRK_intro.Rnw’ using knitr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 353-357 (FRK_intro.Rnw) 
Error: processing vignette 'FRK_intro.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘FRK_intro.Rnw’

SUMMARY: processing the following file failed:
  ‘FRK_intro.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘Rmpfr’ ‘partitions’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Bell : nways: no visible global function definition for ‘setparts’
Bell: no visible global function definition for ‘restrictedparts’
CalIncLapInt : Deriv: no visible global function definition for ‘D’
CalIncLapInt: no visible global function definition for ‘is.whole’
CalIncLapInt: no visible global function definition for ‘mpfr’
CalIncLapInt: no visible global function definition for ‘chooseMpfr’
derivErfc : Deriv: no visible global function definition for ‘D’
derivErfc : Erfc: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  D chooseMpfr is.whole mpfr pnorm restrictedparts setparts
Consider adding
  importFrom("stats", "D", "pnorm")
to your NAMESPACE file.
ROCscore: no visible global function definition for ‘par’
ROCscore: no visible global function definition for ‘axis’
ROCscore: no visible global function definition for ‘mtext’
ROCscore: no visible global function definition for ‘legend’
alphafrontier.2d: no visible global function definition for ‘par’
alphafrontier.2d: no visible global function definition for ‘polygon’
alphafrontier.2d: no visible global function definition for ‘lines’
alphafrontier.2d: no visible global function definition for ‘points’
alphafrontier.3d: no visible global function definition for ‘layout’
alphafrontier.3d: no visible global function definition for ‘barplot’
alphafrontier.3d: no visible global function definition for ‘axis’
alphafrontier.3d: no visible global function definition for ‘lines’
alphafrontier.3d: no visible global function definition for ‘na.omit’
ordermfrontier.2d: no visible global function definition for ‘par’
ordermfrontier.2d: no visible global function definition for ‘polygon’
ordermfrontier.2d: no visible global function definition for ‘lines’
ordermfrontier.2d: no visible global function definition for ‘points’
ordermscore.boot: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axis barplot layout legend lines mtext na.omit par points polygon sd
Consider adding
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "points", "polygon")
  importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘splines’
  Please remove these calls from your code.
Non-standard files/directories found at top level:
  ‘COPYRIGHT’ ‘pmden.R’
Copyright information should be in file inst/COPYRIGHTS
Packages in Depends field not imported from:
  ‘Rcpp’ ‘snowfall’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fugeR.evo: no visible global function definition for ‘runif’
fugeR.sfRun: no visible global function definition for ‘sfInit’
fugeR.sfRun: no visible global function definition for ‘sfLibrary’
fugeR.sfRun: no visible global function definition for ‘sfExport’
fugeR.sfRun: no visible global function definition for ‘sfLapply’
fugeR.sfRun: no visible global function definition for ‘sfStop’
Undefined global functions or variables:
  runif sfExport sfInit sfLapply sfLibrary sfStop
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘copying’
bic.generation: no visible global function definition for ‘lm’
bic.generation: no visible global function definition for ‘BIC’
bic.generation : <anonymous>: no visible global function definition for
  ‘lm’
bic.generation : <anonymous>: no visible global function definition for
  ‘BIC’
data.generation : <anonymous> : <anonymous>: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  BIC lm sd
Consider adding
  importFrom("stats", "BIC", "lm", "sd")
to your NAMESPACE file.
Running examples in ‘funData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.funData
> ### Title: Visualize functional data objects using ggplot
> ### Aliases: autoplot.funData autolayer.funData
> 
> ### ** Examples
> 
> # Install / load package ggplot2 before running the examples
> library("ggplot2")

Attaching package: ‘ggplot2’

The following object is masked from ‘package:funData’:

    ggplot

> 
> # One-dimensional
> argvals <- seq(0,2*pi,0.01)
> object <- funData(argvals,
+                    outer(seq(0.75, 1.25, length.out = 11), sin(argvals)))
> 
> g <- autoplot(object) # returns ggplot object
> g # plot the object
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [7s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(funData)
  
  Attaching package: 'funData'
  
  The following object is masked from 'package:stats':
  
      integrate
  
  > 
  > test_check("funData")
  ── 1. Error: ggplots (@test_plotMethods.R#159)  ────────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_equal(length(autoplot(multiFunData(object1D, 2 * object1D), plotGrid = TRUE)), 
         2) at testthat/test_plotMethods.R:159
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: autoplot(multiFunData(object1D, 2 * object1D), plotGrid = TRUE)
  5: autoplot.multiFunData(multiFunData(object1D, 2 * object1D), plotGrid = TRUE)
  6: gridExtra::grid.arrange(grobs = p, nrow = 1)
  7: grid.draw(g)
  8: grid.draw.gTree(g)
  9: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  10: drawGTree(x)
  ...
  18: pushgrobvp(x$vp)
  19: pushgrobvp.viewport(x$vp)
  20: pushViewport(vp, recording = FALSE)
  21: lapply(vps, push.vp, recording)
  22: FUN(X[[i]], ...)
  23: push.vp.vpStack(X[[i]], ...)
  24: lapply(vp, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.viewport(X[[i]], ...)
  27: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 470 SKIPPED: 0 FAILED: 1
  1. Error: ggplots (@test_plotMethods.R#159) 
  
  Error: testthat unit tests failed
  Execution halted
.FunFEM.main: no visible global function definition for ‘kmeans’
.FunFEM.main: no visible global function definition for ‘rmultinom’
.FunFEM.main: no visible global function definition for ‘cutree’
.FunFEM.main: no visible global function definition for ‘hclust’
.FunFEM.main: no visible global function definition for ‘dist’
.FunFEM.main: no visible global function definition for ‘par’
.FunFEM.main: no visible global function definition for ‘plot’
.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov cutree dist hclust kmeans par plot rmultinom
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "cov", "cutree", "dist", "hclust", "kmeans",
             "rmultinom")
to your NAMESPACE file.
Running examples in ‘funHDDC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict.funHDDC
> ### Title: Predict new results from a funHDDC model
> ### Aliases: predict.funHDDC
> 
> ### ** Examples
> 
> ##Univariate example
>     data("trigo")
>     basis<- create.bspline.basis(c(0,1), nbasis=25)
>     z<-sample(1:100,0.8*100,replace=FALSE)
>     var1_train<-smooth.basis(argvals=seq(0,1,length.out = 100),y=t(trigo[z,1:100]),
+                              fdParobj=basis)$fd
>     var1_test<-smooth.basis(argvals=seq(0,1,length.out = 100),y=t(trigo[-z,1:100]),
+                             fdParobj=basis)$fd
> 
>     model<-funHDDC(var1_train,K=2)
      model K threshold complexity         BIC
1 AKJBKQKDK 2       0.2        103 -373,867.94

SELECTED: model  AKJBKQKDK  with  2  clusters.
Selection Criterion: BIC.
>     pred<-predict(model,var1_test)
> 
> ##Multivariate example
>     data("triangle")
>     basis<- create.bspline.basis(c(1,21), nbasis=25)
>     z<-sample(1:100,0.8*100,replace=FALSE)
>     var1_train<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[z,1:101]),
+                               fdParobj=basis)$fd
>     var1_test<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[-z,1:101]),
+                             fdParobj=basis)$fd
>     var2_train<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[z,102:202]),
+                             fdParobj=basis)$fd
>     var2_test<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[-z,102:202]),
+                             fdParobj=basis)$fd
> 
>     model<-funHDDC(list(var1_train,var2_train),K=3)
Warning in funHDDC(list(var1_train, var2_train), K = 3) :
  All models diverged.
>     pred<-predict(model,list(var1_test,var2_test))
Error in UseMethod("predict") : 
  no applicable method for 'predict' applied to an object of class "list"
Calls: predict
Execution halted
Running examples in ‘funModeling-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: freq
> ### Title: Frequency table for categorical variables
> ### Aliases: freq
> 
> ### ** Examples
> 
> freq(data=heart_disease$thal)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: freq ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘funModeling_quickstart.Rmd’ using rmarkdown
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, units

funModeling v.1.7 :)
Examples and tutorials at livebook.datascienceheroes.com

Quitting from lines 64-65 (funModeling_quickstart.Rmd) 
Error: processing vignette 'funModeling_quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘funModeling_quickstart.Rmd’

SUMMARY: processing the following file failed:
  ‘funModeling_quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘funnelR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: funplot
> ### Title: Create a funnel plot
> ### Aliases: funplot
> 
> ### ** Examples
> 
> #My sample data
> my_data  <- data.frame(id=c('A','B','C','D','E'), n=c(2,5,10,15,18), d=c(20,20,20,20,20))
> 
> #Process sample data through fundata
> my_fpdata <- fundata(my_data, alpha=0.95, alpha2=0.998, method='approximate', step=0.5)
> 
> #Use sample data and fundata to make the plot.
> my_plot <- funplot(my_data, my_fpdata)
> 
> #View plot
> my_plot
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 61-74 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rarity_indices.Rmd’ using rmarkdown
Quitting from lines 279-340 (rarity_indices.Rmd) 
Error: processing vignette 'rarity_indices.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rarity_indices.Rmd’

--- re-building ‘sparse_matrices.Rmd’ using rmarkdown
--- finished re-building ‘sparse_matrices.Rmd’

SUMMARY: processing the following file failed:
  ‘rarity_indices.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘subgroup_fusion.Rmd’ using rmarkdown
Quitting from lines 87-98 (subgroup_fusion.Rmd) 
Error: processing vignette 'subgroup_fusion.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘subgroup_fusion.Rmd’

SUMMARY: processing the following file failed:
  ‘subgroup_fusion.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘FusionLearn.Rmd’ using rmarkdown
Quitting from lines 231-247 (FusionLearn.Rmd) 
Error: processing vignette 'FusionLearn.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘FusionLearn.Rmd’

SUMMARY: processing the following file failed:
  ‘FusionLearn.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘RUnit’ ‘futile.options’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.validateGuardExpression: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘futureheatwaves-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: map_grid
> ### Title: Create a map of model grid
> ### Aliases: map_grid
> 
> ### ** Examples
> 
> out <- system.file("extdata/example_results", package = "futureheatwaves")
> map_grid(plot_model = "bcc1", out = out)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘futureheatwaves.Rmd’ using rmarkdown
Quitting from lines 579-581 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘futureheatwaves.Rmd’

--- re-building ‘starting_from_netcdf.Rmd’ using rmarkdown
--- finished re-building ‘starting_from_netcdf.Rmd’

SUMMARY: processing the following file failed:
  ‘futureheatwaves.Rmd’

Error: Vignette re-building failed.
Execution halted
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  ‘d’ to ‘digits’
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  ‘d’ to ‘digits’
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  ‘d’ to ‘digits’
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
NeedsCompilation field must take value ‘yes’ or ‘no’
'library' or 'require' call to ‘splines’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gensurf: no visible global function definition for ‘persp’
gensurf: no visible global function definition for ‘rainbow’
plotMF: no visible global function definition for ‘plot.new’
plotMF: no visible global function definition for ‘plot.window’
plotMF: no visible global function definition for ‘runif’
plotMF: no visible global function definition for ‘predict’
plotMF: no visible global function definition for ‘interpSpline’
plotMF: no visible global function definition for ‘lines’
plotMF: no visible global function definition for ‘text’
plotMF: no visible global function definition for ‘title’
plotMF: no visible global function definition for ‘axis’
plotMF: no visible global function definition for ‘box’
Undefined global functions or variables:
  axis box interpSpline lines persp plot.new plot.window predict
  rainbow runif text title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "persp", "plot.new",
             "plot.window", "text", "title")
  importFrom("stats", "predict", "runif")
to your NAMESPACE file.
alpha: no visible global function definition for ‘var’
coefH: no visible global function definition for ‘var’
coefZ: no visible global function definition for ‘var’
coefZ: no visible binding for global variable ‘var’
fs.MSA: no visible global function definition for ‘runif’
fs.MSA: no visible global function definition for ‘boxplot’
plot.fs.class: no visible global function definition for ‘lines’
plot.fs.class: no visible global function definition for ‘text’
plot.fs.class: no visible global function definition for ‘axis’
plot.fs.class: no visible global function definition for ‘segments’
plot.fs.class: no visible global function definition for ‘title’
plot.fs.class: no visible global function definition for
  ‘devAskNewPage’
plot.fs.class : <anonymous>: no visible global function definition for
  ‘quantile’
plot.fs.n1.class: no visible global function definition for ‘segments’
plot.fs.n1.class: no visible global function definition for ‘axis’
plot.fs.n1.class: no visible global function definition for ‘lines’
plot.fs.n1.class: no visible global function definition for ‘legend’
search.normal: no visible global function definition for ‘var’
search.normal: no visible binding for global variable ‘var’
search.normal: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  axis boxplot devAskNewPage legend lines qnorm quantile runif segments
  text title var
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "axis", "boxplot", "legend", "lines",
             "segments", "text", "title")
  importFrom("stats", "qnorm", "quantile", "runif", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘foreach’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fxreturns: no visible binding for global variable ‘FXRatesCHF’
fxreturns : <anonymous>: no visible global function definition for
  ‘tail’
gbreakpoints: no visible global function definition for ‘%dopar%’
gbreakpoints: no visible global function definition for ‘foreach’
Undefined global functions or variables:
  %dopar% FXRatesCHF foreach tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DBNScoreStep1: no visible global function definition for ‘lm’
DBNScoreStep1: no visible global function definition for ‘rlm’
DBNScoreStep1: no visible global function definition for ‘pt’
DBNScoreStep2: no visible global function definition for ‘lm’
DBNScoreStep2: no visible global function definition for ‘rlm’
DBNScoreStep2: no visible global function definition for ‘pt’
SimulGeneExpressionAR1: no visible global function definition for
  ‘rnorm’
SimulGeneExpressionAR1: no visible global function definition for ‘ts’
SimulNetworkAdjMatrix: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  lm pt rlm rnorm runif ts
Consider adding
  importFrom("stats", "lm", "pt", "rnorm", "runif", "ts")
to your NAMESPACE file.
Running examples in ‘G2Sd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: granplot
> ### Title: Histogram with a cumulative percentage curve
> ### Aliases: granplot
> 
> ### ** Examples
> 
> data(granulo)
> granplot(granulo,xc=1,hist=TRUE,cum=TRUE,main="Grain-size Distribution",
+ 			col.hist="gray",col.cum="red")
>       
> granplot(granulo,xc=2:4,main="Grain-size Distribution")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: granplot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
crossover: no visible global function definition for ‘runif’
exchangeSols: no visible global function definition for ‘runif’
fps: no visible global function definition for ‘runif’
mutation: no visible global function definition for ‘runif’
plotBicluster: no visible global function definition for ‘gray’
plotBicluster: no visible global function definition for ‘heatmap’
reproduction: no visible global function definition for ‘runif’
Undefined global functions or variables:
  gray heatmap runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "heatmap", "runif")
to your NAMESPACE file.
FPTsimul: no visible global function definition for ‘runif’
histplot: no visible global function definition for ‘dev.new’
histplot: no visible global function definition for ‘hist’
histplot: no visible global function definition for ‘par’
histplot: no visible global function definition for ‘plot’
histplot: no visible global function definition for ‘legend’
mdt: no visible binding for global variable ‘deltat’
plot.FPTdensity: no visible global function definition for ‘dev.new’
plot.FPTdensity: no visible global function definition for ‘plot’
res_summary: no visible global function definition for ‘write.table’
res_summary: no visible global function definition for ‘sd’
res_summary: no visible global function definition for ‘median’
vdt: no visible binding for global variable ‘deltat’
Undefined global functions or variables:
  deltat dev.new hist legend median par plot runif sd write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "legend", "par", "plot")
  importFrom("stats", "deltat", "median", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in ‘GADMTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: choropleth
> ### Title: Draw a choropleth on selected regions
> ### Aliases: choropleth
> ### Keywords: ~documentation
> 
> ### ** Examples
> 
> library(GADMTools)
> data("Corsica")
> Cantons <- listNames(Corsica, 4)
> pop <- floor(runif(length(Cantons), min=15200, max=23500))
> DAT <- data.frame(Cantons, pop)
> 
> choropleth(Corsica, DAT,
+            adm.join = "Cantons",
+            value = "pop",
+            breaks = "sd",
+            palette="Oranges",
+            legend = "Population",
+            title="Population Cantons de Corse")
Warning: Column `NAME_4` joining character vector and factor, coercing into character vector
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
CI.RMSEA: no visible global function definition for ‘qchisq’
CI.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘par’
GAIPE.RMSEA: no visible global function definition for ‘plot’
GAIPE.RMSEA: no visible global function definition for ‘abline’
GAIPE.RMSEA: no visible global function definition for ‘colors’
GAIPE.RMSEA: no visible global function definition for ‘text’
GAIPE.RMSEA: no visible global function definition for ‘arrows’
GAIPE.RMSEA: no visible global function definition for ‘points’
GAIPE.RMSEA: no visible global function definition for ‘axis’
GAIPE.RMSEA: no visible global function definition for ‘lines’
GAIPE.RMSEA: no visible global function definition for ‘legend’
GAIPE.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘qchisq’
GAIPE.RMSEA: no visible global function definition for ‘mtext’
GAIPE.RMSEA: no visible global function definition for ‘title’
PA.RMSEA: no visible global function definition for ‘pchisq’
PA.RMSEA: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  abline arrows axis colors legend lines mtext par pchisq plot points
  qchisq text title
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "par", "plot", "points", "text", "title")
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘gama.Rmd’ using rmarkdown
Package 'gama', version 1.0.3
Type 'citation("gama")' for citing this R package in publications.
Quitting from lines 119-127 (gama.Rmd) 
Error: processing vignette 'gama.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gama.Rmd’

SUMMARY: processing the following file failed:
  ‘gama.Rmd’

Error: Vignette re-building failed.
Execution halted
cvriskMSM: no visible global function definition for ‘predict’
plotcvriskMSM: no visible global function definition for ‘plot’
plotcvriskMSM: no visible binding for global variable ‘lines’
plotcvriskMSM: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot predict
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘changeLog’ ‘gnugpl2.txt’
'library' or 'require' calls in package code:
  ‘parallel’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘Matrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GAMBoost: no visible global function definition for ‘binomial’
GAMBoost: no visible global function definition for ‘gaussian’
GAMBoost: no visible global function definition for ‘poisson’
GAMBoost: no visible binding for global variable ‘sd’
GAMBoost: no visible global function definition for ‘Matrix’
calc.confidence.bands: no visible global function definition for
  ‘predict’
cv.GAMBoost: no visible global function definition for ‘binomial’
cv.GAMBoost : eval.fold: no visible global function definition for
  ‘predict’
cv.GAMBoost: no visible global function definition for ‘mclapply’
cv.GAMBoost: no visible binding for global variable ‘var’
estimPVal: no visible global function definition for ‘mclapply’
plot.GAMBoost: no visible global function definition for ‘plot’
plot.GAMBoost: no visible global function definition for ‘lines’
Undefined global functions or variables:
  Matrix binomial gaussian lines mclapply plot poisson predict sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "binomial", "gaussian", "poisson", "predict", "sd",
             "var")
to your NAMESPACE file.
Running examples in ‘gameofthrones-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gotMap
> ### Title: Game of Thrones Colour Map.
> ### Aliases: gotMap got got_pal gameofthrones
> 
> ### ** Examples
> 
> library(ggplot2)
> library(hexbin)
> 
> dat <- data.frame(x = rnorm(1e4), y = rnorm(1e4))
> 
> ggplot(dat, aes(x = x, y = y)) +
+   geom_hex() + coord_fixed() +
+   scale_fill_gradientn(colours = got(128, option = "targaryen")) +
+   theme_minimal()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package in Depends field not imported from: ‘gamlss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘gamlss:::.gamlss.bi.list’
  See the note in ?`:::` about the use of this operator.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found the following calls to attach():
File ‘gamlss.nl/R/nlgamlss.R’:
  attach(data)
See section ‘Good practice’ in ‘?attach’.
Non-standard file/directory found at top level:
  ‘Read-and-delete-me’
Package in Depends field not imported from: ‘GANPAdata’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘gapfill-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Image
> ### Title: Image Panels
> ### Aliases: Image
> 
> ### ** Examples
> 
> library("abind")
> t1 <- array(rep(c(1,0), each = 5), c(5,5))
> t1[5,3] <- 2 
> t2 <- abind(t1, t1, along = 3)
> t3 <- abind(t2, t2, along = 4)
> Image(t1)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘gapmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gapmap
> ### Title: Function to draw a gapped cluster heatmap
> ### Aliases: gapmap
> 
> ### ** Examples
> 
> set.seed(1234)
> #generate sample data
> x <- rnorm(10, mean=rep(1:5, each=2), sd=0.4)
> y <- rnorm(10, mean=rep(c(1,2), each=5), sd=0.4)
> dataFrame <- data.frame(x=x, y=y, row.names=c(1:10))
> #calculate distance matrix. default is Euclidean distance
> distxy <- dist(dataFrame)
> #perform hierarchical clustering. default is complete linkage.
> hc <- hclust(distxy)
> dend <- as.dendrogram(hc)
> #make a cluster heatmap plot
> gapmap(m = as.matrix(distxy), d_row= rev(dend), d_col=dend)
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: gapmap ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_example.Rmd’ using knitr
Loading required package: ggplot2
Loading required package: reshape2
Quitting from lines 35-37 (simple_example.Rmd) 
Error: processing vignette 'simple_example.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simple_example.Rmd’

--- re-building ‘tcga_example.Rmd’ using knitr
Quitting from lines 43-45 (tcga_example.Rmd) 
Error: processing vignette 'tcga_example.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tcga_example.Rmd’

SUMMARY: processing the following files failed:
  ‘simple_example.Rmd’ ‘tcga_example.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  hap_c.c:380:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  hap_c.c:392:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gap.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘orthopolynom’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘orthopolynom’ ‘polynom’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
contindic.gb2: no visible global function definition for ‘contour’
contindic.gb2: no visible global function definition for ‘box’
contindic.gb2: no visible global function definition for ‘mtext’
contprof.gb2: no visible global function definition for ‘image’
contprof.gb2: no visible global function definition for ‘heat.colors’
contprof.gb2: no visible global function definition for ‘contour’
contprof.gb2: no visible global function definition for ‘text’
contprof.gb2: no visible global function definition for ‘box’
dplot.cavgb2: no visible global function definition for ‘par’
dplot.cavgb2: no visible global function definition for ‘curve’
dplot.cavgb2: no visible global function definition for ‘legend’
dplot.cavgb2: no visible global function definition for ‘plot’
dplot.cavgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘curve’
dplot.cgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘legend’
plotsML.gb2: no visible global function definition for ‘par’
plotsML.gb2: no visible global function definition for ‘plot’
plotsML.gb2: no visible global function definition for ‘abline’
plotsML.gb2: no visible global function definition for ‘curve’
plotsML.gb2: no visible global function definition for ‘legend’
saveplot : <local>: no visible global function definition for ‘dev.set’
saveplot : <local>: no visible global function definition for
  ‘dev.print’
saveplot : <local>: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  abline box contour curve dev.print dev.set heat.colors image legend
  lines mtext par pdf plot text
Consider adding
  importFrom("grDevices", "dev.print", "dev.set", "heat.colors", "pdf")
  importFrom("graphics", "abline", "box", "contour", "curve", "image",
             "legend", "lines", "mtext", "par", "plot", "text")
to your NAMESPACE file.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
coeplot: no visible global function definition for ‘plot’
coeplot: no visible global function definition for ‘axis’
coeplot: no visible global function definition for ‘lines’
coeplot: no visible global function definition for ‘title’
coeplot: no visible global function definition for ‘legend’
corplot: no visible global function definition for ‘par’
corplot: no visible global function definition for ‘pairs’
corplot: no visible global function definition for ‘strwidth’
lm.estimate: no visible global function definition for ‘as.formula’
lm.estimate: no visible global function definition for ‘glm’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
panel.smooth.r: no visible global function definition for ‘par’
panel.smooth.r: no visible global function definition for ‘points’
panel.smooth.r: no visible global function definition for ‘lines’
posplot: no visible global function definition for ‘par’
posplot: no visible global function definition for ‘barplot’
posplot: no visible global function definition for ‘plot’
posplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  as.formula axis barplot cor glm legend lines pairs par plot points
  strwidth text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "pairs",
             "par", "plot", "points", "strwidth", "text", "title")
  importFrom("stats", "as.formula", "cor", "glm")
to your NAMESPACE file.
Running examples in ‘GCalignR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw_chromatogram
> ### Title: Visualise peak lists as a pseudo-chromatogram
> ### Aliases: draw_chromatogram
> 
> ### ** Examples
> 
> ## load data
> path <- (system.file("extdata", "simulated_peak_data.txt", package = "GCalignR"))
> ## run with defaults
> x <- draw_chromatogram(data = path, rt_col_name = "rt")
Computing chromatograms ...

  |                                                  | 0 % elapsed =00s  
  |+++++++++++++                                     | 25% elapsed =00s, remaining ~00s
  |+++++++++++++++++++++++++                         | 50% elapsed =00s, remaining ~00s
  |++++++++++++++++++++++++++++++++++++++            | 75% elapsed =00s, remaining ~00s
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed =00s, remaining ~00s

Drawing chromatograms ...Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: draw_chromatogram ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GCalignR_How_does_the_Algorithm_work.Rmd’ using rmarkdown
Quitting from lines 35-42 (GCalignR_How_does_the_Algorithm_work.Rmd) 
Error: processing vignette 'GCalignR_How_does_the_Algorithm_work.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GCalignR_How_does_the_Algorithm_work.Rmd’

--- re-building ‘GCalignR_step_by_step.Rmd’ using rmarkdown
Quitting from lines 196-197 (GCalignR_step_by_step.Rmd) 
Error: processing vignette 'GCalignR_step_by_step.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GCalignR_step_by_step.Rmd’

SUMMARY: processing the following files failed:
  ‘GCalignR_How_does_the_Algorithm_work.Rmd’
  ‘GCalignR_step_by_step.Rmd’

Error: Vignette re-building failed.
Execution halted
gcat.test: no visible global function definition for ‘pnorm’
generate_sub: no visible global function definition for ‘runif’
pfcn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm runif
Consider adding
  importFrom("stats", "pnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gputools’
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DownloadGdelt: no visible global function definition for
  ‘packageVersion’
DownloadGdelt: no visible global function definition for
  ‘download.file’
GdeltZipToDataframe: no visible global function definition for
  ‘read.delim’
GdeltZipToDataframe: no visible global function definition for ‘unzip’
GetSizeOfGDELT: no visible global function definition for ‘read.delim’
IsValidGDELT: no visible global function definition for ‘read.delim’
IsValidGDELT: no visible global function definition for ‘md5sum’
NormEventCounts: no visible global function definition for
  ‘download.file’
NormEventCounts: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  download.file md5sum packageVersion read.csv read.delim unzip
Consider adding
  importFrom("utils", "download.file", "packageVersion", "read.csv",
             "read.delim", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  Gdmlib.cpp:2352:19: warning: ‘%lf’ directive writing between 3 and 317 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gdm.Rcheck/00install.out’ for details.
Running examples in ‘GD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gdrisk
> ### Title: Geographical detectors: risk detector.
> ### Aliases: gdrisk print.gdrisk plot.gdrisk
> 
> ### ** Examples
> 
> gr1 <- gdrisk(NDVIchange ~ Climatezone + Mining, data = ndvi_40)
> gr1
Climatezone
  interval  Bsk  Bwk  Dwa  Dwb  Dwc
1      Bsk <NA> <NA> <NA> <NA> <NA>
2      Bwk    Y <NA> <NA> <NA> <NA>
3      Dwa    Y    Y <NA> <NA> <NA>
4      Dwb    Y    Y    N <NA> <NA>
5      Dwc    Y    Y    Y    Y <NA>

Mining
   interval high  low medium very high very low
1      high <NA> <NA>   <NA>      <NA>     <NA>
2       low    Y <NA>   <NA>      <NA>     <NA>
3    medium    N    Y   <NA>      <NA>     <NA>
4 very high    Y    Y      Y      <NA>     <NA>
5  very low    Y    Y      Y         N     <NA>

> plot(gr1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Non-standard files/directories found at top level:
  ‘README.too’ ‘blurb’
Running examples in ‘gemtc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: blobbogram
> ### Title: Plot a blobbogram (AKA forest plot)
> ### Aliases: blobbogram forest
> 
> ### ** Examples
> 
> data <- read.table(textConnection('
+ id               group pe       ci.l ci.u style      value.A    value.B 
+ "Study 1"  1         0.35 0.08 0.92 "normal" "2/46"     "7/46" 
+ "Study 2"  1         0.43 0.15 1.14 "normal" "4/50"     "8/49" 
+ "Study 3"  2         0.31 0.07 0.74 "normal" "2/97"     "10/100"
+ "Study 4"  2         0.86 0.34 2.90 "normal" "9/104"    "6/105" 
+ "Study 5"  2         0.33 0.10 0.72 "normal" "4/74"     "14/74" 
+ "Study 6"  2         0.47 0.23 0.91 "normal" "11/120" "22/129"
+ "Pooled"     NA      0.42 0.15 1.04 "pooled" NA             NA 
+ '), header=TRUE)
> data$pe <- log(data$pe)
> data$ci.l <- log(data$ci.l)
> data$ci.u <- log(data$ci.u)
> 
> blobbogram(data, group.labels=c('GROUP 1', 'GROUP 2'),
+     columns=c('value.A', 'value.B'), column.labels=c('r/n', 'r/n'),
+     column.groups=c(1, 2), grouped=TRUE,
+     column.group.labels=c('Intervention', 'Control'),
+     id.label="Trial", ci.label="Odds Ratio (95% CrI)", log.scale=TRUE)
Error in FUN(X[[i]], ...) : object is not coercible to a unit
Calls: blobbogram -> Summary.unit -> unlist -> lapply -> FUN
Execution halted
plot.rbga: no visible global function definition for ‘par’
plot.rbga: no visible global function definition for ‘hist’
plot.rbga: no visible global function definition for ‘plot’
plot.rbga: no visible global function definition for ‘lines’
rbga: no visible global function definition for ‘runif’
rbga: no visible global function definition for ‘dnorm’
rbga.bin: no visible global function definition for ‘dnorm’
rbga.bin: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm hist lines par plot runif
Consider adding
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
Running examples in ‘genBaRcode-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generateKirchenplot
> ### Title: Plotting a Kirchenplot
> ### Aliases: generateKirchenplot
> 
> ### ** Examples
> 
> data(BC_dat)
> generateKirchenplot(BC_dat, ori_BCs, loga = TRUE, col_type = NULL)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
clopper.pearson.ci: no visible global function definition for ‘qbeta’
cm.clopper.pearson.ci: no visible global function definition for
  ‘uniroot’
cm.clopper.pearson.ci : <anonymous>: no visible global function
  definition for ‘pbeta’
cm.n.clopper.pearson: no visible global function definition for
  ‘uniroot’
cm.n.clopper.pearson : <anonymous>: no visible global function
  definition for ‘pbeta’
n.clopper.pearson: no visible global function definition for ‘uniroot’
n.clopper.pearson : <anonymous>: no visible global function definition
  for ‘pbeta’
rgbinom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  pbeta qbeta runif uniroot
Consider adding
  importFrom("stats", "pbeta", "qbeta", "runif", "uniroot")
to your NAMESPACE file.
genmvnorm: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘genderdata’
Error(s) in re-building vignettes:
  ...
--- re-building ‘predicting-gender.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 15-27 (predicting-gender.Rmd) 
Error: processing vignette 'predicting-gender.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘predicting-gender.Rmd’

SUMMARY: processing the following file failed:
  ‘predicting-gender.Rmd’

Error: Vignette re-building failed.
Execution halted
gPopCreate: no visible global function definition for ‘rnorm’
periodogram.freq: no visible global function definition for ‘spectrum’
periodogram.freq: no visible global function definition for ‘frequency’
periodogram.spec.single: no visible global function definition for
  ‘spectrum’
periodogram.spec.single: no visible global function definition for
  ‘fft’
robust.g.test: no visible global function definition for ‘read.table’
robust.g.test: no visible global function definition for ‘density’
robust.spectrum: no visible global function definition for ‘density’
robust.spectrum.single: no visible global function definition for ‘fft’
spearman: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor density fft frequency read.table rnorm spectrum
Consider adding
  importFrom("stats", "cor", "density", "fft", "frequency", "rnorm",
             "spectrum")
  importFrom("utils", "read.table")
to your NAMESPACE file.
t1p1: no visible global function definition for ‘var’
t1p1: no visible global function definition for ‘pt’
t1p2: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt var
Consider adding
  importFrom("stats", "pt", "var")
to your NAMESPACE file.
load.genelist: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RHugin’
fit.dbn: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package unavailable to check Rd xrefs: ‘GeneticsDesign’
ForImp.Mahala: no visible global function definition for ‘combn’
ForImp.Mahala: no visible global function definition for ‘var’
ForImp.Mahala: no visible global function definition for ‘quantile’
ForImp.Mahala : <anonymous>: no visible global function definition for
  ‘var’
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for ‘var’
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for ‘quantile’
ForImp.PCA: no visible global function definition for ‘cov’
ForImp.PCA: no visible global function definition for ‘princomp’
ForImp.PCA: no visible global function definition for ‘combn’
ForImp.PCA: no visible global function definition for ‘quantile’
ForImp.PCA : <anonymous> : <anonymous>: no visible global function
  definition for ‘quantile’
Undefined global functions or variables:
  combn cov princomp quantile var
Consider adding
  importFrom("stats", "cov", "princomp", "quantile", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package in Depends field not imported from: ‘KernSmooth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KernSec: no visible global function definition for ‘na.omit’
KernSur: no visible global function definition for ‘na.fail’
KernSur: no visible global function definition for ‘na.omit’
bandwidthselect: no visible global function definition for ‘na.omit’
bandwidthselect: no visible global function definition for ‘dpik’
correlationselect: no visible global function definition for ‘cor’
nearest: no visible global function definition for ‘na.fail’
nearest: no visible global function definition for ‘na.omit’
per: no visible global function definition for ‘na.fail’
Undefined global functions or variables:
  cor dpik na.fail na.omit
Consider adding
  importFrom("stats", "cor", "na.fail", "na.omit")
to your NAMESPACE file.
MOSS_GWAS: no visible global function definition for ‘complete.cases’
MOSS_GWAS_main: no visible global function definition for ‘rbinom’
MOSS_GWAS_main: no visible global function definition for ‘na.omit’
MOSS_GWAS_main: no visible global function definition for ‘glm’
MOSS_GWAS_main: no visible global function definition for ‘poisson’
MOSS_Hierarchical: no visible global function definition for
  ‘as.formula’
MOSS_Hierarchical: no visible global function definition for ‘rbinom’
cvFunc: no visible global function definition for ‘na.omit’
findDualGenerators: no visible global function definition for ‘na.omit’
findGenerators: no visible global function definition for ‘na.omit’
findLogMargLik: no visible global function definition for ‘na.omit’
findModel: no visible global function definition for ‘as.formula’
findNeighbours: no visible global function definition for ‘na.omit’
fitInteractionModels: no visible global function definition for
  ‘na.omit’
fitInteractionModels: no visible global function definition for ‘glm’
fitInteractionModels: no visible global function definition for
  ‘poisson’
getSubsets: no visible global function definition for ‘na.omit’
logLaplace: no visible global function definition for ‘as.formula’
logLaplace: no visible global function definition for ‘model.matrix’
logLaplace: no visible global function definition for ‘glm’
logLaplace: no visible global function definition for ‘poisson’
mWindow: no visible global function definition for ‘complete.cases’
prettyFormula: no visible global function definition for ‘na.omit’
randomHierModel: no visible global function definition for ‘rbinom’
recode_data: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  as.formula complete.cases glm model.matrix na.omit poisson rbinom
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "glm",
             "model.matrix", "na.omit", "poisson", "rbinom")
to your NAMESPACE file.
Running examples in ‘genogeographer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: error_bar_plot
> ### Title: Plot log likelihoods of profiles with approximate confidence
> ###   intervals
> ### Aliases: error_bar_plot
> 
> ### ** Examples
> 
> df_ <- simulate_pops(pop_n = 20, aims_n = 50)
> df_db <- pops_to_DB(df_)
> profile <- random_AIMs_profile(df_db, keep_pop = TRUE)
> profile$pop[1] # The true population
[1] "pop_11"
> result <- genogeo(profile[,c("locus","x0")], df = df_db)
> error_bar_plot(result)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘genomeplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genomeplot-package
> ### Title: 'Plot genome wide values for all chromosomes'
> ### Aliases: genomeplot-package
> ### Keywords: package
> 
> ### ** Examples
> 
> data(sample_data)
> select <- 1
> genomeplot(sample_data,select)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘genoPlotR.Rnw’ using Sweave
Loading required package: ade4
Loading required package: grid

Error: processing vignette 'genoPlotR.Rnw' failed with diagnostics:
 chunk 49 (label = ex7_plotwithsegplots) 
Error in unit(3, "grobwidth", data = seg_plot_yaxis_grobs[[longest_segment]]) : 
  data must be either NULL, have length 1, or match the length of the final unit vector

--- failed re-building ‘genoPlotR.Rnw’

SUMMARY: processing the following file failed:
  ‘genoPlotR.Rnw’

Error: Vignette re-building failed.
Execution halted
splineAnalyze: no visible global function definition for ‘var’
splineAnalyze: no visible global function definition for ‘par’
splineAnalyze: no visible global function definition for ‘plot’
splineAnalyze: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par plot var
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "var")
to your NAMESPACE file.
PAEA : <anonymous>: no visible global function definition for
  ‘integrate’
PAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
PAEAAnalysis : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
PAEAAnalysis: no visible global function definition for ‘par’
PAEAAnalysis: no visible global function definition for ‘barplot’
chdirSig: no visible global function definition for ‘prcomp’
chdirSig: no visible global function definition for ‘rchisq’
chdirSig: no visible global function definition for ‘txtProgressBar’
chdirSig : <anonymous> : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
chdirplots : <anonymous>: no visible global function definition for
  ‘par’
chdirplots : <anonymous>: no visible global function definition for
  ‘plot’
chdirplots : <anonymous>: no visible global function definition for
  ‘arrows’
chdirplots : <anonymous>: no visible global function definition for
  ‘barplot’
multigmtPAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘data’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘write.table’
Undefined global functions or variables:
  arrows barplot data integrate par plot prcomp rchisq
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("graphics", "arrows", "barplot", "par", "plot")
  importFrom("stats", "integrate", "prcomp", "rchisq")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Running examples in ‘geofacet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: grid_preview
> ### Title: Plot a preview of a grid
> ### Aliases: grid_preview
> 
> ### ** Examples
> 
> grid_preview(us_state_grid2)
Note: You provided a user-specified grid. If this is a generally-useful
  grid, please consider submitting it to become a part of the geofacet
  package. You can do this easily by calling:
  grid_submit(__grid_df_name__)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: grid_preview ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(geofacet)
  Registered S3 method overwritten by 'geofacet':
    method from   
    +.gg   ggplot2
  > 
  > test_check("geofacet")
  ── 1. Error: grids all load and work correctly (@test-grids.R#6)  ──────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: grid_preview(grd) at testthat/test-grids.R:6
  2: plot(p)
  3: plot.ggplot(p)
  4: grid.draw(gtable)
  5: grid.draw.gTree(gtable)
  6: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  7: drawGTree(x)
  8: preDraw(x)
  9: preDraw.gTree(x)
  10: pushvpgp(x)
  11: pushgrobvp(x$vp)
  12: pushgrobvp.viewport(x$vp)
  13: pushViewport(vp, recording = FALSE)
  14: lapply(vps, push.vp, recording)
  15: FUN(X[[i]], ...)
  16: push.vp.viewport(X[[i]], ...)
  17: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 4 FAILED: 1
  1. Error: grids all load and work correctly (@test-grids.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
SimTangleData: no visible global function definition for ‘runif’
SimTangleData: no visible global function definition for ‘dist’
SimTangleData: no visible global function definition for ‘rnorm’
SimTangleData: no visible global function definition for ‘qgamma’
SimTangleData: no visible global function definition for ‘pnorm’
SimTangleData: no visible global function definition for ‘rmultinom’
TangleInference: no visible global function definition for ‘rnorm’
TangleInferenceGauss : thetaOpt: no visible global function definition
  for ‘dist’
TangleInferenceGauss : thetaOpt: no visible global function definition
  for ‘optim’
TangleInferenceGauss : predError: no visible global function definition
  for ‘dist’
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
Running examples in ‘GeomComb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.foreccomb_res
> ### Title: Plot results from forecast combination model
> ### Aliases: plot.foreccomb_res
> 
> ### ** Examples
> 
> obs <- rnorm(100)
> preds <- matrix(rnorm(1000, 1), 100, 10)
> train_o<-obs[1:80]
> train_p<-preds[1:80,]
> test_o<-obs[81:100]
> test_p<-preds[81:100,]
> 
> data<-foreccomb(train_o, train_p, test_o, test_p)
> fit <- comb_EIG1(data)
> plot(fit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘geomnet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: football
> ### Title: College football games network (undirected)
> ### Aliases: football
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # data step: merge vertices and edges
> ftnet <- merge(
+   football$edges, football$vertices,
+   by.x = "from", by.y = "label", all = TRUE
+ )
> 
> # label independent schools
> ftnet$schools <- ifelse(ftnet$value == "Independents", ftnet$from, "")
> 
> library(geomnet)
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> # create data plot
> ggplot(data = ftnet,
+        aes(from_id = from, to_id = to)) +
+   geom_net(
+     aes(
+       colour = value, group = value,
+       linetype = factor(1-same.conf),
+       label = schools
+     ),
+     linewidth = 0.5,
+     size = 5, vjust = -0.75, alpha = 0.3,
+     layout.alg = 'fruchtermanreingold'
+   ) +
+   theme_net() +
+   theme(legend.position = "bottom") +
+   scale_colour_brewer("Conference", palette = "Paired")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
geoscaleBox: no visible global function definition for ‘boxplot’
geoscaleBox: no visible global function definition for ‘par’
geoscaleBox: no visible global function definition for ‘plot’
geoscaleBox: no visible global function definition for ‘text’
geoscaleBox: no visible global function definition for ‘segments’
geoscaleBox: no visible global function definition for ‘rect’
geoscaleBox: no visible global function definition for ‘rgb’
geoscaleBox: no visible global function definition for ‘polygon’
geoscaleBox: no visible global function definition for ‘points’
geoscaleBox: no visible global function definition for ‘axis’
geoscalePlot: no visible global function definition for ‘par’
geoscalePlot: no visible global function definition for ‘plot’
geoscalePlot: no visible global function definition for ‘text’
geoscalePlot: no visible global function definition for ‘segments’
geoscalePlot: no visible global function definition for ‘rect’
geoscalePlot: no visible global function definition for ‘rgb’
geoscalePlot: no visible global function definition for ‘points’
geoscalePlot: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis boxplot par plot points polygon rect rgb segments text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "boxplot", "par", "plot", "points",
             "polygon", "rect", "segments", "text")
to your NAMESPACE file.
ImagePoly: no visible global function definition for ‘plot’
performSinglePlot: no visible global function definition for
  ‘heat.colors’
Undefined global functions or variables:
  heat.colors plot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "plot")
to your NAMESPACE file.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Running examples in ‘geotoolsR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gboot_solow
> ### Title: Solow bootstrap
> ### Aliases: gboot_solow
> ### Keywords: Bootstrap Solow Spatial
> 
> ### ** Examples
> 
> # Example 1
> 
> ## transforming the data.frame in an object of class geodata
> data<- as.geodata(soilmoisture)
> 
> points(data) ## data visualization
> 
> var<- variog(data, max.dist = 140) ## Obtaining the variogram
variog: computing omnidirectional variogram
> plot(var)
> 
> ## Fitting the model
> mod<- variofit(var,ini.cov.pars = c(2,80),nugget = 2,cov.model = "sph")
variofit: covariance model used is spherical 
variofit: weights used: npairs 
variofit: minimisation function used: optim 
> lines(mod, col=2, lwd=2) ##fitted model
> 
> ## Bootstrap procedure
> 
> boot<- gboot_solow(data,var,mod,B=10)
> ## For better Confidence interval, try B=1000
> 
> gboot_CI(boot,digits = 4) ## Bootstrap Confidence Interval
Parameters confidence interval (95%): 
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: gboot_CI ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started.Rmd’ using rmarkdown
Theta parameter estimates have converged...
Theta parameter estimates have converged...
Theta parameter estimates have converged...
Lambda parameter estimates have converged...
Parameter estimates simulate networks that are statistically indistinguishable from observed network on the statistics specified by the user. 
Quitting from lines 207-219 (getting_started.Rmd) 
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘getting_started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting_started.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GerminaR.Rmd’ using rmarkdown
Quitting from lines 214-225 (GerminaR.Rmd) 
Error: processing vignette 'GerminaR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GerminaR.Rmd’

SUMMARY: processing the following file failed:
  ‘GerminaR.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘germinationmetrics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gcdata
> ### Title: Germination count data
> ### Aliases: gcdata
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(gcdata)
> library(ggplot2)
> library(reshape2)
> 
> # Plot partial germination counts over time
> #----------------------------------------------------------------------------
> # Convert wide-from to long-form
> gcdatamelt <- melt(gcdata[, !names(gcdata) %in% c("Total Seeds")],
+                    id.vars = c("Genotype", "Rep"))
> 
> ggplot(gcdatamelt, aes(x = variable, y = value,
+                        group = interaction(Genotype, Rep),
+                        colour = Genotype)) +
+   geom_point(alpha = 0.7) +
+   geom_line(alpha = 0.7) +
+   ylab("Germination count (Partial)") +
+   xlab("Intervals") +
+   theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Quitting from lines 351-351 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
GESTr: no visible global function definition for ‘rnorm’
GESTr: no visible global function definition for ‘sd’
GESTr : <anonymous>: no visible global function definition for ‘pnorm’
TranSAM : magChange: no visible global function definition for ‘median’
TranSAM : dstat: no visible global function definition for ‘sd’
TranSAM: no visible binding for global variable ‘sd’
TranSAM: no visible global function definition for ‘quantile’
findReplicateGroups: no visible global function definition for ‘qnorm’
findReplicateGroups: no visible global function definition for ‘sd’
fitGMM : simulateData: no visible global function definition for
  ‘rnorm’
fitGMM : simulateData: no visible global function definition for ‘sd’
fitGMM: no visible global function definition for ‘median’
fitGMM: no visible global function definition for ‘ks.test’
fitRockeDurbin: no visible global function definition for ‘dist’
fitRockeDurbin : findLowGenes: no visible global function definition
  for ‘median’
fitRockeDurbin : findLowGenes: no visible global function definition
  for ‘mad’
fitRockeDurbin: no visible binding for global variable ‘sd’
getMonotonicConfidences_multiclass: no visible global function
  definition for ‘pnorm’
getMonotonicConfidences_multiclass: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  dist ks.test mad median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "dist", "ks.test", "mad", "median", "pnorm",
             "qnorm", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ghfd-vignette-LOB.Rmd’ using rmarkdown
--- finished re-building ‘ghfd-vignette-LOB.Rmd’

--- re-building ‘ghfd-vignette-Orders.Rmd’ using rmarkdown
--- finished re-building ‘ghfd-vignette-Orders.Rmd’

--- re-building ‘ghfd-vignette-Trades.Rmd’ using rmarkdown
Quitting from lines 75-80 (ghfd-vignette-Trades.Rmd) 
Error: processing vignette 'ghfd-vignette-Trades.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ghfd-vignette-Trades.Rmd’

SUMMARY: processing the following file failed:
  ‘ghfd-vignette-Trades.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gld_vignette-ReadLattes.Rmd’ using rmarkdown
Quitting from lines 83-91 (gld_vignette-ReadLattes.Rmd) 
Error: processing vignette 'gld_vignette-ReadLattes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gld_vignette-ReadLattes.Rmd’

SUMMARY: processing the following file failed:
  ‘gld_vignette-ReadLattes.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘getmstatistic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getmstatistic
> ### Title: Quantifying Systematic Heterogeneity in Meta-Analysis.
> ### Aliases: getmstatistic getm getmstat Rgetmstatistic
> ###   getmstatistic.default
> 
> ### ** Examples
> 
> library(getmstatistic)
> library(gridExtra)
> 
> 
> # Basic M analysis using the heartgenes214 dataset.
> # heartgenes214 is a multi-ethnic GWAS meta-analysis dataset for coronary artery disease.
> # To learn more about the heartgenes214 dataset ?heartgenes214
> 
> # Running an M analysis on 20 GWAS significant variants (p < 5e-08) in the first 10 studies
> 
> heartgenes44_10studies <- subset(heartgenes214, studies <= 10 & fdr214_gwas46 == 2) 
> heartgenes20_10studies <- subset(heartgenes44_10studies, 
+     variants %in% unique(heartgenes44_10studies$variants)[1:20])
> 
> getmstatistic_results <- getmstatistic(heartgenes20_10studies$beta_flipped, 
+                                         heartgenes20_10studies$gcse, 
+                                         heartgenes20_10studies$variants, 
+                                         heartgenes20_10studies$studies)

Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: getmstatistic ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' call to ‘party’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘party’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gTree: no visible global function definition for ‘ctree’
gTree: no visible global function definition for ‘ctree_control’
guttmanErrors: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ctree ctree_control runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘getTBinR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: map_tb_burden
> ### Title: Map TB Burden
> ### Aliases: map_tb_burden
> 
> ### ** Examples
> 
> 
> ## Map raw incidence rates
> map_tb_burden()
Loading data from: /home/hornik/tmp/scratch/RtmpaRdRBu/TB_burden.rds
Loading data from: /home/hornik/tmp/scratch/RtmpaRdRBu/MDR_TB.rds
Joining TB burden data and MDR TB data.
Loading data from: /home/hornik/tmp/scratch/RtmpaRdRBu/TB_data_dict.rds
1 results found for your variable search for e_inc_100k
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gtdd-vignette_GetTDData.Rmd’ using rmarkdown
Quitting from lines 44-49 (gtdd-vignette_GetTDData.Rmd) 
Error: processing vignette 'gtdd-vignette_GetTDData.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gtdd-vignette_GetTDData.Rmd’

--- re-building ‘gtdd-vignette_YieldCurve.Rmd’ using rmarkdown
Quitting from lines 26-36 (gtdd-vignette_YieldCurve.Rmd) 
Error: processing vignette 'gtdd-vignette_YieldCurve.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gtdd-vignette_YieldCurve.Rmd’

SUMMARY: processing the following files failed:
  ‘gtdd-vignette_GetTDData.Rmd’ ‘gtdd-vignette_YieldCurve.Rmd’

Error: Vignette re-building failed.
Execution halted
Missing or unexported object: ‘stable::dstable.quick’
'library' or 'require' call to ‘multtest’ which was already attached by Depends.
  Please remove these calls from your code.
src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
Running examples in ‘ggallin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: %of%
> ### Title: Composition of scale transforms.
> ### Aliases: %of%
> ### Keywords: plotting
> 
> ### ** Examples
> 
> set.seed(1234)
> # compose transformatins with %of%:
> ggplot(data.frame(x=rnorm(100),y=exp(rnorm(100,mean=-2,sd=4))),aes(x=x,y=y)) + 
+   geom_point() + 
+   scale_y_continuous(trans=scales::reverse_trans() %of% scales::log10_trans())
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggalluvial.rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 33-43 (ggalluvial.rmd) 
Error: processing vignette 'ggalluvial.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggalluvial.rmd’

--- re-building ‘labels.rmd’ using rmarkdown
Quitting from lines 31-40 (labels.rmd) 
Error: processing vignette 'labels.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘labels.rmd’

SUMMARY: processing the following files failed:
  ‘ggalluvial.rmd’ ‘labels.rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘GGally-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getPlot
> ### Title: getPlot
> ### Aliases: getPlot [.ggmatrix
> ### Keywords: hplot
> 
> ### ** Examples
> 
>  data(tips, package = "reshape")
>  plotMatrix2 <- ggpairs(tips[, 3:2], upper = list(combo = "denstrip"))
>  plotMatrix2[1, 2]
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 22 rows containing missing values (geom_bar).
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘ggalt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate_textp
> ### Title: Text annotations in plot coordinate system
> ### Aliases: annotate_textp
> 
> ### ** Examples
> 
> p <- ggplot(mtcars, aes(x = wt, y = mpg)) + geom_point()
> p <- p + geom_smooth(method = "lm", se = FALSE)
> p + annotate_textp(x = 0.9, y = 0.35, label="A relative linear\nrelationship", hjust=1, color="red")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggalt_examples.Rmd’ using rmarkdown
Quitting from lines 33-71 (ggalt_examples.Rmd) 
Error: processing vignette 'ggalt_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggalt_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘ggalt_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gganimate.Rmd’ using rmarkdown
Quitting from lines 38-45 (gganimate.Rmd) 
Error: processing vignette 'gganimate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gganimate.Rmd’

SUMMARY: processing the following file failed:
  ‘gganimate.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggasym-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: continuous_scale_asym
> ### Title: Continuous scale constructor for 'ggasym'
> ### Aliases: continuous_scale_asym
> 
> ### ** Examples
> 
> library(tibble)
> library(ggplot2)
> tib <- tibble(g1 = c("A", "A", "B"),
+               g2 = c("B", "C", "C"),
+               val_1 = c(1, 2, 3),
+               val_2 = c(-1, 0, 1))
> 
> tib
# A tibble: 3 x 4
  g1    g2    val_1 val_2
  <chr> <chr> <dbl> <dbl>
1 A     B         1    -1
2 A     C         2     0
3 B     C         3     1
> 
> tib <- asymmetrise(tib, g1, g2)
> ggplot(tib) +
+ geom_asymmat(aes(x = g1, y = g2, fill_tl = val_1, fill_br = val_2)) +
+     scale_fill_tl_gradient(low = "lightpink", high = "tomato") +
+     scale_fill_br_gradient(low = "lightblue1", high = "dodgerblue") +
+     labs(fill_tl =  "top-left fill", fill_br = "bottom-right fill")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggasym-stats.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 86-90 (ggasym-stats.Rmd) 
Error: processing vignette 'ggasym-stats.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggasym-stats.Rmd’

SUMMARY: processing the following file failed:
  ‘ggasym-stats.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggbeeswarm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_beeswarm
> ### Title: Points, jittered to reduce overplotting using the beeswarm
> ###   package
> ### Aliases: geom_beeswarm
> 
> ### ** Examples
> 
> 
>   ggplot2::qplot(class, hwy, data = ggplot2::mpg, geom='beeswarm')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘usageExamples.Rnw’ using Sweave
Loading required package: ggplot2
Error: processing vignette 'usageExamples.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘usageExamples.Rnw’

SUMMARY: processing the following file failed:
  ‘usageExamples.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggbuildr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_plot
> ### Title: Incrementally build and save layers of a ggplot object into
> ###   numbered files
> ### Aliases: build_plot
> 
> ### ** Examples
> 
> X <- rnorm(20)
> Y <- X + rnorm(20)
> 
> set.seed(1)
> pd <- data.frame(X, Y)
> p <- ggplot(pd, aes(X, Y)) +
+   geom_smooth() +
+   geom_point()
> 
> # Plot smooth, and then point
> build_plot(p, build_order = list(1, 2))
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: build_plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggbuildr)
  Loading required package: ggplot2
  > 
  > test_check("ggbuildr")
  ── 1. Error: build_plot creates correct number of files (@test-build_plot.R#28) 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: build_plot(p, filepath, build_order = list(1, 2)) at testthat/test-build_plot.R:28
  2: .write_plot(plot, file.path(dir, paste0(filename, ".", ext)), ...)
  3: ggsave(plotpath, plot = p, ...)
  4: grid.draw(plot)
  5: grid.draw.ggplot(plot)
  6: print(x)
  7: print.ggplot(x)
  8: grid.draw(gtable)
  9: grid.draw.gTree(gtable)
  10: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  11: drawGTree(x)
  12: preDraw(x)
  13: preDraw.gTree(x)
  14: pushvpgp(x)
  15: pushgrobvp(x$vp)
  16: pushgrobvp.viewport(x$vp)
  17: pushViewport(vp, recording = FALSE)
  18: lapply(vps, push.vp, recording)
  19: FUN(X[[i]], ...)
  20: push.vp.viewport(X[[i]], ...)
  21: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: build_plot creates correct number of files (@test-build_plot.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ggChernoff-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_chernoff
> ### Title: Chernoff faces in ggplot2
> ### Aliases: geom_chernoff
> 
> ### ** Examples
> 
> library(ggplot2)
> ggplot(iris, aes(Sepal.Width, Sepal.Length, smile = Petal.Length, fill = Species)) +
+   geom_chernoff()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggconf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme2
> ### Title: an enhanced version of ggplot2::theme()
> ### Aliases: theme2
> 
> ### ** Examples
> 
> 
> if (requireNamespace("ggplot2", quietly = TRUE)) {
+ 
+ library(ggplot2)
+ ggplot(mtcars) + geom_point(aes(wt, hp, color=as.factor(cyl))) +
+   theme2(
+     text(f="bold", z=24, fmly="Times New Roman"),
+     pnl.bg(fill="white"),
+     lgd.box.margin(.2, .2, .2, .2, "cm"),
+     lgd.box.bg(c="black"),
+     lgd.key(fill="white"),
+     lgd.position("bottom"),
+     lgd.txt(z=rel(.8)),
+     lgd.title(fmly="Consolas", c="royalblue"),  
+     axs.title(fmly="Consolas", c="royalblue"),  
+     axs.title.y(angle=0, vjust=.5),             
+     axs.txt(z=rel(1.1)),
+     axs.line(arrow=arrow(type="open", angle=20), z=2),
+     axs.tick(z=1),                              
+     axs.tick.len(.5, "cm"),
+     plt.subttl(f="plain", hjust=1),
+     plt.margin(.3, .3, .3, .1, "inch")          
+   )
+ 
+ 
+ ggplot(mtcars) + geom_point(aes(wt, hp, color=cyl)) +
+    theme2(a.txt(family = c("Consolas", "Times")[1]))
+ 
+ # all of the following three generate the same plot
+ 
+ ggplot(mtcars) + geom_point(aes(wt, hp, color=cyl)) +
+    theme(text = element_text(size=20, face="bold"),
+    axis.line = element_line(size=2),
+    legend.key = element_rect(color="black"))
+ 
+ ggplot(mtcars) + geom_point(aes(wt, hp, color=cyl)) +
+    theme2(text(size=20, face="bold"), axis.line(size=2),
+           legend.key(color="black"))
+ 
+ ggplot(mtcars) + geom_point(aes(wt, hp, color=cyl)) +
+    theme2(txt(sz=20, f="bold"), aline(sz=2), l.key(c="black"))
+ 
+ 
+ 
+ }
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-ggconf.Rmd’ using rmarkdown
Quitting from lines 22-24 (Introduction-to-ggconf.Rmd) 
Error: processing vignette 'Introduction-to-ggconf.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction-to-ggconf.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-ggconf.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggdag-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Covariate Adjustment Sets
> ### Title: Covariate Adjustment Sets
> ### Aliases: 'Covariate Adjustment Sets' dag_adjustment_sets
> ###   ggdag_adjustment_set
> 
> ### ** Examples
> 
> dag <- dagify(y ~ x + z2 + w2 + w1,
+   x ~ z1 + w1,
+   z1 ~ w1 + v,
+   z2 ~ w2 + v,
+   w1 ~~ w2,
+   exposure = "x",
+   outcome = "y")
> 
> tidy_dagitty(dag) %>% dag_adjustment_sets()
# A tibble: 36 x 10
   name      x     y direction to     xend  yend circular adjusted   set       
   <chr> <dbl> <dbl> <fct>     <chr> <dbl> <dbl> <lgl>    <chr>      <chr>     
 1 v      23.5  16.9 ->        z1     22.6  16.0 FALSE    unadjusted w1, w2, z2
 2 v      23.5  16.9 ->        z2     24.5  15.9 FALSE    unadjusted w1, w2, z2
 3 w1     23.4  15.1 ->        x      22.5  14.7 FALSE    adjusted   w1, w2, z2
 4 w1     23.4  15.1 ->        y      23.9  14.6 FALSE    adjusted   w1, w2, z2
 5 w1     23.4  15.1 ->        z1     22.6  16.0 FALSE    adjusted   w1, w2, z2
 6 w1     23.4  15.1 <->       w2     24.8  14.9 FALSE    adjusted   w1, w2, z2
 7 w2     24.8  14.9 ->        y      23.9  14.6 FALSE    adjusted   w1, w2, z2
 8 w2     24.8  14.9 ->        z2     24.5  15.9 FALSE    adjusted   w1, w2, z2
 9 x      22.5  14.7 ->        y      23.9  14.6 FALSE    unadjusted w1, w2, z2
10 z1     22.6  16.0 ->        x      22.5  14.7 FALSE    unadjusted w1, w2, z2
# … with 26 more rows
> 
> ggdag_adjustment_set(dag)
Error in Summary.unit(c(4.8, 4.8), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘ggdark-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dark_mode
> ### Title: Activate dark mode on a 'ggplot2' theme
> ### Aliases: dark_mode
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> p1 <- ggplot(iris, aes(Sepal.Width, Sepal.Length, color = Species)) +
+   geom_point()
> 
> p1  # theme returned by theme_get()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggdendro-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dendro_data
> ### Title: Extract cluster data from a model into a list of data frames.
> ### Aliases: dendro_data dendro_data.default dendro_data.dendrogram
> ###   dendro_data.hclust dendro_data.twins
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
> 
> ### Demonstrate dendro_data.dendrogram
> 
> model <- hclust(dist(USArrests), "ave")
> dendro <- as.dendrogram(model)
> 
> # Rectangular lines
> ddata <- dendro_data(dendro, type="rectangle")
> ggplot(segment(ddata)) + 
+   geom_segment(aes(x=x, y=y, xend=xend, yend=yend)) + 
+   coord_flip() + 
+   scale_y_reverse(expand=c(0.2, 0)) + 
+   theme_dendro()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggdendro.Rmd’ using knitr
Quitting from lines 42-44 (ggdendro.Rmd) 
Error: processing vignette 'ggdendro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggdendro.Rmd’

SUMMARY: processing the following file failed:
  ‘ggdendro.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggdistribute-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate_corner
> ### Title: Write text to one of four corners of a plot
> ### Aliases: annotate_corner
> 
> ### ** Examples
> 
> posterior_plot() + annotate_corner("Hi.", "bottomright")
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘geom_posterior.Rmd’ using rmarkdown
Quitting from lines 54-58 (geom_posterior.Rmd) 
Error: processing vignette 'geom_posterior.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘geom_posterior.Rmd’

SUMMARY: processing the following file failed:
  ‘geom_posterior.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggdmc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_prior
> ### Title: Plot prior distributions
> ### Aliases: plot_prior plot.prior
> 
> ### ** Examples
> 
> p.prior <- BuildPrior(
+            dists = rep("tnorm", 7),
+            p1    = c(a = 2,   v.f1 = 4,  v.f2 = 3,  z = 0.5, sv = 1,
+                      sz = 0.3, t0 = 0.3),
+            p2    = c(a = 0.5, v.f1 = .5, v.f2 = .5, z = 0.1, sv = .3,
+                      sz = 0.1, t0 = 0.05),
+            lower = c(0,-5, -5, 0, 0, 0, 0),
+            upper = c(5, 7,  7, 1, 2, 1, 1))
> 
> plot_prior("a", p.prior)
Error in Summary.unit(c(6.4, 6.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_prior ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘GGEBiplots-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CompareGens
> ### Title: Compare two genotypes biplot
> ### Aliases: CompareGens
> ### Keywords: GGE
> 
> ### ** Examples
> 
> library(GGEBiplotGUI)
Loading required package: rgl
Loading required package: tcltk
Loading required package: tkrplot
> data(Ontario)
> GGE1<-GGEModel(Ontario)
> CompareGens(GGE1,"cas","luc")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggedit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.ggedit
> ### Title: Try to coerce a ggplot object into a ggedit object
> ### Aliases: as.ggedit
> 
> ### ** Examples
> 
> 
> p  <- ggplot2::ggplot(iris,ggplot2::aes(x =Sepal.Length,y=Sepal.Width))
> 
> p1 <- p + 
+ ggplot2::geom_point(ggplot2::aes(colour=Species)) + 
+ ggplot2::geom_line()
> 
> p2 <- p + 
+ ggplot2::geom_point() + 
+ ggplot2::geom_smooth(method='loess')
> 
> p3 <- list(p1,p2)
> 
> p4 <- as.ggedit(p3)
> 
> p4
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggeffects-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_title
> ### Title: Get titles and labels from data
> ### Aliases: get_title get_x_title get_y_title get_legend_title
> ###   get_legend_labels get_x_labels get_complete_df
> 
> ### ** Examples
> 
> data(efc)
> efc$c172code <- sjmisc::to_factor(efc$c172code)
> fit <- lm(barthtot ~ c12hour + neg_c_7 + c161sex + c172code, data = efc)
> 
> mydf <- ggpredict(fit, terms = c("c12hour", "c161sex", "c172code"))
> 
> library(ggplot2)
> ggplot(mydf, aes(x = x, y = predicted, colour = group)) +
+   stat_smooth(method = "lm") +
+   facet_wrap(~facet, ncol = 2) +
+   labs(
+     x = get_x_title(mydf),
+     y = get_y_title(mydf),
+     colour = get_legend_title(mydf)
+   )
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘ggenealogy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotAncDes
> ### Title: Returns the image object to show the ancestors and descendants
> ###   of a variety
> ### Aliases: plotAncDes
> 
> ### ** Examples
> 
> data(sbGeneal)
> plotAncDes("Tokyo", sbGeneal, vColor = "red")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggenealogy.Rnw’ using Sweave
dfToIG               package:ggenealogy                R Documentation

_P_r_o_c_e_s_s _t_h_e _g_e_n_e_a_l_o_g_y _g_r_a_p_h

_D_e_s_c_r_i_p_t_i_o_n:

     Processes the genealogy into an igraph object with appropriate
     vertex information, graph type, and edge weights.

_U_s_a_g_e:

     dfToIG(geneal, vertexinfo = NULL, edgeweights = 1, isDirected = FALSE)
     
_A_r_g_u_m_e_n_t_s:

  geneal: the full genealogy (in data frame format)

vertexinfo: (default NULL) either names of columns in the genealogy
          which should be added to the database as vertex information
          or a data frame with information for all vertices such that
          the first column contains vertex names.

edgeweights: (default 1) name of a column which contains edge weights

isDirected: (default FALSE) should the graph be a directed graph?

_S_e_e _A_l_s_o:

     <URL: https://www.r-project.org> for iGraph information


Error: processing vignette 'ggenealogy.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggenealogy.Rnw’

SUMMARY: processing the following file failed:
  ‘ggenealogy.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggetho-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_peak
> ### Title: Visualise peaks in a power spectrum or periodogram
> ### Aliases: geom_peak
> 
> ### ** Examples
> 
> # We make a data frame by hand with five rows
> # There are two peaks: in position 4 and 2
> 
> df <- data.frame(x = hours(1:5),
+                  y = c(1, 2, 0, 4, 1),
+                  peak = c(0, 2, 0, 1, 0))
> #  We draw the plot as a line
> pl <-  ggplot(df, aes(x, y, peak = peak)) +
+                   geom_line() +
+                   scale_x_hours()
> pl
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggExtra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggMarginal
> ### Title: Add marginal density/histogram to ggplot2 scatterplots
> ### Aliases: ggMarginal
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # basic usage
> p <- ggplot(mtcars, aes(wt, mpg)) + geom_point()
> ggMarginal(p)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggExtra.Rmd’ using rmarkdown
Quitting from lines 81-85 (ggExtra.Rmd) 
Error: processing vignette 'ggExtra.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggExtra.Rmd’

SUMMARY: processing the following file failed:
  ‘ggExtra.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggfan-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_fan
> ### Title: Fan plot visualising intervals of a distribution
> ### Aliases: geom_fan
> 
> ### ** Examples
> 
> 
> # Basic use. The data frame must have multiple y values for each
> # x
> library(ggplot2)
> 
> ggplot(fake_df, aes(x=x,y=y)) +geom_fan()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘geom_fan.Rmd’ using rmarkdown
Quitting from lines 59-62 (geom_fan.Rmd) 
Error: processing vignette 'geom_fan.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘geom_fan.Rmd’

--- re-building ‘ggfan_stan.Rmd’ using rmarkdown
Quitting from lines 107-108 (ggfan_stan.Rmd) 
Error: processing vignette 'ggfan_stan.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggfan_stan.Rmd’

SUMMARY: processing the following files failed:
  ‘geom_fan.Rmd’ ‘ggfan_stan.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggfocus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggfocus
> ### Title: ggfocus
> ### Aliases: ggfocus
> 
> ### ** Examples
> 
> library(ggplot2)
> p <- ggplot(iris,aes(x=Sepal.Length,y=Petal.Length)) + geom_point()
> ggfocus(p, Species, "versicolor")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘a-quick-guide-to-ggfocus.Rmd’ using rmarkdown
Quitting from lines 42-48 (a-quick-guide-to-ggfocus.Rmd) 
Error: processing vignette 'a-quick-guide-to-ggfocus.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘a-quick-guide-to-ggfocus.Rmd’

SUMMARY: processing the following file failed:
  ‘a-quick-guide-to-ggfocus.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggforce-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: facet_grid_paginate
> ### Title: Split facet_grid over multiple plots
> ### Aliases: facet_grid_paginate
> 
> ### ** Examples
> 
> # Draw a small section of the grid
> ggplot(diamonds) +
+   geom_point(aes(carat, price), alpha = 0.1) +
+   facet_grid_paginate(color ~ cut:clarity, ncol = 3, nrow = 3, page = 4)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Visual_Guide.Rmd’ using rmarkdown
Quitting from lines 72-96 (Visual_Guide.Rmd) 
Error: processing vignette 'Visual_Guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Visual_Guide.Rmd’

SUMMARY: processing the following file failed:
  ‘Visual_Guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggformula-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_lm
> ### Title: Linear Model Displays
> ### Aliases: stat_lm geom_lm
> 
> ### ** Examples
> 
> ggplot(data = mosaicData::KidsFeet, aes(y = length, x = width, color = sex)) +
+   geom_lm() +
+   geom_point()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggformula-blog.Rmd’ using rmarkdown
Quitting from lines 144-146 (ggformula-blog.Rmd) 
Error: processing vignette 'ggformula-blog.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggformula-blog.Rmd’

--- re-building ‘ggformula.Rmd’ using rmarkdown
Quitting from lines 94-96 (ggformula.Rmd) 
Error: processing vignette 'ggformula.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggformula.Rmd’

SUMMARY: processing the following files failed:
  ‘ggformula-blog.Rmd’ ‘ggformula.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggfortify-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.aareg
> ### Title: Autoplot 'survival::aareg'
> ### Aliases: autoplot.aareg
> 
> ### ** Examples
> 
> library(survival)
> autoplot(aareg(Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1))
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘gggenes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_gene_arrow
> ### Title: A 'ggplot2' geom to draw genes as arrows
> ### Aliases: geom_gene_arrow
> 
> ### ** Examples
> 
> 
> ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
+                                             y = molecule, fill = gene)) +
+ geom_gene_arrow() +
+ ggplot2::facet_wrap(~ molecule, scales = "free")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-gggenes.Rmd’ using rmarkdown
Quitting from lines 37-43 (introduction-to-gggenes.Rmd) 
Error: processing vignette 'introduction-to-gggenes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction-to-gggenes.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-gggenes.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggghost-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: -.gg
> ### Title: Remove a call from a ggghost object
> ### Aliases: -.gg
> 
> ### ** Examples
> 
> ## create a ggghost object
> tmpdata <- data.frame(x = 1:100, y = rnorm(100))
> 
> z %g<% ggplot(tmpdata, aes(x,y))
> z <- z + geom_point(col = "steelblue")
> z <- z + theme_bw()
> z <- z + labs(title = "My cool ggplot")
> z <- z + labs(x = "x axis", y = "y axis")
> z <- z + geom_smooth()
> 
> ## remove the geom_smooth
> z - geom_smooth()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggguitar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tablature
> ### Title: Create guitar chord tablature chart.
> ### Aliases: tablature
> 
> ### ** Examples
> 
> tablature('G Major', c(3, 2, 0, 0, 0, 3))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 40-41 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘gghalfnorm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gghalfnorm
> ### Title: Half Normal Plot
> ### Aliases: gghalfnorm
> 
> ### ** Examples
> 
> set.seed(100)
> gghalfnorm(x = rnorm(100), nlab = 10)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘gghighlight-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gghighlight
> ### Title: Highlight Data With Predicate
> ### Aliases: gghighlight
> 
> ### ** Examples
> 
> d <- data.frame(
+   idx = c( 1, 1, 1, 2, 2, 2, 3, 3, 3),
+   value = c( 1, 2, 3,10,11,12, 9,10,11),
+   category = rep(c("a","b","c"), 3),
+   stringsAsFactors = FALSE
+ )
> 
> # highlight the lines whose max values are larger than 10
> ggplot(d, aes(idx, value, colour = category)) +
+   geom_line() + gghighlight(max(value) > 10)
label_key: category
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gghighlight.Rmd’ using rmarkdown
Quitting from lines 39-43 (gghighlight.Rmd) 
Error: processing vignette 'gghighlight.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gghighlight.Rmd’

SUMMARY: processing the following file failed:
  ‘gghighlight.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggimage-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_image
> ### Title: geom_image
> ### Aliases: geom_image
> 
> ### ** Examples
> 
> library("ggplot2")
> library("ggimage")
> set.seed(2017-02-21)
> d <- data.frame(x = rnorm(10),
+                 y = rnorm(10),
+                 image = sample(c("https://www.r-project.org/logo/Rlogo.png",
+                                 "https://jeroenooms.github.io/images/frink.png"),
+                               size=10, replace = TRUE)
+                )
> ggplot(d, aes(x, y)) + geom_image(aes(image=image))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggimage.Rmd’ using rmarkdown
Quitting from lines 35-54 (ggimage.Rmd) 
Error: processing vignette 'ggimage.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggimage.Rmd’

SUMMARY: processing the following file failed:
  ‘ggimage.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘gginference-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggaov
> ### Title: Anova F test plot
> ### Aliases: ggaov
> 
> ### ** Examples
> 
> # 21-th day
> chick21 <- ChickWeight[ChickWeight$Time == 21,]
> chickaov <- aov(weight~Diet, data = chick21)
> summary(chickaov)
            Df Sum Sq Mean Sq F value  Pr(>F)   
Diet         3  57164   19055   4.655 0.00686 **
Residuals   41 167839    4094                   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> 
> ggaov(chickaov, colaccept = "grey89", colreject = "black")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘gginnards-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: delete_layers
> ### Title: Layer manipulation.
> ### Aliases: delete_layers append_layers move_layers shift_layers
> ###   which_layers extract_layers top_layer bottom_layer num_layers
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> df <- data.frame(
+   gp = factor(rep(letters[1:3], each = 10)),
+   y = rnorm(30)
+ )
> p <- ggplot(df, aes(gp, y)) +
+      geom_point() +
+      stat_summary(fun.data = "mean_se", colour = "red")
> p
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide-1.Rmd’ using rmarkdown
Quitting from lines 62-63 (user-guide-1.Rmd) 
Error: processing vignette 'user-guide-1.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide-1.Rmd’

--- re-building ‘user-guide-2.Rmd’ using rmarkdown
Quitting from lines 109-114 (user-guide-2.Rmd) 
Error: processing vignette 'user-guide-2.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide-2.Rmd’

SUMMARY: processing the following files failed:
  ‘user-guide-1.Rmd’ ‘user-guide-2.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggiraphExtra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggAncova
> ### Title: Make an interactive plot for an ANCOVA model
> ### Aliases: ggAncova ggAncova.default ggAncova.formula ggAncova.lm
> 
> ### ** Examples
> 
> require(moonBook)
Loading required package: moonBook

Attaching package: ‘moonBook’

The following objects are masked from ‘package:ggiraphExtra’:

    addLabelDf, getMapping

> require(ggplot2)
Loading required package: ggplot2
> require(ggiraph)
Loading required package: ggiraph
> ggAncova(radial,aes(age,NTAV,color=sex),interactive=TRUE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ggAncova ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggPredict.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 38-40 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘ggPredict.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggiraph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_bar_interactive
> ### Title: interactive bars
> ### Aliases: geom_bar_interactive
> 
> ### ** Examples
> 
> library(ggplot2)
> g <- ggplot(mpg, aes( x = class, tooltip = class,
+         data_id = class ) ) +
+   geom_bar_interactive()
> ggiraph(code = print(g))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ggiraph ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Running examples in ‘gglogo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: letterToPolygon
> ### Title: Convert an image file to a polygon
> ### Aliases: letterToPolygon
> 
> ### ** Examples
> 
> library(ggplot2)

Attaching package: ‘ggplot2’

The following object is masked from ‘package:gglogo’:

    fortify

> letter <- letterToPolygon("R", fontfamily="Helvetica")
> qplot(x, y, geom="polygon", data = letter, fill=I("black"), alpha=I(0.8))+
+      coord_equal()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gglogo-alphabet.Rmd’ using rmarkdown

Attaching package: 'gglogo'

The following object is masked from 'package:ggplot2':

    fortify

Quitting from lines 34-37 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gglogo-alphabet.Rmd’

SUMMARY: processing the following file failed:
  ‘gglogo-alphabet.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 107-110 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘gglorenz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_lorenz
> ### Title: Values of Ordinary Lorenz Curve
> ### Aliases: stat_lorenz
> 
> ### ** Examples
> 
> library(gglorenz)
> 
> ggplot(billionaires, aes(TNW)) +
+     stat_lorenz()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggimage
> ### Title: Plot an image using ggplot2
> ### Aliases: ggimage
> 
> ### ** Examples
> 
> 
> img <- matrix(1:16, 4, 4)
> image(img)
> ggimage(t(img[,4:1]), fullpage = FALSE, scale_axes = TRUE)
rescaling mat to [0,1]...
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggmcmc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggmcmc
> ### Title: Wrapper function that creates a single pdf file with all plots
> ###   that ggmcmc can produce.
> ### Aliases: ggmcmc ggmcmc-package
> 
> ### ** Examples
> 
> data(linear)
> ggmcmc(ggs(s))  # Directly from a coda object
Plotting histograms
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ggmcmc ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_ggmcmc.Rmd’ using rmarkdown
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: tidyr
Loading required package: ggplot2
Quitting from lines 133-134 (using_ggmcmc.Rmd) 
Error: processing vignette 'using_ggmcmc.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using_ggmcmc.Rmd’

--- re-building ‘v70i09.Rnw’ using knitr
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: tidyr
Loading required package: ggplot2
Loading required package: gridExtra

Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine

Quitting from lines 240-245 (v70i09.Rnw) 
Error: processing vignette 'v70i09.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘v70i09.Rnw’

SUMMARY: processing the following files failed:
  ‘using_ggmcmc.Rmd’ ‘v70i09.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggmosaic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_mosaic
> ### Title: Mosaic plots.
> ### Aliases: geom_mosaic stat_mosaic
> 
> ### ** Examples
> 
> 
> data(Titanic)
> titanic <- as.data.frame(Titanic)
> titanic$Survived <- factor(titanic$Survived, levels=c("Yes", "No"))
> 
> 
> ggplot(data=titanic) +
+   geom_mosaic(aes(weight=Freq, x=product(Class), fill=Survived))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggmosaic.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 128-131 (ggmosaic.Rmd) 
Error: processing vignette 'ggmosaic.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggmosaic.Rmd’

SUMMARY: processing the following file failed:
  ‘ggmosaic.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggmuller-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Muller_plot
> ### Title: Draw a Muller plot of frequencies using ggplot2
> ### Aliases: Muller_plot
> 
> ### ** Examples
> 
> # include all genotypes:
> Muller_df1 <- get_Muller_df(example_edges, example_pop_df)
> Muller_plot(Muller_df1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggmuller.Rmd’ using rmarkdown
Quitting from lines 26-29 (ggmuller.Rmd) 
Error: processing vignette 'ggmuller.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggmuller.Rmd’

SUMMARY: processing the following file failed:
  ‘ggmuller.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggnetwork.Rmd’ using rmarkdown
network: Classes for Relational Data
Version 1.14-377 created on 2019-03-04.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.

Loading required package: statnet.common

Attaching package: 'statnet.common'

The following object is masked from 'package:base':

    order

sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.

Quitting from lines 130-133 (ggnetwork.Rmd) 
Error: processing vignette 'ggnetwork.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggnetwork.Rmd’

SUMMARY: processing the following file failed:
  ‘ggnetwork.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggnewscale-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: new_scale
> ### Title: Adds a new scale to a plot
> ### Aliases: new_scale new_scale_fill new_scale_color new_scale_colour
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # Equivalent to melt(volcano), but we don't want to depend on reshape2
> topography <- expand.grid(x = 1:nrow(volcano),
+                           y = 1:ncol(volcano))
> topography$z <- c(volcano)
> 
> # point measurements of something at a few locations
> measurements <- data.frame(x = runif(30, 1, 80),
+                            y = runif(30, 1, 60),
+                            thing = rnorm(30))
> 
> ggplot(mapping = aes(x, y)) +
+   geom_contour(data = topography, aes(z = z, color = stat(level))) +
+   # Color scale for topography
+   scale_color_viridis_c(option = "D") +
+   # geoms below will use another color scale
+   new_scale_color() +
+   geom_point(data = measurements, size = 3, aes(color = thing)) +
+   # Color scale applied to geoms added after new_scale_color()
+   scale_color_viridis_c(option = "A")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggnormalviolin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_normalviolin
> ### Title: Creates normal violins with specified means and standard
> ###   deviations
> ### Aliases: geom_normalviolin
> 
> ### ** Examples
> 
> library(ggplot2)
> library(ggnormalviolin)
> 
> d <- data.frame(
+   Distribution = c("A", "B"),
+   Distribution_mean = c(80, 90),
+   Distribution_sd = c(15, 10)
+ )
> 
> ggplot(data = d, aes(x = Distribution)) +
+   geom_normalviolin(aes(mu = Distribution_mean,
+                       sigma = Distribution_sd))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggparallel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genes
> ### Title: Data linking genes and pathways.
> ### Aliases: genes
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> library(RColorBrewer)
> genes$chrom <- factor(genes$chrom, levels=c(paste("chr", 1:22, sep=""),
+   "chrX", "chrY"))
> ggparallel(
+   list("path", "chrom"),
+   text.offset = c(0.03, 0,-0.03),
+   data = genes,
+   width = 0.1,
+   order = c(1, 0),
+   angle = 0,
+   color = "white",
+   factorlevels =  c(sapply(unique(genes$chrom), as.character),unique(genes$path))
+ ) +
+  scale_fill_manual(
+    values = c(brewer.pal("YlOrRd", n = 9), rep("grey80", 24)),
+    guide = "none"
+  ) +
+  scale_colour_manual(
+    values = c(brewer.pal("YlOrRd", n = 9), rep("grey80", 24)),
+    guide = "none"
+  ) +
+  coord_flip()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggparliament-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw_majoritythreshold
> ### Title: Draw majority threshold
> ### Aliases: draw_majoritythreshold
> 
> ### ** Examples
> 
> data <- election_data[
+   election_data$country == "USA" &
+   election_data$house == "Representatives" &
+   election_data$year == "2016",
+ ]
> usa_data <- parliament_data(
+   election_data = data,
+   type = "semicircle",
+   party_seats = data$seats,
+   parl_rows = 8
+ )
> ggplot2::ggplot(usa_data, ggplot2::aes(x, y, colour = party_long)) +
+   geom_parliament_seats() +
+   draw_majoritythreshold(
+     n = 218,
+     label = TRUE,
+     type = 'semicircle'
+   ) +
+   theme_ggparliament()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggperiodic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: periodic
> ### Title: Add or remove periodic variables
> ### Aliases: periodic periodic.default periodic.data.frame setperiodic
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> x <- seq(0, 360 - 20, by = 20)
> df <- data.frame(x = x, y = cos(x*pi/180))
> df_p <- periodic(df, x = c(0, 360))
> 
> ggplot(df_p, aes(x, y)) +
+    geom_line() +            # periodic data
+    geom_point(data = df)    # non periodic data
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wraping-around-ggplot2.Rmd’ using rmarkdown
Quitting from lines 36-40 (wraping-around-ggplot2.Rmd) 
Error: processing vignette 'wraping-around-ggplot2.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘wraping-around-ggplot2.Rmd’

SUMMARY: processing the following file failed:
  ‘wraping-around-ggplot2.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggplot2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aes
> ### Title: Construct aesthetic mappings
> ### Aliases: aes
> 
> ### ** Examples
> 
> aes(x = mpg, y = wt)
Aesthetic mapping: 
* `x` -> `mpg`
* `y` -> `wt`
> aes(mpg, wt)
Aesthetic mapping: 
* `x` -> `mpg`
* `y` -> `wt`
> 
> # You can also map aesthetics to functions of variables
> aes(x = mpg ^ 2, y = wt / cyl)
Aesthetic mapping: 
* `x` -> `mpg^2`
* `y` -> `wt/cyl`
> 
> # Or to constants
> aes(x = 1, colour = "smooth")
Aesthetic mapping: 
* `x`      -> 1
* `colour` -> "smooth"
> 
> # Aesthetic names are automatically standardised
> aes(col = x)
Aesthetic mapping: 
* `colour` -> `x`
> aes(fg = x)
Aesthetic mapping: 
* `colour` -> `x`
> aes(color = x)
Aesthetic mapping: 
* `colour` -> `x`
> aes(colour = x)
Aesthetic mapping: 
* `colour` -> `x`
> 
> # aes() is passed to either ggplot() or specific layer. Aesthetics supplied
> # to ggplot() are used as defaults for every layer.
> ggplot(mpg, aes(displ, hwy)) + geom_point()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending-ggplot2.Rmd’ using rmarkdown
Quitting from lines 87-90 (extending-ggplot2.Rmd) 
Error: processing vignette 'extending-ggplot2.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘extending-ggplot2.Rmd’

--- re-building ‘ggplot2-specs.Rmd’ using rmarkdown
Quitting from lines 56-67 (ggplot2-specs.Rmd) 
Error: processing vignette 'ggplot2-specs.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggplot2-specs.Rmd’

SUMMARY: processing the following files failed:
  ‘extending-ggplot2.Rmd’ ‘ggplot2-specs.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggpmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot
> ### Title: Create a new ggplot plot from time series data
> ### Aliases: ggplot ggplot.ts ggplot.xts
> 
> ### ** Examples
> 
> library(ggplot2)
> ggplot(lynx) + geom_line()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Quitting from lines 66-67 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggpol-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GeomConfmat
> ### Title: Confusion Matrix
> ### Aliases: GeomConfmat geom_confmat stat_confmat
> 
> ### ** Examples
> 
> x <- sample(LETTERS[seq(4)], 50, replace = TRUE)
> y <- sample(LETTERS[seq(4)], 50, replace = TRUE)
> 
> ggplot() + 
+   geom_confmat(aes(x = x, y = y), normalize = TRUE, text.perc = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggpolypath-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dathome
> ### Title: Simple polygon data
> ### Aliases: dathome maphome
> 
> ### ** Examples
> 
> ggplot(maphome) + aes(x = x_, y = y_, group = branch_, fill = object_) +
+ geom_polypath() + facet_wrap(~object_, nrow = nrow(dathome))
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggpolypath.Rmd’ using rmarkdown
Quitting from lines 16-21 (ggpolypath.Rmd) 
Error: processing vignette 'ggpolypath.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggpolypath.Rmd’

SUMMARY: processing the following file failed:
  ‘ggpolypath.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggpubr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_summary
> ### Title: Add Summary Statistics onto a ggplot.
> ### Aliases: add_summary mean_se_ mean_sd mean_ci mean_range median_iqr
> ###   median_mad median_range
> 
> ### ** Examples
> 
> 
> # Basic violin plot
> p <- ggviolin(ToothGrowth, x = "dose", y = "len", add = "none")
> p
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggpval-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_pval
> ### Title: Add p-values to ggplot objects.
> ### Aliases: add_pval
> 
> ### ** Examples
> 
> library(ggplot2)
> library(ggpval)
> data("PlantGrowth")
> plt <- ggplot(PlantGrowth, aes(group, weight)) +
+   geom_boxplot()
> add_pval(plt, pairs = list(c(1, 3)), test='wilcox.test')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggpval.Rmd’ using knitr
Quitting from lines 61-66 (ggpval.Rmd) 
Error: processing vignette 'ggpval.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggpval.Rmd’

SUMMARY: processing the following file failed:
  ‘ggpval.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggQC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_mR
> ### Title: Generate mR chart in ggplot
> ### Aliases: stat_mR
> 
> ### ** Examples
> 
> #########################
> #  Example 1: mR Chart  #
> #########################
> 
> # Load Libraries ----------------------------------------------------------
>  require(ggQC)
>  require(ggplot2)
Loading required package: ggplot2
> 
> # Setup Data --------------------------------------------------------------
>  set.seed(5555)
>  Process1 <- data.frame(processID = as.factor(rep(1,100)),
+                         metric_value = rnorm(100,0,1),
+                         subgroup_sample=rep(1:20, each=5),
+                         Process_run_id = 1:100)
>  set.seed(5556)
>  Process2 <- data.frame(processID = as.factor(rep(2,100)),
+                         metric_value = rnorm(100,5, 1),
+                         subgroup_sample=rep(1:10, each=10),
+                         Process_run_id = 101:200)
> 
>  Both_Processes <- rbind(Process1, Process2)
> 
> # One Plot Both Processes -------------------------------------------------
>  ggplot(Both_Processes, aes(x=Process_run_id, y = metric_value)) +
+    stat_mR() + ylab("Moving Range")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘XbarR_HOTTO.Rmd’ using rmarkdown
Quitting from lines 46-54 (XbarR_HOTTO.Rmd) 
Error: processing vignette 'XbarR_HOTTO.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘XbarR_HOTTO.Rmd’

--- re-building ‘XmR_HOWTO.Rmd’ using rmarkdown
Quitting from lines 35-43 (XmR_HOWTO.Rmd) 
Error: processing vignette 'XmR_HOWTO.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘XmR_HOWTO.Rmd’

SUMMARY: processing the following files failed:
  ‘XbarR_HOTTO.Rmd’ ‘XmR_HOWTO.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggQQunif-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_QQ_unif
> ### Title: geom_QQ_unif
> ### Aliases: geom_QQ_unif
> 
> ### ** Examples
> 
> library(ggplot2)
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> 
> set.seed(27599)
> d <- data.frame(s = runif(n = 5e3))
> 
> d %>%
+ ggplot(mapping = aes(sample = s)) +
+  geom_QQ_unif() +
+  scale_x_QQ() +
+  scale_y_QQ() +
+  theme_minimal()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggquickeda-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GeomKm
> ### Title: Display Kaplan Meier Curve
> ### Aliases: GeomKm geom_km
> ### Keywords: internal
> 
> ### ** Examples
> 
> library(ggplot2)
> sex <- rbinom(250, 1, .5)
> df <- data.frame(time = exp(rnorm(250, mean = sex)), status = rbinom(250, 1, .75), sex = sex)
> ggplot(df, aes(time = time, status = status, color = factor(sex))) + geom_km()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggquiver-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_quiver
> ### Title: Quiver plots for ggplot2
> ### Aliases: geom_quiver GeomQuiver stat_quiver StatQuiver
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> # Quiver plots of mathematical functions
> expand.grid(x=seq(0,pi,pi/12), y=seq(0,pi,pi/12)) %>%
+   ggplot(aes(x=x,y=y,u=cos(x),v=sin(y))) +
+   geom_quiver()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggRandomForests-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_error
> ### Title: randomForestSRC error rate data object
> ### Aliases: gg_error gg_error.randomForest gg_error.randomForest.formula
> ###   gg_error.rfsrc
> 
> ### ** Examples
> 
> ## Examples from RFSRC package...
> ## ------------------------------------------------------------
> ## classification example
> ## ------------------------------------------------------------
> ## ------------- iris data
> ## You can build a randomForest
> rfsrc_iris <- rfsrc(Species ~ ., data = iris)
> # ... or load a cached randomForestSRC object
> # data(rfsrc_iris, package="ggRandomForests")
> 
> # Get a data.frame containing error rates
> gg_dta<- gg_error(rfsrc_iris)
> 
> # Plot the gg_error object
> plot(gg_dta)
Warning: Removed 3996 rows containing missing values (geom_path).
geom_path: Each group consists of only one observation. Do you need to adjust
the group aesthetic?
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggraph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: facet_edges
> ### Title: Create small multiples based on edge attributes
> ### Aliases: facet_edges
> 
> ### ** Examples
> 
> library(igraph)

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

> gr <- graph_from_data_frame(highschool)
> 
> ggraph(gr) +
+     geom_edge_link() +
+     geom_node_point() +
+     facet_edges(~year)
Using `nicely` as default layout
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Edges.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 76-78 (Edges.Rmd) 
Error: processing vignette 'Edges.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Edges.Rmd’

--- re-building ‘Layouts.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Using `nicely` as default layout
Quitting from lines 31-40 (Layouts.Rmd) 
Error: processing vignette 'Layouts.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Layouts.Rmd’

--- re-building ‘Nodes.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 23-30 (Nodes.Rmd) 
Error: processing vignette 'Nodes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Nodes.Rmd’

SUMMARY: processing the following files failed:
  ‘Edges.Rmd’ ‘Layouts.Rmd’ ‘Nodes.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggridges-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_density_line
> ### Title: Smoothed density estimates drawn with a ridgeline rather than
> ###   area
> ### Aliases: geom_density_line GeomDensityLine
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)

Attaching package: ‘ggplot2’

The following object is masked from ‘package:ggridges’:

    scale_discrete_manual

> ggplot(diamonds, aes(carat)) +
+   geom_density_line()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggridges)
  > 
  > test_check("ggridges")
  ── 1. Error: basic tests (@test_scale_cyclical.R#26)  ──────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_equal("guide-box" %in% ggplotGrob(p)$layout$name, TRUE) at testthat/test_scale_cyclical.R:26
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: "guide-box" %in% ggplotGrob(p)$layout$name
  5: ggplotGrob(p)
  6: ggplot_gtable(ggplot_build(x))
  7: ggplot_gtable.ggplot_built(ggplot_build(x))
  8: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  9: guides_gengrob(gdefs, theme)
  10: lapply(gdefs, guide_gengrob, theme)
  ...
  19: pushvpgp(x)
  20: pushgrobvp(x$vp)
  21: pushgrobvp.viewport(x$vp)
  22: pushViewport(vp, recording = FALSE)
  23: lapply(vps, push.vp, recording)
  24: FUN(X[[i]], ...)
  25: push.vp.vpTree(X[[i]], ...)
  26: push.vp(vp$parent, recording)
  27: push.vp.viewport(vp$parent, recording)
  28: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 55 SKIPPED: 5 FAILED: 1
  1. Error: basic tests (@test_scale_cyclical.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gallery.Rmd’ using rmarkdown
Picking joint bandwidth of 6.68
Warning: Removed 250 rows containing non-finite values (stat_density_ridges).
Quitting from lines 25-31 (gallery.Rmd) 
Error: processing vignette 'gallery.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gallery.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown

Attaching package: 'ggridges'

The following object is masked from 'package:ggplot2':

    scale_discrete_manual

Quitting from lines 25-31 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘gallery.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ggplot2’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ggroc: no visible global function definition for ‘ggplot’
ggroc: no visible global function definition for ‘aes’
ggroc: no visible global function definition for ‘geom_point’
ggroc: no visible global function definition for ‘geom_line’
ggroc: no visible global function definition for ‘theme’
ggroc: no visible global function definition for ‘element_text’
ggroc: no visible global function definition for ‘labs’
ggroc: no visible global function definition for ‘ggsave’
Undefined global functions or variables:
  aes element_text geom_line geom_point ggplot ggsave labs theme
Running examples in ‘ggROC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggROC-package
> ### Title: package for roc curve plot with ggplot2
> ### Aliases: ggROC-package ggROC
> ### Keywords: roc
> 
> ### ** Examples
> 
> 	data(roc)
> 	ggroc(roc, 0.01,"green",19,output="roc.pdf")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ggroc ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggsci-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_color_aaas
> ### Title: AAAS Journal Color Scales
> ### Aliases: scale_color_aaas scale_colour_aaas scale_fill_aaas
> 
> ### ** Examples
> 
> library("ggplot2")
> data("diamonds")
> 
> ggplot(subset(diamonds, carat >= 2.2),
+        aes(x = table, y = price, colour = cut)) +
+   geom_point(alpha = 0.7) +
+   geom_smooth(method = "loess", alpha = 0.1, size = 1, span = 1) +
+   theme_bw() + scale_color_aaas()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggsci.Rmd’ using rmarkdown
Quitting from lines 136-139 (ggsci.Rmd) 
Error: processing vignette 'ggsci.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggsci.Rmd’

SUMMARY: processing the following file failed:
  ‘ggsci.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggseas-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggsdc
> ### Title: Visualise seasonal decomposition
> ### Aliases: ggsdc
> 
> ### ** Examples
> 
> # sample time series data in data frame
> ap_df <- tsdf(AirPassengers)
> 
> ggsdc(ap_df, aes(x = x, y = y), method = "decompose") +
+    geom_line()
Calculating frequency of 12 from the data.
Warning: Removed 6 rows containing missing values (geom_path).
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggseas.Rmd’ using rmarkdown
Quitting from lines 47-49 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggseas.Rmd’

SUMMARY: processing the following file failed:
  ‘ggseas.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggseqlogo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggseqlogo
> ### Title: Quick sequence logo plot
> ### Aliases: ggseqlogo
> 
> ### ** Examples
> 
> # Load sample data
> data(ggseqlogo_sample)
> 
> # Plot a single DNA sequence logo
> p1 = ggseqlogo( seqs_dna[[1]] )
> print(p1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 35-39 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggsolvencyii-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_sii_riskconnection
> ### Title: geom_sii_riskconnection
> ### Aliases: geom_sii_riskconnection
> 
> ### ** Examples
> 
> library(ggsolvencyii)
> library(ggplot2)
> 
> sii_z_ex3_data[sii_z_ex3_data$description == "SCR", ]
  time ratio description     value id comparewithid
1    3   231         SCR  93.50000  1             2
2    1   234         SCR  92.18182  2            NA
3    3   227         SCR 138.06446  3             2
> 
> ggplot() + geom_sii_riskconnection(data = sii_z_ex3_data, mapping = aes(
+   comparewithid = comparewithid,
+   x = time,
+   y = ratio,
+   id = id,
+   ),
+ color = "red",
+ lwd = 0.7,
+ arrow = arrow()
+ )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘coding_overview.Rmd’ using rmarkdown
--- finished re-building ‘coding_overview.Rmd’

--- re-building ‘ggsolvencyii.Rmd’ using rmarkdown
Quitting from lines 70-194 (ggsolvencyii.Rmd) 
Error: processing vignette 'ggsolvencyii.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggsolvencyii.Rmd’

--- re-building ‘plotdetails.Rmd’ using rmarkdown
--- finished re-building ‘plotdetails.Rmd’

--- re-building ‘showcase.Rmd’ using rmarkdown
Quitting from lines 51-176 (showcase.Rmd) 
Error: processing vignette 'showcase.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘showcase.Rmd’

SUMMARY: processing the following files failed:
  ‘ggsolvencyii.Rmd’ ‘showcase.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggsom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggsom_line
> ### Title: ggsom_line
> ### Aliases: ggsom_line
> 
> ### ** Examples
> 
> 
> library(ggthemes)
> library(ggsom)
> library(ggplot2)
> library(kohonen)
> 
> iris_som <- som(scale(iris[1:4]), grid = somgrid(6, 4, 'rectangular'))
> 
> ggsom_line(aes_som(iris_som), TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggsom.Rmd’ using rmarkdown
Quitting from lines 19-27 (ggsom.Rmd) 
Error: processing vignette 'ggsom.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggsom.Rmd’

SUMMARY: processing the following file failed:
  ‘ggsom.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggspatial-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotation_map_tile
> ### Title: Add background OSM tiles
> ### Aliases: annotation_map_tile GeomMapTile
> ### Keywords: datasets
> 
> ### ** Examples
> 
> load_longlake_data()
> 
> ggplot() +
+   annotation_map_tile(zoom = 13, cachedir = system.file("rosm.cache", package = "ggspatial")) +
+   geom_sf(data = longlake_waterdf, fill = NA, col = "grey50")
Zoom: 13
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggspatial.Rmd’ using rmarkdown
Quitting from lines 36-39 (ggspatial.Rmd) 
Error: processing vignette 'ggspatial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggspatial.Rmd’

SUMMARY: processing the following file failed:
  ‘ggspatial.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggspectra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.filter_spct
> ### Title: Create a complete ggplot for a filter spectrum.
> ### Aliases: autoplot.filter_spct autoplot.filter_mspct
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 
> autoplot(yellow_gel.spct)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘userguide1-grammar.Rmd’ using rmarkdown
Quitting from lines 144-145 (userguide1-grammar.Rmd) 
Error: processing vignette 'userguide1-grammar.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘userguide1-grammar.Rmd’

--- re-building ‘userguide2-autoplot-methods.Rmd’ using rmarkdown
Quitting from lines 62-63 (userguide2-autoplot-methods.Rmd) 
Error: processing vignette 'userguide2-autoplot-methods.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘userguide2-autoplot-methods.Rmd’

SUMMARY: processing the following files failed:
  ‘userguide1-grammar.Rmd’ ‘userguide2-autoplot-methods.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggstance-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_boxploth
> ### Title: Horizontal box and whiskers plot.
> ### Aliases: geom_boxploth
> 
> ### ** Examples
> 
> library("ggplot2")

Attaching package: ‘ggplot2’

The following objects are masked from ‘package:ggstance’:

    GeomErrorbarh, geom_errorbarh

> 
> # With ggplot2 we need coord_flip():
> ggplot(mpg, aes(class, hwy, fill = factor(cyl))) +
+   geom_boxplot() +
+   coord_flip()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggstatsplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: combine_plots
> ### Title: Combining and arranging multiple plots in a grid
> ### Aliases: combine_plots
> 
> ### ** Examples
> 
> # loading the necessary libraries
> library(ggplot2)
> 
> # preparing the first plot
> p1 <-
+   ggplot2::ggplot(
+     data = subset(iris, iris$Species == "setosa"),
+     aes(x = Sepal.Length, y = Sepal.Width)
+   ) +
+   geom_point() +
+   labs(title = "setosa")
> 
> # preparing the second plot
> p2 <-
+   ggplot2::ggplot(
+     data = subset(iris, iris$Species == "versicolor"),
+     aes(x = Sepal.Length, y = Sepal.Width)
+   ) +
+   geom_point() +
+   labs(title = "versicolor")
> 
> # combining the plot with a title and a caption
> combine_plots(
+   p1,
+   p2,
+   labels = c("(a)", "(b)"),
+   title.text = "Dataset: Iris Flower dataset",
+   caption.text = "Note: Only two species of flower are displayed",
+   title.color = "red",
+   caption.color = "blue"
+ )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggstatsplot)
  > 
  > test_check("ggstatsplot")
  ── 1. Error: `theme_pie()` works (@test_theme_ggstatsplot.R#68)  ───────────────
  subscript out of bounds
  1: testthat::expect_identical(as.character(df3$value[[35]][1]), "0cm") at testthat/test_theme_ggstatsplot.R:68
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: as.character(df3$value[[35]][1])
  5: as.character.unit(df3$value[[35]][1])
  6: vapply(as.unit(x), unitDesc, character(1))
  7: FUN(X[[i]], ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 24 SKIPPED: 184 FAILED: 1
  1. Error: `theme_pie()` works (@test_theme_ggstatsplot.R#68) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ggswissmaps-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: maps2
> ### Title: A list with 8 'ggplot2' objects of swiss territory boundaries,
> ###   at various levels.
> ### Aliases: maps2
> ### Keywords: datasets
> 
> ### ** Examples
> 
> class(maps2)
[1] "list"
> length(maps2)
[1] 8
> names(maps2)
[1] "g1b15"      "g1g15_encl" "g1g15_li"   "g1g15"      "g1k15"     
[6] "g1l15"      "g1r15"      "g1s15"     
> # str(maps2[["g1k15"]])
> 
> # By name
> maps2[["g1k15"]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggswissmaps_intro.Rmd’ using rmarkdown
Quitting from lines 35-42 (ggswissmaps_intro.Rmd) 
Error: processing vignette 'ggswissmaps_intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggswissmaps_intro.Rmd’

SUMMARY: processing the following file failed:
  ‘ggswissmaps_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggtern-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate
> ### Title: Create an annotation layer (ggtern version).
> ### Aliases: annotate
> 
> ### ** Examples
> 
> ggtern() + 
+ annotate(geom  = 'text',
+               x     = c(0.5,1/3,0.0),
+               y     = c(0.5,1/3,0.0),
+               z     = c(0.0,1/3,1.0),
+               angle = c(0,30,60),
+               vjust = c(1.5,0.5,-0.5),
+               label = paste("Point",c("A","B","C")),
+               color = c("green","red",'blue')) +
+   theme_dark() + 
+   theme_nomask()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ggthemes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bank_slopes
> ### Title: Bank Slopes to 45 degrees
> ### Aliases: bank_slopes
> 
> ### ** Examples
> 
> library("ggplot2")
> 
> # Use the classic sunspot data from Cleveland's original paper
> x <- seq_along(sunspot.year)
> y <- as.numeric(sunspot.year)
> # Without banking
> m <- ggplot(data.frame(x = x, y = y), aes(x = x, y = y)) +
+    geom_line()
> m
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggthemes)
  > 
  > test_check("ggthemes")
  ── 1. Error: theme_few draws correctly (@test-few.R#65)  ───────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_doppelganger("theme_few", plot + theme_few()) at testthat/test-few.R:65
  2: vdiffr::expect_doppelganger(title, fig, path = path, ..., user_fonts = user_fonts, 
         verbose = verbose) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggthemes.Rcheck/tests/testthat/helper-vdiffr.R:18
  3: writer(fig, testcase, title)
  4: print_plot(plot, title)
  5: print_plot.ggplot(plot, title)
  6: print(p)
  7: print.ggplot(p)
  8: ggplot_gtable(data)
  9: ggplot_gtable.ggplot_built(data)
  10: layout$render(geom_grobs, data, theme, plot$labels)
  11: f(..., self = self)
  12: self$facet$draw_panels(panels, self$layout, self$panel_scales_x, self$panel_scales_y, 
         self$panel_params, self$coord, data, theme, self$facet_params)
  13: f(...)
  14: render_strips(structure(labels_df, type = "rows"), structure(labels_df, type = "cols"), 
         params$labeller, theme)
  15: build_strip(x, labeller, theme, TRUE)
  16: ggstrip(grobs, theme, element, gp, horizontal, clip = "on")
  17: Summary.unit(structure(c(4.8, 4.8), unit = 8L, class = c("margin", "unit")), na.rm = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 275 SKIPPED: 0 FAILED: 1
  1. Error: theme_few draws correctly (@test-few.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ggTimeSeries-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot_calendar_heatmap
> ### Title: Plots a calendar heatmap
> ### Aliases: ggplot_calendar_heatmap
> 
> ### ** Examples
> 
> {
+ library(data.table)
+ library(ggplot2)
+ set.seed(1)
+ dtData = data.table(
+       DateCol = seq(
+          as.Date("1/01/2014", "%d/%m/%Y"),
+          as.Date("31/12/2015", "%d/%m/%Y"),
+          "days"
+       ),
+       ValueCol = runif(730)
+    )
+ # you could also try categorical data with
+ # ValueCol = sample(c('a','b','c'), 730, replace = T)
+ p1 = ggplot_calendar_heatmap(
+    dtData,
+    'DateCol',
+    'ValueCol'
+ )
+ p1
+ # add new geoms
+ p1 +
+ geom_text(label = '!!!') +
+ scale_colour_continuous(low = 'red', high = 'green')
+ }
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggTimeSeries.Rmd’ using rmarkdown
Quitting from lines 38-62 (ggTimeSeries.Rmd) 
Error: processing vignette 'ggTimeSeries.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggTimeSeries.Rmd’

SUMMARY: processing the following file failed:
  ‘ggTimeSeries.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggupset-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: axis_combmatrix
> ### Title: Convert delimited text labels into a combination matrix axis
> ### Aliases: axis_combmatrix
> 
> ### ** Examples
> 
>   library(ggplot2)
>   mtcars$combined <- paste0("Cyl: ", mtcars$cyl, "_Gears: ", mtcars$gear)
>   head(mtcars)
                   mpg cyl disp  hp drat    wt  qsec vs am gear carb
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1
                         combined
Mazda RX4         Cyl: 6_Gears: 4
Mazda RX4 Wag     Cyl: 6_Gears: 4
Datsun 710        Cyl: 4_Gears: 4
Hornet 4 Drive    Cyl: 6_Gears: 3
Hornet Sportabout Cyl: 8_Gears: 3
Valiant           Cyl: 6_Gears: 3
>   ggplot(mtcars, aes(x=combined)) +
+     geom_bar() +
+     axis_combmatrix(sep = "_")
Error: No method for merging unit into margin
Execution halted
Running examples in ‘ggvoronoi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fortify_voronoi
> ### Title: Create Data Frame from voronoi_polygons output
> ### Aliases: fortify_voronoi
> ### Keywords: choropleth voronoi,
> 
> ### ** Examples
> 
> set.seed(45056)
> x <- sample(1:200,100)
> y <- sample(1:200,100)
> points <- data.frame(x, y,
+                      distance = sqrt((x-100)^2 + (y-100)^2))
> circle <- data.frame(x = 100*(1+cos(seq(0, 2*pi, length.out = 2500))),
+                      y = 100*(1+sin(seq(0, 2*pi, length.out = 2500))),
+                      group = rep(1,2500))
> 
> vor_spdf <- voronoi_polygon(data=points,x="x",y="y",outline=circle)
> vor_df <- fortify_voronoi(vor_spdf)
> 
> ggplot(vor_df) +
+     geom_polygon(aes(x=x,y=y,fill=distance,group=group))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggvoronoi.Rmd’ using rmarkdown
Quitting from lines 36-49 (ggvoronoi.Rmd) 
Error: processing vignette 'ggvoronoi.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggvoronoi.Rmd’

SUMMARY: processing the following file failed:
  ‘ggvoronoi.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ggwordcloud-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_text_wordcloud
> ### Title: word cloud text geoms
> ### Aliases: geom_text_wordcloud geom_text_wordcloud_area
> 
> ### ** Examples
> 
> set.seed(42)
> data("love_words_small")
> 
> ggplot(love_words_small, aes(label = word, size = speakers)) +
+ geom_text_wordcloud() +
+ scale_size_area(max_size = 20) +
+ theme_minimal()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggwordcloud.Rmd’ using rmarkdown
Quitting from lines 61-65 (ggwordcloud.Rmd) 
Error: processing vignette 'ggwordcloud.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggwordcloud.Rmd’

SUMMARY: processing the following file failed:
  ‘ggwordcloud.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ghibli-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot2-scales-continuous
> ### Title: Continuous scales to use for ggplot2
> ### Aliases: ggplot2-scales-continuous scale_colour_ghibli_c
> ###   scale_color_ghibli_c scale_fill_ghibli_c
> 
> ### ** Examples
> 
> 
> if (require('ggplot2')) {
+ 
+   ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, colour = Petal.Length)) +
+     geom_point() +
+     scale_colour_ghibli_c("PonyoMedium")
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ghibli-guide.Rmd’ using rmarkdown
Loading required package: ghibli
Quitting from lines 43-53 (ghibli-guide.Rmd) 
Error: processing vignette 'ghibli-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ghibli-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘ghibli-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace with empty importFrom: ‘statmod’
acovamcmc: no visible global function definition for ‘rnorm’
acovamcmc: no visible global function definition for ‘rgamma’
acovamcmc: no visible binding for global variable ‘quantile’
acovamcmc: no visible global function definition for ‘quantile’
acovamcmc: no visible global function definition for ‘var’
plot.acovamcmc: no visible global function definition for ‘dev.new’
plot.acovamcmc: no visible global function definition for ‘par’
plot.acovamcmc: no visible global function definition for ‘plot’
plot.acovamcmc: no visible global function definition for ‘density’
plot.acovamcmc: no visible global function definition for ‘acf’
plot.acovamcmc: no visible global function definition for ‘contour’
plot.acovamcmc: no visible global function definition for ‘image’
plot.acovamcmc: no visible global function definition for ‘persp’
Undefined global functions or variables:
  acf contour density dev.new image par persp plot quantile rgamma
  rnorm var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "contour", "image", "par", "persp", "plot")
  importFrom("stats", "acf", "density", "quantile", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘gibbs.met/R/firstlib.R’:
  .First.lib calls:
    cat("Naive Gibbs Sampling with Metropolis steps(gibbs.met) loaded\n",     "COPYRIGHT 2008 (c) Longhai Li (http://math.usask.ca/~longhai)\n",     "Type ?begin.gibbs.met for help to this package\n", sep = "")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

met_gaussian : one_transition: no visible global function definition
  for ‘rnorm’
met_gaussian : one_transition: no visible global function definition
  for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
ssa.btl: no visible global function definition for ‘rbinom’
ssa.btl: no visible global function definition for ‘rpois’
ssa.btl.diag: no visible global function definition for ‘rbinom’
ssa.btl.diag: no visible global function definition for ‘rpois’
ssa.d: no visible global function definition for ‘runif’
ssa.d.diag: no visible global function definition for ‘runif’
ssa.etl: no visible global function definition for ‘rpois’
ssa.etl.diag: no visible global function definition for ‘rpois’
ssa.otl: no visible global function definition for ‘runif’
ssa.otl: no visible global function definition for ‘rpois’
ssa.otl.diag: no visible global function definition for ‘runif’
ssa.otl.diag: no visible global function definition for ‘rpois’
ssa.plot: no visible global function definition for ‘rainbow’
ssa.plot: no visible global function definition for ‘matplot’
ssa.plot: no visible global function definition for ‘title’
ssa.plot: no visible global function definition for ‘legend’
ssa.plot: no visible global function definition for ‘mtext’
ssa.run: no visible global function definition for ‘flush.console’
ssa.terminate: no visible global function definition for ‘sd’
Undefined global functions or variables:
  flush.console legend matplot mtext rainbow rbinom rpois runif sd
  title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "mtext", "title")
  importFrom("stats", "rbinom", "rpois", "runif", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
choro.legend: no visible global function definition for ‘strwidth’
choro.legend: no visible global function definition for ‘legend’
choro.legend: no visible global function definition for ‘text’
jitter.points: no visible global function definition for ‘rnorm’
level.plot: no visible global function definition for ‘.filled.contour’
map.scale: no visible global function definition for ‘par’
map.scale: no visible global function definition for ‘rect’
map.scale: no visible global function definition for ‘lines’
map.scale: no visible global function definition for ‘text’
map.scale: no visible global function definition for ‘strheight’
north.arrow: no visible global function definition for ‘polygon’
north.arrow: no visible global function definition for ‘text’
north.arrow: no visible global function definition for ‘strheight’
poly.labels: no visible global function definition for ‘slot’
poly.labels : <anonymous>: no visible global function definition for
  ‘slot’
quantileCuts: no visible global function definition for ‘quantile’
sdCuts: no visible global function definition for ‘sd’
Undefined global functions or variables:
  .filled.contour legend lines par polygon quantile rect rnorm sd slot
  strheight strwidth text
Consider adding
  importFrom("graphics", ".filled.contour", "legend", "lines", "par",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("methods", "slot")
  importFrom("stats", "quantile", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘gitter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.gitter
> ### Title: Plot a gitter dat file
> ### Aliases: plot.gitter
> ### Keywords: bubble display heatmap plot visualize
> 
> ### ** Examples
> 
> f = system.file("extdata", "sample.jpg.dat", package="gitter")
> # Read in path as a gitter data object
> g = gitter.read(f)
> # Plot a heatmap
> plot(g, type="heatmap")
Warning: `axis.ticks.margin` is deprecated. Please set `margin` property  of `axis.text` instead
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
fptcdf: no visible global function definition for ‘dnorm’
fptcdf: no visible global function definition for ‘pnorm’
fptpdf: no visible global function definition for ‘pnorm’
fptpdf: no visible global function definition for ‘dnorm’
lba: no visible global function definition for ‘as.formula’
lba: no visible global function definition for ‘model.frame’
lba : logl: no visible global function definition for ‘head’
lba: no visible global function definition for ‘optim’
pmod: no visible global function definition for ‘model.frame’
pmod: no visible global function definition for ‘model.matrix’
rlba: no visible global function definition for ‘pnorm’
rlba: no visible global function definition for ‘rnorm’
rlba: no visible global function definition for ‘runif’
tablba: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula dnorm head model.frame model.matrix optim pnorm rnorm
  runif
Consider adding
  importFrom("stats", "as.formula", "dnorm", "model.frame",
             "model.matrix", "optim", "pnorm", "rnorm", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
Running examples in ‘glmertree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glmertree
> ### Title: (Generalized) Linear Mixed Model Trees
> ### Aliases: lmertree glmertree print.lmertree plot.lmertree coef.lmertree
> ###   ranef.lmertree logLik.lmertree model.frame.lmertree predict.lmertree
> ###   terms.lmertree as.party.lmertree residuals.lmertree resid.lmertree
> ###   VarCorr.lmertree print.glmertree plot.glmertree coef.glmertree
> ###   ranef.glmertree logLik.glmertree model.frame.glmertree
> ###   predict.glmertree terms.glmertree as.party.glmertree
> ###   residuals.glmertree resid.glmertree VarCorr.glmertree
> ### Keywords: tree
> 
> ### ** Examples
> 
> ## artificial example data
> data("DepressionDemo", package = "glmertree")
> 
> ## fit normal linear regression LMM tree for continuous outcome
> lt <- lmertree(depression ~ treatment | cluster | age + anxiety + duration,
+   data = DepressionDemo)
> plot(lt, which = "all") # default behavior, may also be "tree" or "ranef" 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘glmertree.Rnw’ using Sweave
Loading required package: lme4
Loading required package: Matrix
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm

Error: processing vignette 'glmertree.Rnw' failed with diagnostics:
 chunk 9 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building ‘glmertree.Rnw’

SUMMARY: processing the following file failed:
  ‘glmertree.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘spatial-glms.Rmd’ using rmarkdown
Loading required package: Rcpp

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 38-53 (spatial-glms.Rmd) 
Error: processing vignette 'spatial-glms.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘spatial-glms.Rmd’

SUMMARY: processing the following file failed:
  ‘spatial-glms.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘glmmTMB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: profile.glmmTMB
> ### Title: Compute likelihood profiles for a fitted model
> ### Aliases: profile.glmmTMB confint.profile.glmmTMB
> 
> ### ** Examples
> 
> ## Not run: 
> ##D m1 <- glmmTMB(count~ mined + (1|site), 
> ##D        zi=~mined, family=poisson, data=Salamanders)
> ##D salamander_prof1 <- profile(m1, parallel="multicore",
> ##D                             ncpus=2, trace=1)
> ##D ## testing
> ##D salamander_prof1 <- profile(m1, trace=1,parm=1)
> ##D salamander_prof1M <- profile(m1, trace=1,parm=1, npts = 4)
> ##D salamander_prof2 <- profile(m1, parm="theta_")
> ##D 
> ## End(Not run)
> salamander_prof1 <- readRDS(system.file("example_files","salamander_prof1.rds",package="glmmTMB"))
> if (require("ggplot2")) {
+     ggplot(salamander_prof1,aes(.focal,sqrt(value))) +
+         geom_point() + geom_line()+
+         facet_wrap(~.par,scale="free_x")+
+     geom_hline(yintercept=1.96,linetype=2)
+ }
Loading required package: ggplot2
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘covstruct.rmd’ using rmarkdown

Attaching package: 'TMB'

The following object is masked from 'package:glmmTMB':

    tmbroot

--- finished re-building ‘covstruct.rmd’

--- re-building ‘mcmc.rmd’ using rmarkdown
Quitting from lines 87-89 (mcmc.rmd) 
Error: processing vignette 'mcmc.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mcmc.rmd’

--- re-building ‘miscEx.rmd’ using rmarkdown
--- finished re-building ‘miscEx.rmd’

--- re-building ‘model_evaluation.rmd’ using rmarkdown
Loading required package: carData
lattice theme set by effectsTheme()
See ?effectsTheme for details.
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

The following object is masked from 'package:MASS':

    geyser


Attaching package: 'multcomp'

The following object is masked from 'package:emmeans':

    cld

Loading required package: ggplot2
--- finished re-building ‘model_evaluation.rmd’

--- re-building ‘sim.rmd’ using rmarkdown
Quitting from lines 47-49 (sim.rmd) 
Error: processing vignette 'sim.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sim.rmd’

--- re-building ‘troubleshooting.rmd’ using rmarkdown
--- finished re-building ‘troubleshooting.rmd’

--- re-building ‘glmmTMB.Rnw’ using knitr
Loading required package: stats4
Warning in qt((1 - level)/2, df) : NaNs produced
Quitting from lines 300-306 (glmmTMB.Rnw) 
Error: processing vignette 'glmmTMB.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘glmmTMB.Rnw’

SUMMARY: processing the following files failed:
  ‘mcmc.rmd’ ‘sim.rmd’ ‘glmmTMB.Rnw’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glmulti.Rcheck/00install.out’ for details.
globalboosttest: no visible global function definition for ‘predict’
globalboosttest: no visible global function definition for ‘lm’
globalboosttest: no visible global function definition for ‘glm’
globalboosttest: no visible binding for global variable ‘binomial’
globalboosttest: no visible global function definition for ‘points’
globalboosttest: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC binomial glm lm points predict
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "AIC", "binomial", "glm", "lm", "predict")
to your NAMESPACE file.
.nPerms: no visible global function definition for ‘terms’
expr.dev.test: no visible global function definition for ‘terms’
expr.dev.test: no visible global function definition for ‘model.matrix’
expr.dev.test: no visible global function definition for ‘pchisq’
lancaster: no visible global function definition for ‘pgamma’
liptak: no visible global function definition for ‘pnorm’
summary.dev.test : ci: no visible global function definition for
  ‘qnorm’
varwiselogLik : <anonymous>: no visible global function definition for
  ‘deviance’
varwiselogLik.regression: no visible global function definition for
  ‘glm.fit’
Undefined global functions or variables:
  deviance glm.fit model.matrix pchisq pgamma pnorm qnorm terms
Consider adding
  importFrom("stats", "deviance", "glm.fit", "model.matrix", "pchisq",
             "pgamma", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
CreateFormula: no visible global function definition for ‘as.formula’
GeneratePvalues: no visible binding for global variable ‘binomial’
globalARTP: no visible binding for global variable ‘binomial’
globalFisher: no visible binding for global variable ‘binomial’
globalFisher: no visible global function definition for ‘pchisq’
globalSimes: no visible binding for global variable ‘binomial’
pvalFmla: no visible binding for global variable ‘binomial’
pvalFmla: no visible global function definition for ‘glm’
pvalFmla: no visible global function definition for ‘anova’
runPermut: no visible binding for global variable ‘binomial’
runPvalues: no visible binding for global variable ‘binomial’
Undefined global functions or variables:
  anova as.formula binomial glm pchisq
Consider adding
  importFrom("stats", "anova", "as.formula", "binomial", "glm", "pchisq")
to your NAMESPACE file.
ScoreTest: no visible global function definition for ‘pchisq’
Var1: no visible global function definition for ‘runif’
gLRT1: no visible global function definition for ‘pchisq’
gLRT2: no visible global function definition for ‘pchisq’
gLRT3: no visible global function definition for ‘pchisq’
gLRT4: no visible global function definition for ‘pf’
Undefined global functions or variables:
  pchisq pf runif
Consider adding
  importFrom("stats", "pchisq", "pf", "runif")
to your NAMESPACE file.
Running examples in ‘GmAMisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: outlier
> ### Title: R function for univariate outliers detection
> ### Aliases: outlier
> ### Keywords: outlier
> 
> ### ** Examples
> 
> # create a toy dataset
> mydata <- c(2,3,4,5,6,7,8,9,50,50)
> 
> # locate outlier(s) using the median-based method
> outlier(mydata, method="median", addthres=TRUE)
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: outlier ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
plot.bGAMM: no visible global function definition for ‘par’
plot.bGAMM: no visible global function definition for ‘plot’
plot.bGAMM: no visible global function definition for ‘lines’
plot.bGAMM: no visible global function definition for ‘rug’
Undefined global functions or variables:
  lines par plot rug
Consider adding
  importFrom("graphics", "lines", "par", "plot", "rug")
to your NAMESPACE file.
Running examples in ‘gMOIP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cornerPoints
> ### Title: Calculate the corner points for the polytope Ax<=b, x>=0 (used
> ###   some code from the 'intpoint' package)
> ### Aliases: cornerPoints
> 
> ### ** Examples
> 
> # Define the LP max/min coeff*x st. Ax<=b, x>=0
> A <- matrix(c(9,10,2,4,-3,2), ncol = 2, byrow = TRUE)
> b <- c(90,27,3)
> coeff <- c(7.75, 10)
> 
> # Corner points of the polytope
> cPoints<-cornerPoints(A, b)
> # Integer points in the polytope
> iPoints<-integerPoints(A, b)
> 
> # Plot of the polytope
> plotPolytope(cPoints)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘GMSimpute-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MAR.est
> ### Title: Missing At Random (MAR) proportion estimation based on technical
> ###   replicates.
> ### Aliases: MAR.est
> 
> ### ** Examples
> 
> data('replicates')
> # replicates contains mass specturm log abundance of 85 peptides
> # with missing values for 4 pairs of technical replicates.
> 
> 
> MAR=MAR.est(replicates,sample=rep(1:4,each=2),log.scale=FALSE,violin.plot=TRUE)
No id variables; using all as measure variables
> # Estimates the MAR proportion in the 4 pairs of replicates and output violin/box plots object.
> 
> print(MAR$plot)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
File ‘gnmf/libs/gnmf.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘lava’ ‘numDeriv’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cumres.lvmfit : myres: no visible global function definition for ‘vars’
cumres.lvmfit: no visible global function definition for ‘iid’
plot.cumres : sampleproc: no visible global function definition for
  ‘lines’
plot.cumres : predband : <anonymous>: no visible binding for global
  variable ‘rgb’
plot.cumres : predband : <anonymous>: no visible global function
  definition for ‘col2rgb’
plot.cumres : predband: no visible global function definition for
  ‘lines’
plot.cumres : predband: no visible global function definition for
  ‘polygon’
Undefined global functions or variables:
  col2rgb iid lines polygon rgb vars
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "lines", "polygon")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GANPA’ ‘WGCNA’
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  ‘GANPA’ ‘WGCNA’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘GANPA’ ‘WGCNA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GOGANPA: no visible global function definition for ‘GSE.Test.Main’
selectRho: no visible global function definition for
  ‘scaleFreeFitIndex’
Undefined global functions or variables:
  GSE.Test.Main scaleFreeFitIndex
Packages in Depends field not imported from:
  ‘fGarch’ ‘fastICA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
UprodR: no visible global function definition for ‘combn’
goinit: no visible global function definition for ‘as.formula’
ccor,GoGARCH : <anonymous>: no visible global function definition for
  ‘cov2cor’
ccor,Gopredict : <anonymous>: no visible global function definition for
  ‘cov2cor’
goest,Goestica: no visible global function definition for ‘fastICA’
goest,Goestml: no visible global function definition for ‘nlminb’
goest,Goestmm : <anonymous>: no visible global function definition for
  ‘combn’
goest,Goestnls: no visible global function definition for ‘optim’
show,Goinit: no visible global function definition for ‘head’
show,Gopredict: no visible global function definition for ‘head’
update,GoGARCH: no visible global function definition for
  ‘update.formula’
update,Goestica: no visible global function definition for
  ‘update.formula’
update,Goestml: no visible global function definition for
  ‘update.formula’
update,Goestmm: no visible global function definition for
  ‘update.formula’
update,Goestnls: no visible global function definition for
  ‘update.formula’
Undefined global functions or variables:
  as.formula combn cov2cor fastICA head nlminb optim update.formula
Consider adding
  importFrom("stats", "as.formula", "cov2cor", "nlminb", "optim",
             "update.formula")
  importFrom("utils", "combn", "head")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘GOplot_vignette.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: ggdendro
Loading required package: gridExtra
Loading required package: RColorBrewer
Quitting from lines 72-74 (GOplot_vignette.Rmd) 
Error: processing vignette 'GOplot_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GOplot_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘GOplot_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
gpairs: no visible global function definition for ‘hclust’
gpairs: no visible global function definition for ‘dist’
gpairs : scatterplot.panel: no visible global function definition for
  ‘lm’
gpairs : scatterplot.panel: no visible global function definition for
  ‘predict’
gpairs : scatterplot.panel: no visible global function definition for
  ‘prcomp’
gpairs : scatterplot.panel: no visible global function definition for
  ‘cor’
gpairs : scatterplot.panel: no visible global function definition for
  ‘cor.test’
gpairs : scatterplot.panel: no visible global function definition for
  ‘hsv’
gpairs : scatterplot.panel: no visible global function definition for
  ‘na.omit’
gpairs : scatterplot.panel: no visible global function definition for
  ‘pf’
gpairs : scatterplot.panel: no visible global function definition for
  ‘grey’
Undefined global functions or variables:
  cor cor.test dist grey hclust hsv lm na.omit pf prcomp predict
Consider adding
  importFrom("grDevices", "grey", "hsv")
  importFrom("stats", "cor", "cor.test", "dist", "hclust", "lm",
             "na.omit", "pf", "prcomp", "predict")
to your NAMESPACE file.
Random.Start: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
CumulativeVarPlot: no visible global function definition for ‘plot’
CumulativeVarPlot: no visible global function definition for ‘axis’
PCplot: no visible global function definition for ‘par’
PCplot: no visible global function definition for ‘plot’
PCplot: no visible global function definition for ‘rainbow’
PCplot: no visible global function definition for ‘density’
gDist: no visible global function definition for ‘plot’
gDist: no visible global function definition for ‘density’
gDist: no visible global function definition for ‘abline’
gPCA.batchdetect: no visible global function definition for ‘var’
Undefined global functions or variables:
  abline axis density par plot rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "par", "plot")
  importFrom("stats", "density", "var")
to your NAMESPACE file.
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
Warning: no function found corresponding to methods exports from ‘gpclib’ for: ‘coerce’, ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
read.polyfile: no visible global function definition for ‘as’
write.polyfile: no visible global function definition for ‘is’
write.polyfile: no visible global function definition for ‘as’
[,gpc.poly: no visible global function definition for ‘new’
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for ‘new’
coerce,data.frame-gpc.poly: no visible global function definition for
  ‘as’
coerce,list-gpc.poly: no visible global function definition for ‘as’
coerce,matrix-gpc.poly: no visible global function definition for ‘new’
coerce,numeric-gpc.poly: no visible global function definition for
  ‘new’
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for ‘new’
intersect,gpc.poly-gpc.poly: no visible global function definition for
  ‘as’
intersect,gpc.poly-gpc.poly: no visible global function definition for
  ‘new’
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  ‘as’
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  ‘new’
tristrip,gpc.poly: no visible global function definition for ‘as’
union,gpc.poly-gpc.poly: no visible global function definition for ‘as’
union,gpc.poly-gpc.poly: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespaces with empty importFrom:
  ‘scatterplot3d’ ‘sqldf’
Resdata : prepdata: no visible global function definition for ‘sqldf’
gpca : Build3d: no visible global function definition for ‘dev.new’
gpca : Build3d: no visible global function definition for
  ‘scatterplot3d’
gpca : Build3d: no visible global function definition for ‘text’
gpca : Build3d: no visible global function definition for ‘plot’
gpca : Build3d: no visible global function definition for ‘abline’
gpca : Build3d: no visible global function definition for ‘rect’
gpca: no visible global function definition for ‘cor’
gpca: no visible global function definition for ‘dev.new’
gpca: no visible global function definition for ‘plot’
gpca: no visible global function definition for ‘text’
gpca: no visible global function definition for ‘abline’
gpca: no visible global function definition for ‘rect’
gpca: no visible global function definition for ‘scatterplot3d’
gpca: no visible global function definition for ‘segments’
gpca: no visible global function definition for ‘points’
gpca: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline cor dev.new plot points rect scatterplot3d segments sqldf text
  write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot", "points", "rect", "segments",
             "text")
  importFrom("stats", "cor")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Missing or unexported object: ‘TSA::tsdiag.Arima’
.r1: no visible global function definition for ‘cor’
.r2: no visible global function definition for ‘cor’
rgp: no visible global function definition for ‘runif’
rgp: no visible global function definition for ‘rexp’
Undefined global functions or variables:
  cor rexp runif
Consider adding
  importFrom("stats", "cor", "rexp", "runif")
to your NAMESPACE file.
gpfr: no visible global function definition for ‘rnorm’
gpfr: no visible global function definition for ‘runif’
gpfrpred : <anonymous>: no visible global function definition for
  ‘predict’
gpfrtrain: no visible global function definition for ‘nlminb’
gppredict: no visible global function definition for ‘predict’
gpr: no visible global function definition for ‘rnorm’
gpr: no visible global function definition for ‘runif’
gpr: no visible global function definition for ‘lm’
gpr: no visible global function definition for ‘resid’
gpr: no visible global function definition for ‘nlminb’
main1: no visible global function definition for ‘lm’
main1: no visible global function definition for ‘resid’
main2 : <anonymous>: no visible global function definition for
  ‘predict’
main2: no visible global function definition for ‘predict’
main3: no visible global function definition for ‘lm’
main3: no visible global function definition for ‘resid’
plot.gpfr: no visible global function definition for ‘polygon’
plot.gpfr: no visible global function definition for ‘rgb’
plot.gpfr: no visible global function definition for ‘matpoints’
plot.gpfr: no visible global function definition for ‘matlines’
plot.gpfr: no visible global function definition for ‘lines’
plot.gpr: no visible global function definition for ‘plot’
plot.gpr: no visible global function definition for ‘polygon’
plot.gpr: no visible global function definition for ‘rgb’
plot.gpr: no visible global function definition for ‘points’
plot.gpr: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines lm matlines matpoints nlminb plot points polygon predict resid
  rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "matlines", "matpoints", "plot",
             "points", "polygon")
  importFrom("stats", "lm", "nlminb", "predict", "resid", "rnorm",
             "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Checking should be performed on sources prepared by ‘R CMD build’.
Packages in Depends field not imported from:
  ‘foreach’ ‘ggplot2’ ‘isotone’ ‘plyr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘gpmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.gpmap
> ### Title: Functions for creating lineplots of genotype-phenotype (GP) maps
> ### Aliases: plot.gpmap plot.gpmap.decomp.mono
> 
> ### ** Examples
> 
> data(GPmaps)
> 
> #plot additive gpmap
> plot(A)
[[1]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘genotype_test.R’ [1s/1s]
  Comparing ‘genotype_test.Rout’ to ‘genotype_test.Rout.save’ ... OK
  Running ‘test_code_example.R’ [1s/2s]
Running the tests in ‘tests/test_code_example.R’ failed.
Complete output:
  > ## Test code example 1 from 
  > ## Gjuvsland AB, Wang Y, Plahte E, Omholt SW (2013) Monotonicity is a key feature of genotype-phenotype maps. Submitted to Frontiers in Genetics
  > 
  > library(gpmap)
  Loading required package: isotone
  Loading required package: plyr
  Loading required package: ggplot2
  Loading required package: foreach
  > data(GPmaps)
  > gp <- mouseweight
  > 
  > ## Tabulate genotypic values
  > cbind(gp$genotype,gp$values)
    Locus_B Locus_A LG_JxSM_J
  1    B1B1    A1A1    36.839
  2    B1B2    A1A1    36.527
  3    B2B2    A1A1    33.824
  4    B1B1    A1A2    37.951
  5    B1B2    A1A2    35.898
  6    B2B2    A1A2    34.125
  7    B1B1    A2A2    34.118
  8    B1B2    A2A2    34.894
  9    B2B2    A2A2    31.234
  > 
  > ## Plot the GP map
  > plot(gp)		
  [[1]]
  Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
    VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
  Execution halted
Running examples in ‘gppm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.LongData
> ### Title: Plot a Long Data Frame
> ### Aliases: plot.LongData
> 
> ### ** Examples
> 
> data("demoLGCM")
> plot(demoLGCM,plotIds=c(1,2,3))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘gprofiler2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gostplot
> ### Title: Manhattan plot of functional enrichment results.
> ### Aliases: gostplot
> 
> ### ** Examples
> 
>  gostres <- gost(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")
>  gostplot(gostres)
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: gostplot ... unitConvert -> <Anonymous> -> convertUnit -> grid.Call
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Quitting from lines 39-51 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘granovaGG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: granovagg.1w
> ### Title: Elemental Graphic Display for One-Way ANOVA
> ### Aliases: granovagg.1w
> ### Keywords: hplot htest
> 
> ### ** Examples
> 
> data(arousal)
> #Drug A
> granovagg.1w(arousal[,1:2], h.rng = 1.6, v.rng = 0.5)

By-group summary statistics for your input data (ordered by group means)
    group group.mean trimmed.mean contrast variance standard.deviation
1 Placebo      20.43        20.30    -1.92     5.83               2.41
2  Drug.A      24.27        24.45     1.92     7.89               2.81
  group.size
1         10
2         10

Below is a t-test summary of your input data

	Two Sample t-test

data:  unstacked.data[, 1] and unstacked.data[, 2]
t = -3.2786, df = 18, p-value = 0.004174
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -6.300681 -1.379319
sample estimates:
mean of x mean of y 
    20.43     24.27 

Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' calls in package code:
  ‘mgcv’ ‘rgl’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
KL: no visible global function definition for ‘complete.cases’
MergeNodes: no visible global function definition for ‘colors’
cross.validate: no visible global function definition for ‘runif’
fit.APFA: no visible global function definition for ‘complete.cases’
fit.APFA: no visible global function definition for ‘aggregate’
select.beagle: no visible global function definition for ‘write.table’
select.beagle: no visible global function definition for ‘aggregate’
select.beagle: no visible global function definition for ‘colors’
simulateAPFA: no visible global function definition for ‘runif’
st: no visible global function definition for ‘colors’
Undefined global functions or variables:
  aggregate colors complete.cases runif write.table
Consider adding
  importFrom("grDevices", "colors")
  importFrom("stats", "aggregate", "complete.cases", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘custom_generators.Rmd’ using rmarkdown
Quitting from lines 50-56 (custom_generators.Rmd) 
Error: processing vignette 'custom_generators.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘custom_generators.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 42-51 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘piping.Rmd’ using rmarkdown
Quitting from lines 26-37 (piping.Rmd) 
Error: processing vignette 'piping.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘piping.Rmd’

SUMMARY: processing the following files failed:
  ‘custom_generators.Rmd’ ‘introduction.Rmd’ ‘piping.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Sxslt’
Package in Depends field not imported from: ‘Matrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GrassmannOptim: no visible global function definition for ‘rnorm’
GrassmannOptim: no visible global function definition for ‘runif’
GrassmannOptim : <anonymous>: no visible global function definition for
  ‘expm’
GrassmannOptim : <anonymous>: no visible global function definition for
  ‘Matrix’
Undefined global functions or variables:
  Matrix expm rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Running examples in ‘gratia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: appraise
> ### Title: Model diagnostic plots
> ### Aliases: appraise
> 
> ### ** Examples
> 
> library(mgcv)
Loading required package: nlme
This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
> ## Don't show: 
> set.seed(2)
> ## End(Don't show)
> ## simulate some data...
> dat <- gamSim(1, n = 400, dist = "normal", scale = 2)
Gu & Wahba 4 term additive model
> mod <- gam(y ~ s(x0) + s(x1) + s(x2) + s(x3), data = dat)
> ## run some basic model checks, including checking
> ## smoothing basis dimensions...
> appraise(mod)
Error in pSummary(..., op = "max") : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: appraise ... plot_grid -> align_plots -> do.call -> <Anonymous> -> pSummary
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘printCrudeAndAdjustedModel.Rmd’ using rmarkdown
Loading required package: forestplot
Loading required package: grid
Loading required package: magrittr
Loading required package: checkmate
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, units

--- finished re-building ‘printCrudeAndAdjustedModel.Rmd’

--- re-building ‘timeSplitter.Rmd’ using rmarkdown
Loading required package: forestplot
Loading required package: grid
Loading required package: checkmate
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning in coxpenal.fit(X, Y, strats, offset, init = init, control, weights = weights,  :
  Inner loop failed to coverge for iterations 3
Quitting from lines 500-523 (timeSplitter.Rmd) 
Error: processing vignette 'timeSplitter.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘timeSplitter.Rmd’

SUMMARY: processing the following file failed:
  ‘timeSplitter.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘gremlin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gremlin-package
> ### Title: Mixed-Effects REML Incorporating Generalized Inverses
> ### Aliases: gremlin-package _PACKAGE
> 
> ### ** Examples
> 
>   require(nadiv)
Loading required package: nadiv
>   Ainv <- makeAinv(Mrode3[-c(1:2), 1:3])$Ainv
>   mod11 <- gremlinR(WWG11 ~ sex - 1,
+ random = ~ calf,
+ data = Mrode11,
+ ginverse = list(calf = Ainv),
+ Gstart = matrix(0.2), Rstart = matrix(0.4),
+ maxit = 10, v = 2)
gremlin started:		 19:55:14 
   1 of max 10 			 19:55:14 
	EM to find next theta
Element 0.2124631 must be a symmetric matrix or a number
Error in FUN(X[[i]], ...) : 
Calls: gremlinR -> sapply -> lapply -> FUN
Execution halted
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
bestcut2: no visible global function definition for ‘pchisq’
cov.func: no visible global function definition for ‘rbinom’
cov.func: no visible global function definition for ‘cov’
cov.func: no visible global function definition for ‘pnorm’
cox.summary: no visible global function definition for ‘predict’
em.func: no visible global function definition for ‘quantile’
genSurvData: no visible global function definition for ‘rweibull’
greyzone.func: no visible global function definition for ‘points’
greyzone.func: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov pchisq pnorm points predict quantile rbinom rweibull
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "cov", "pchisq", "pnorm", "predict", "quantile",
             "rbinom", "rweibull")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘arrangeGrob.rmd’ using rmarkdown
Quitting from lines 24-33 (arrangeGrob.rmd) 
Error: processing vignette 'arrangeGrob.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘arrangeGrob.rmd’

--- re-building ‘gtable.Rmd’ using rmarkdown
Loading required package: knitr
Loading required package: gridExtra
Loading required package: grid
Loading required package: gtable
Loading required package: ggplot2
Quitting from lines 52-55 (gtable.Rmd) 
Error: processing vignette 'gtable.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gtable.Rmd’

--- re-building ‘ngonGrob.Rmd’ using rmarkdown
--- finished re-building ‘ngonGrob.Rmd’

--- re-building ‘tableGrob.Rmd’ using rmarkdown
--- finished re-building ‘tableGrob.Rmd’

SUMMARY: processing the following files failed:
  ‘arrangeGrob.rmd’ ‘gtable.Rmd’

Error: Vignette re-building failed.
Execution halted
grid.graph: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘gridsampler-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw_multiple_n_persons_x_times
> ### Title: Draw and redraw results of simulation
> ### Aliases: draw_multiple_n_persons_x_times
> 
> ### ** Examples
> 
> ## simulate
> prob <-  dexp(1:30, .05)      # probabilities for categories
> N <- seq(10, 80, by = 10)     # smaple sizes to simulate
> r <- sim_n_persons_x_times_many_n(prob, n = N, a = 7, times = 100, progress = "none")
> 
> # calculate and draw
> M <- 1:5                      # minimal number of categories to evaluate
> p <- c(0.9, .95, 1)           # proportion of categories for which minimal m holds
> d <- calc_probabilities(r, n = N, ms = M, min.props = p)
> draw_multiple_n_persons_x_times(d)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Non-standard file/directory found at top level:
  ‘R.css’
Package in Depends field not imported from: ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GriegSmith: no visible global function definition for ‘is.ppp’
envelopes: no visible binding for global variable ‘quantile’
plot.GriegSmith: no visible global function definition for ‘plot’
plot.GriegSmith: no visible global function definition for ‘lines’
plot.GriegSmith: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis is.ppp lines plot quantile
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Growthcurver-vignette.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 397-414 (Growthcurver-vignette.Rmd) 
Error: processing vignette 'Growthcurver-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Growthcurver-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Growthcurver-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
PCgamma : <anonymous>: no visible global function definition for
  ‘prcomp’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘glm’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘update’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘pchisq’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘lm’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘anova’
PCgamma: no visible global function definition for ‘qgamma’
PCgamma: no visible global function definition for ‘pgamma’
RNAgamma : rnafunc: no visible global function definition for
  ‘model.matrix’
RNAgamma : rnafunc: no visible global function definition for
  ‘as.formula’
RNAgamma: no visible global function definition for ‘qgamma’
RNAgamma: no visible global function definition for ‘pgamma’
STTtoShapeParameter : f: no visible global function definition for
  ‘qgamma’
STTtoShapeParameter: no visible global function definition for
  ‘optimize’
Undefined global functions or variables:
  anova as.formula glm lm model.matrix optimize pchisq pgamma prcomp
  qgamma update
Consider adding
  importFrom("stats", "anova", "as.formula", "glm", "lm", "model.matrix",
             "optimize", "pchisq", "pgamma", "prcomp", "qgamma",
             "update")
to your NAMESPACE file.
.gsa.assignGATKTableToEnvironment: no visible global function
  definition for ‘type.convert’
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
'library' or 'require' call to ‘impute’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GSA: no visible global function definition for ‘impute.knn’
Undefined global functions or variables:
  impute.knn
garsim: no visible global function definition for ‘rnorm’
garsim: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  rnorm rpois
Consider adding
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
plotgsCP: no visible global function definition for ‘opts’
plotgsPower: no visible global function definition for ‘opts’
qplotit: no visible global function definition for ‘opts’
Undefined global functions or variables:
  opts
Error(s) in re-building vignettes:
  ...
--- re-building ‘gsSurvTemplate.rnw’ using knitr
Loading required package: gsDesign
Loading required package: xtable
Loading required package: ggplot2
Quitting from lines 146-147 (gsSurvTemplate.rnw) 
Error: processing vignette 'gsSurvTemplate.rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gsSurvTemplate.rnw’

--- re-building ‘gsSurvTemplateInstructions.rnw’ using knitr
Loading required package: gsDesign
Loading required package: xtable
Loading required package: ggplot2
Quitting from lines 183-184 (gsSurvTemplateInstructions.rnw) 
Error: processing vignette 'gsSurvTemplateInstructions.rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gsSurvTemplateInstructions.rnw’

SUMMARY: processing the following files failed:
  ‘gsSurvTemplate.rnw’ ‘gsSurvTemplateInstructions.rnw’

Error: Vignette re-building failed.
Execution halted
Missing or unexported object: ‘cellWise::DetectDeviatingCells’
Missing link or links in documentation object 'TSGS.Rd':
  ‘DetectDeviatingCells’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Running examples in ‘GSE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TSGS
> ### Title: Two-Step Generalized S-Estimator for cell- and case-wise
> ###   outliers
> ### Aliases: TSGS
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> # Generate 5% cell-wise contaminated normal data
> # using a random correlation matrix with condition number 100
> x <- generate.cellcontam(n=100, p=10, cond=100, contam.size=5, contam.prop=0.05)
> 
> ## Using MLE
> slrt( cov(x$x), x$A)
[1] 69.01395
> 
> ## Using Fast-S
> slrt( rrcov:::CovSest(x$x)@cov, x$A)
[1] 44.9836
> 
> ## Using 2SGS
> slrt( TSGS(x$x)@S, x$A)
Error: 'DetectDeviatingCells' is not an exported object from 'namespace:cellWise'
Execution halted
binding: no visible global function definition for ‘rnorm’
binding: no visible binding for global variable ‘var’
binding: no visible global function definition for ‘uniroot’
equivonly: no visible global function definition for ‘rnorm’
equivonly: no visible binding for global variable ‘var’
equivonly: no visible global function definition for ‘uniroot’
figureE: no visible global function definition for ‘rgb’
figureEF: no visible global function definition for ‘rgb’
nfix : f: no visible global function definition for ‘pnorm’
nfix : f: no visible global function definition for ‘qnorm’
nfix: no visible global function definition for ‘uniroot’
nonbinding: no visible global function definition for ‘rnorm’
nonbinding: no visible binding for global variable ‘var’
nonbinding: no visible global function definition for ‘uniroot’
oc: no visible global function definition for ‘rnorm’
oc: no visible global function definition for ‘var’
Undefined global functions or variables:
  pnorm qnorm rgb rnorm uniroot var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "pnorm", "qnorm", "rnorm", "uniroot", "var")
to your NAMESPACE file.
Namespaces with empty importFrom:
  ‘gee’ ‘geepack’
Running examples in ‘gsloid-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lisiecki2005
> ### Title: LR04 Global Pliocene-Pleistocene Benthic d18O Stack (5.3-Myr).
> ### Aliases: lisiecki2005
> ### Keywords: datasets
> 
> ### ** Examples
> 
> names(lisiecki2005)
[1] "Time"  "d18O"  "Error"
> head(lisiecki2005)
  Time d18O Error
1    0 3.23  0.03
2    1 3.23  0.04
3    2 3.18  0.03
4    3 3.29  0.03
5    4 3.30  0.03
6    5 3.26  0.03
> # plot for 0-250 ka:
> if (require("ggplot2")) {
+    ggplot(lisiecki2005,
+           aes(Time,
+               d18O)) +
+      geom_line() +
+      scale_x_continuous(limits = c(0, 250),
+                         name = "x 1000 years ago") +
+      scale_y_reverse(name = bquote(delta^18*O)) +
+      theme_bw()
+    }
Loading required package: ggplot2
Warning: Removed 1864 rows containing missing values (geom_path).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning: Removed 1864 rows containing missing values (geom_path).
Quitting from lines 64-75 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GSODR.Rmd’ using rmarkdown
Quitting from lines 129-147 (GSODR.Rmd) 
Error: processing vignette 'GSODR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GSODR.Rmd’

--- re-building ‘Working_with_spatial_and_climate_data.Rmd’ using rmarkdown
--- finished re-building ‘Working_with_spatial_and_climate_data.Rmd’

--- re-building ‘use_case_1.Rmd’ using rmarkdown
--- finished re-building ‘use_case_1.Rmd’

SUMMARY: processing the following file failed:
  ‘GSODR.Rmd’

Error: Vignette re-building failed.
Execution halted
gte: no visible global function definition for ‘model.extract’
gte: no visible global function definition for ‘model.matrix’
gte: no visible binding for global variable ‘sd’
gte: no visible global function definition for ‘dnorm’
plot.gte: no visible global function definition for ‘plot’
plot.gte: no visible global function definition for ‘par’
plot.gte: no visible global function definition for ‘polygon’
plot.gte: no visible global function definition for ‘gray’
plot.gte: no visible global function definition for ‘lines’
plot.gte: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dnorm gray legend lines model.extract model.matrix par plot polygon
  sd
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "legend", "lines", "par", "plot", "polygon")
  importFrom("stats", "dnorm", "model.extract", "model.matrix", "sd")
to your NAMESPACE file.
Found the following possibly unsafe calls:
File ‘gtools/R/unByteCode.R’:
  unlockBinding(name, env = env)
Error(s) in re-building vignettes:
  ...
--- re-building ‘gunsales.Rmd’ using rmarkdown
Quitting from lines 60-61 (gunsales.Rmd) 
Error: processing vignette 'gunsales.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gunsales.Rmd’

SUMMARY: processing the following file failed:
  ‘gunsales.Rmd’

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘TITEL’
calculate.threshold: no visible global function definition for ‘pchisq’
gwerAM: no visible global function definition for ‘rnorm’
gwerAM: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  pchisq quantile rnorm
Consider adding
  importFrom("stats", "pchisq", "quantile", "rnorm")
to your NAMESPACE file.
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘GWG/R/obese.R’:
  data(OB_above)
  data(OB_below)
File ‘GWG/R/overweight.R’:
  data(OW_above)
  data(OW_below)
See section ‘Good practice’ in ‘?data’.
browseDataAsCSV: no visible global function definition for ‘write.csv’
browseDataAsCSV: no visible global function definition for ‘browseURL’
tcltkDialog: no visible global function definition for ‘runif’
tl_get_column_name: no visible global function definition for ‘tail’
.add,gTexttcltk-guiWidgetsToolkittcltk-character: no visible global
  function definition for ‘rnorm’
.font<-,gTexttcltk-guiWidgetsToolkittcltk: no visible global function
  definition for ‘rnorm’
.font<-,tcltkObject-guiWidgetsToolkittcltk: no visible global function
  definition for ‘rnorm’
.gdf,guiWidgetsToolkittcltk: no visible global function definition for
  ‘head’
.visible<-,gGraphicstcltk-guiWidgetsToolkittcltk-ANY: no visible global
  function definition for ‘dev.set’
Undefined global functions or variables:
  browseURL dev.set head rnorm runif tail write.csv
Consider adding
  importFrom("grDevices", "dev.set")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "browseURL", "head", "tail", "write.csv")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘fields’ ‘lars’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gwl.beta: no visible global function definition for ‘lars’
gwl.cv.err: no visible global function definition for ‘lars’
gwl.est: no visible global function definition for ‘lm’
gwr.bw.est: no visible global function definition for ‘lm’
gwr.est: no visible global function definition for ‘lm’
gwr.rsquare: no visible global function definition for ‘cor’
gwrr.est: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cor lars lm
Consider adding
  importFrom("stats", "cor", "lm")
to your NAMESPACE file.
GxMestimator: no visible global function definition for ‘na.omit’
initialization_chol: no visible global function definition for ‘cov’
initialization_corr: no visible global function definition for ‘cov’
initialization_nlmain: no visible global function definition for
  ‘lm.fit’
print.summaryGxMclass: no visible global function definition for
  ‘pnorm’
print.summaryGxMclass: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  cov lm.fit na.omit pnorm printCoefmat
Consider adding
  importFrom("stats", "cov", "lm.fit", "na.omit", "pnorm",
             "printCoefmat")
to your NAMESPACE file.
hf.bt: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
hsTableReader: no visible global function definition for ‘object.size’
hsWriteTable: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  object.size write.table
Consider adding
  importFrom("utils", "object.size", "write.table")
to your NAMESPACE file.
EMvar: no visible global function definition for ‘model.matrix’
RecodeHaplos: no visible global function definition for ‘na.omit’
RecodeHaplos: no visible global function definition for ‘tail’
anova.hapassoc: no visible global function definition for ‘pchisq’
handleMissings: no visible global function definition for ‘na.omit’
hapassoc: no visible global function definition for ‘binomial’
hapassoc: no visible global function definition for ‘formula’
hapassoc: no visible global function definition for ‘glm’
hapassoc : <anonymous>: no visible global function definition for ‘glm’
hapassoc: no visible global function definition for ‘model.frame’
hapassoc: no visible global function definition for ‘model.matrix’
hapassoc: no visible binding for global variable ‘contrasts’
hapassoc: no visible global function definition for ‘glm.control’
hapassoc : <anonymous>: no visible global function definition for
  ‘glm.control’
probY: no visible global function definition for ‘dbinom’
probY: no visible global function definition for ‘dpois’
probY: no visible global function definition for ‘dnorm’
probY: no visible global function definition for ‘dgamma’
summary.hapassoc: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  binomial contrasts dbinom dgamma dnorm dpois formula glm glm.control
  model.frame model.matrix na.omit pchisq tail
Consider adding
  importFrom("stats", "binomial", "contrasts", "dbinom", "dgamma",
             "dnorm", "dpois", "formula", "glm", "glm.control",
             "model.frame", "model.matrix", "na.omit", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
allele.marq: no visible global function definition for ‘na.omit’
depart.LDL: no visible global function definition for ‘aov’
freq.all: no visible global function definition for ‘na.omit’
hapim.LD.add: no visible global function definition for ‘optim’
hapim.LDL.add: no visible global function definition for ‘optim’
obj.haplomax.HS.add: no visible global function definition for ‘aov’
obj.haplomax.add: no visible global function definition for ‘aov’
vrais.LD.add: no visible global function definition for ‘dnorm’
vrais.LDL.add.pere: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  aov dnorm na.omit optim
Consider adding
  importFrom("stats", "aov", "dnorm", "na.omit", "optim")
to your NAMESPACE file.
Running examples in ‘Hapi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hapiCVDistance
> ### Title: Histogram of crossover distance
> ### Aliases: hapiCVDistance
> 
> ### ** Examples
> 
> data(crossover)
> hapiCVDistance(cv=crossover)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘A_Haplin_intro_installation.Rmd’ using rmarkdown
--- finished re-building ‘A_Haplin_intro_installation.Rmd’

--- re-building ‘B_Reading_data.Rmd’ using rmarkdown
--- finished re-building ‘B_Reading_data.Rmd’

--- re-building ‘C_Running_Haplin.Rmd’ using rmarkdown
Read 6 items
Read 1494 items
Read 0 items
Read 8 items
Read 9112 items
Read 0 items
Read 864 items
Read 1433376 items
Read 0 items
Quitting from lines 141-142 (C_Running_Haplin.Rmd) 
Error: processing vignette 'C_Running_Haplin.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘C_Running_Haplin.Rmd’

--- re-building ‘D_Running_Haplin_on_cluster.Rmd’ using rmarkdown
--- finished re-building ‘D_Running_Haplin_on_cluster.Rmd’

SUMMARY: processing the following file failed:
  ‘C_Running_Haplin.Rmd’

Error: Vignette re-building failed.
Execution halted
AssignQTL : <anonymous>: no visible global function definition for
  ‘rgamma’
AssignSingleQTL: no visible global function definition for ‘rgamma’
ListQTL : <anonymous>: no visible global function definition for
  ‘rgamma’
SampleBaseHaplotype: no visible global function definition for ‘runif’
SampleHaplotype: no visible global function definition for ‘rpois’
SampleHaplotype: no visible global function definition for ‘runif’
SampleHaplotype: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom rgamma rpois runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rpois", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘ape’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ape’ ‘hash’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘harrypotter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hp
> ### Title: Harry Potter Colour Map.
> ### Aliases: hp hp_pal harrypotter
> 
> ### ** Examples
> 
> library(ggplot2)
> library(hexbin)
> 
> dat <- data.frame(x = rnorm(1e4), y = rnorm(1e4))
> ggplot(dat, aes(x = x, y = y)) +
+   geom_hex() +
+   coord_fixed() +
+   scale_fill_gradientn(colours = hp(128, option = 'Always'))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [19s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  ── 1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42)  
  RNGkind() not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 2. Failure: gather replaces seed. (@test-gather.R#57)  ──────────────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 3. Failure: get.seed retrieves properly (@test-seeds.R#14)  ─────────────────
  `seed` not identical to `eseed`.
  Mean relative difference: 0.9608917
  
  ── 4. Failure: replace.seed (@test-seeds.R#29)  ────────────────────────────────
  `k` not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 5. Failure: replace.seed (@test-seeds.R#30)  ────────────────────────────────
  `l` not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 6. Failure: withseed replaces previous seed. (@test-seeds.R#56)  ────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 119 SKIPPED: 5 FAILED: 6
  1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42) 
  2. Failure: gather replaces seed. (@test-gather.R#57) 
  3. Failure: get.seed retrieves properly (@test-seeds.R#14) 
  4. Failure: replace.seed (@test-seeds.R#29) 
  5. Failure: replace.seed (@test-seeds.R#30) 
  6. Failure: withseed replaces previous seed. (@test-seeds.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace with empty importFrom: ‘utils’
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘dev’
Found the following significant warnings:
  readstat/readstat_writer.c:82:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/readstat_writer.c:276:5: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
  readstat/readstat_writer.c:331:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/sas/readstat_sas7bcat_write.c:108:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:284:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:337:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 31 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:156:5: warning: ‘strncpy’ output may be truncated copying 9 bytes from a string of length 9 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:164:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 8 [-Wstringop-truncation]
  readstat/spss/readstat_por_write.c:205:5: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/haven.Rcheck/00install.out’ for details.
extract_hazus_functions: no visible global function definition for
  ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘hazus_demo.Rmd’ using knitr
Quitting from lines 109-119 (hazus_demo.Rmd) 
Error: processing vignette 'hazus_demo.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘hazus_demo.Rmd’

SUMMARY: processing the following file failed:
  ‘hazus_demo.Rmd’

Error: Vignette re-building failed.
Execution halted
detect.movement: no visible global function definition for ‘t.test’
generate.random.conf: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm t.test
Consider adding
  importFrom("stats", "rnorm", "t.test")
to your NAMESPACE file.
PoincarePlot: no visible global function definition for ‘plot’
PoincarePlot: no visible global function definition for ‘lines’
PoincarePlot: no visible global function definition for ‘lowess’
hctest: no visible global function definition for ‘cor.test’
rdplot: no visible global function definition for ‘plot’
rdplot: no visible global function definition for ‘lines’
rdplot: no visible global function definition for ‘lowess’
rdplot: no visible global function definition for ‘rgb’
simer: no visible global function definition for ‘runif’
simer: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cor.test lines lowess plot rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "cor.test", "lowess", "rnorm", "runif")
to your NAMESPACE file.
Promax.only: no visible global function definition for ‘lm.fit’
factor.pa.ginv: no visible binding for global variable ‘median’
factor.pa.ginv: no visible global function definition for ‘cor’
factor.pa.ginv: no visible global function definition for ‘varimax’
factor.pa.ginv: no visible global function definition for ‘pchisq’
pairwise.mahalanobis: no visible global function definition for ‘cor’
pairwise.mahalanobis: no visible global function definition for
  ‘mahalanobis’
Undefined global functions or variables:
  cor lm.fit mahalanobis median pchisq varimax
Consider adding
  importFrom("stats", "cor", "lm.fit", "mahalanobis", "median", "pchisq",
             "varimax")
to your NAMESPACE file.
Running examples in ‘hdme-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv_corrected_lasso
> ### Title: Cross-validated Corrected lasso
> ### Aliases: cv_corrected_lasso
> 
> ### ** Examples
> 
> # Gaussian
> set.seed(100)
> n <- 100; p <- 50 # Problem dimensions
> # True (latent) variables
> X <- matrix(rnorm(n * p), nrow = n)
> # Measurement error covariance matrix
> # (typically estimated by replicate measurements)
> sigmaUU <- diag(x = 0.2, nrow = p, ncol = p)
> # Measurement matrix (this is the one we observe)
> W <- X + rnorm(n, sd = diag(sigmaUU))
> # Coefficient
> beta <- c(seq(from = 0.1, to = 1, length.out = 5), rep(0, p-5))
> # Response
> y <- X %*% beta + rnorm(n, sd = 1)
> # Run the corrected lasso
> cvfit <- cv_corrected_lasso(W, y, sigmaUU, no_radii = 5, n_folds = 3)
> plot(cvfit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdme-package.Rmd’ using rmarkdown

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'zeallot'

The following objects are masked from 'package:igraph':

    %->%, %<-%

Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16


Attaching package: 'dplyr'

The following objects are masked from 'package:igraph':

    as_data_frame, groups, union

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 156-162 (hdme-package.Rmd) 
Error: processing vignette 'hdme-package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘hdme-package.Rmd’

SUMMARY: processing the following file failed:
  ‘hdme-package.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘hdm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rlassoEffects
> ### Title: rigorous Lasso for Linear Models: Inference
> ### Aliases: rlassoEffects rlassoEffects.default rlassoEffects.formula
> ###   rlassoEffect
> 
> ### ** Examples
> 
> library(hdm); library(ggplot2)
> set.seed(1)
> n = 100 #sample size
> p = 100 # number of variables
> s = 3 # nubmer of non-zero variables
> X = matrix(rnorm(n*p), ncol=p)
> colnames(X) <- paste("X", 1:p, sep="")
> beta = c(rep(3,s), rep(0,p-s))
> y = 1 + X%*%beta + rnorm(n)
> data = data.frame(cbind(y,X))
> colnames(data)[1] <- "y"
> fm = paste("y ~", paste(colnames(X), collapse="+"))
> fm = as.formula(fm)                 
> lasso.effect = rlassoEffects(X, y, index=c(1,2,3,50))
> lasso.effect = rlassoEffects(fm, I = ~ X1 + X2 + X3 + X50, data=data)
> print(lasso.effect)

Call:
rlassoEffects.formula(formula = fm, data = data, I = ~X1 + X2 + 
    X3 + X50)

Coefficients:
     X1       X2       X3      X50  
2.94448  3.04127  2.97540  0.07196  

> summary(lasso.effect)
[1] "Estimates and significance testing of the effect of target variables"
    Estimate. Std. Error t value Pr(>|t|)    
X1    2.94448    0.08815  33.404   <2e-16 ***
X2    3.04127    0.08389  36.253   <2e-16 ***
X3    2.97540    0.07804  38.127   <2e-16 ***
X50   0.07196    0.07765   0.927    0.354    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1


> confint(lasso.effect)
          2.5 %    97.5 %
X1   2.77171308 3.1172421
X2   2.87685121 3.2056979
X3   2.82244962 3.1283583
X50 -0.08022708 0.2241377
> plot(lasso.effect)
Warning: Ignoring unknown aesthetics: width, h
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘hdnom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hdnom.calibrate
> ### Title: Calibrate High-Dimensional Cox Models
> ### Aliases: hdnom.calibrate
> 
> ### ** Examples
> 
> library("survival")
> 
> # Load imputed SMART data
> data("smart")
> x = as.matrix(smart[, -c(1, 2)])
> time = smart$TEVENT
> event = smart$EVENT
> y = Surv(time, event)
> 
> # Fit Cox model with lasso penalty
> fit = hdcox.lasso(x, y, nfolds = 5, rule = "lambda.1se", seed = 11)
> 
> # Model calibration by fitting the original data directly
> cal.fitting = hdnom.calibrate(
+   x, time, event, model.type = "lasso",
+   alpha = 1, lambda = fit$lasso_best_lambda,
+   method = "fitting",
+   pred.at = 365 * 9, ngroup = 5,
+   seed = 1010)
Start fitting ...
> 
> # Model calibration by 5-fold cross-validation
> cal.cv = hdnom.calibrate(
+   x, time, event, model.type = "lasso",
+   alpha = 1, lambda = fit$lasso_best_lambda,
+   method = "cv", nfolds = 5,
+   pred.at = 365 * 9, ngroup = 5,
+   seed = 1010)
Start fold 1 
Start fold 2 
Start fold 3 
Start fold 4 
Start fold 5 
> 
> print(cal.fitting)
High-Dimensional Cox Model Calibration Object
Random seed: 1010 
Calibration method: fitting
Model type: lasso 
glmnet model alpha: 1 
glmnet model lambda: 0.0235179 
glmnet model penalty factor: not specified
Calibration time point: 3285 
Number of groups formed for calibration: 5 
> summary(cal.fitting)
  Calibration Summary Table
  Predicted  Observed Lower 95% Upper 95%
1 0.6084404 0.4670959 0.3931194 0.5549932
2 0.7010189 0.6906300 0.5617393 0.8490947
3 0.7455827 0.8047966 0.7566516 0.8560051
4 0.7790308 0.8132201 0.7256294 0.9113837
5 0.8169391 0.8988891 0.8646299 0.9345058
> plot(cal.fitting)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdnom.Rmd’ using rmarkdown
Quitting from lines 193-194 (hdnom.Rmd) 
Error: processing vignette 'hdnom.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘hdnom.Rmd’

SUMMARY: processing the following file failed:
  ‘hdnom.Rmd’

Error: Vignette re-building failed.
Execution halted
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Running examples in ‘hdrcde-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hdrscatterplot
> ### Title: Scatterplot showing bivariate highest density regions
> ### Aliases: hdrscatterplot
> ### Keywords: distribution hplot smooth
> 
> ### ** Examples
> 
> 
> x <- c(rnorm(200, 0, 1), rnorm(200, 4, 1))
> y <- c(rnorm(200, 0, 1), rnorm(200, 4, 1))
> hdrscatterplot(x, y)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
coef.HDtweedie: no visible global function definition for ‘rbind2’
coef.cv.HDtweedie: no visible global function definition for ‘coef’
cv.tweediegrppath: no visible global function definition for ‘predict’
cv.tweediegrppath: no visible binding for global variable
  ‘weighted.mean’
cvcompute: no visible binding for global variable ‘weighted.mean’
error.bars: no visible global function definition for ‘segments’
lambda.interp: no visible global function definition for ‘approx’
plot.HDtweedie: no visible global function definition for ‘par’
plot.HDtweedie: no visible binding for global variable ‘plot.default’
plot.HDtweedie: no visible global function definition for ‘gray.colors’
plot.HDtweedie: no visible global function definition for ‘abline’
plot.cv.HDtweedie: no visible global function definition for ‘points’
plot.cv.HDtweedie: no visible global function definition for ‘axis’
plot.cv.HDtweedie: no visible global function definition for ‘abline’
predict.HDtweedie: no visible global function definition for ‘rbind2’
predict.HDtweedie: no visible global function definition for ‘cbind2’
predict.cv.HDtweedie: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  abline approx axis cbind2 coef gray.colors par plot.default points
  predict rbind2 segments weighted.mean
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "abline", "axis", "par", "plot.default",
             "points", "segments")
  importFrom("methods", "cbind2", "rbind2")
  importFrom("stats", "approx", "coef", "predict", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘healthcareai-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: control_chart
> ### Title: Create a control chart
> ### Aliases: control_chart
> 
> ### ** Examples
> 
> d <-
+   tibble::data_frame(
+     day = sample(c("Monday", "Tuesday", "Wednesday", "Thursday", "Friday"),
+                  100, TRUE),
+     person = sample(c("Tom", "Jane", "Alex"), 100, TRUE),
+     count = rbinom(100, 20, ifelse(day == "Friday", .5, .2)),
+     date = Sys.Date() - sample.int(100))
Warning: `data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
> 
> # Minimal arguments are the data and the column to put on the y-axis.
> # If x is not provided, observations will be plotted in order of the rows
> 
> control_chart(d, "count")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: control_chart ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘heatmaply.Rmd’ using rmarkdown
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.15.2

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================

Quitting from lines 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘heatmaply.Rmd’

SUMMARY: processing the following file failed:
  ‘heatmaply.Rmd’

Error: Vignette re-building failed.
Execution halted
heatmap.plus: no visible binding for global variable ‘dist’
heatmap.plus: no visible binding for global variable ‘hclust’
heatmap.plus : <anonymous>: no visible global function definition for
  ‘reorder’
heatmap.plus: no visible global function definition for ‘as.dendrogram’
heatmap.plus: no visible global function definition for
  ‘order.dendrogram’
heatmap.plus: no visible binding for global variable ‘sd’
heatmap.plus: no visible global function definition for ‘par’
heatmap.plus: no visible global function definition for ‘layout’
heatmap.plus: no visible global function definition for ‘image’
heatmap.plus: no visible global function definition for ‘axis’
heatmap.plus: no visible global function definition for ‘mtext’
heatmap.plus: no visible global function definition for ‘plot’
heatmap.plus: no visible global function definition for ‘frame’
heatmap.plus: no visible global function definition for ‘title’
Undefined global functions or variables:
  as.dendrogram axis dist frame hclust image layout mtext
  order.dendrogram par plot reorder sd title
Consider adding
  importFrom("graphics", "axis", "frame", "image", "layout", "mtext",
             "par", "plot", "title")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
Running examples in ‘heatwaveR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: block_average
> ### Title: Calculate yearly means for event metrics.
> ### Aliases: block_average
> 
> ### ** Examples
> 
> ts <- ts2clm(sst_WA, climatologyPeriod = c("1983-01-01", "2012-12-31"))
> res <- detect_event(ts)
> out <- block_average(res)
> summary(glm(count ~ year, out, family = "poisson"))

Call:
glm(formula = count ~ year, family = "poisson", data = out)

Deviance Residuals: 
    Min       1Q   Median       3Q      Max  
-2.3992  -1.5279  -0.5768   0.6122   3.7773  

Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
(Intercept) -105.58986   29.22236  -3.613 0.000302 ***
year           0.05308    0.01459   3.638 0.000275 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for poisson family taken to be 1)

    Null deviance: 89.964  on 32  degrees of freedom
Residual deviance: 75.723  on 31  degrees of freedom
AIC: 133.7

Number of Fisher Scoring iterations: 6

> 
> library(ggplot2)
> 
> ggplot(data = out, aes(x = year, y = count)) +
+   geom_point(colour = "salmon") +
+   geom_line() +
+   labs(x = NULL, y = "Number of events")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘heemod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run_dsa
> ### Title: Run Sensitivity Analysis
> ### Aliases: run_dsa
> 
> ### ** Examples
> 
> param <- define_parameters(
+   p1 = .5,
+   p2 = .2,
+   r = .05
+ )
> mod1 <- define_strategy(
+   transition = define_transition(
+     C, p1,
+     p2, C
+   ),
+   define_state(
+     cost = discount(543, r),
+     ly = 1
+   ),
+   define_state(
+     cost = discount(432, r),
+     ly = .5
+   )
+ )
No named state -> generating names.
No named state -> generating names.
> 
> mod2 <- define_strategy(
+   transition = define_transition(
+     C, p1,
+     p2, C
+   ),
+   define_state(
+     cost = 789,
+     ly = 1
+   ),
+   define_state(
+     cost = 456,
+     ly = .8
+   )
+ )
No named state -> generating names.
No named state -> generating names.
> 
> res2 <- run_model(
+   mod1, mod2,
+   parameters = param,
+   init = c(100, 0),
+   cycles = 10,
+   cost = cost,
+   effect = ly
+ )
No named model -> generating names.
> 
> ds <- define_dsa(
+   p1, .1, .9,
+   p2, .1, .3,
+   r, .05, .1
+ )
> print(ds)
   Low  High
p1 0.1  0.9 
p2 0.1  0.3 
r  0.05 0.1 
> 
> x <- run_dsa(res2, ds)
Running DSA on strategy 'I'...
Running DSA on strategy 'II'...
> 
> plot(x, value = "cost")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running ‘testthat.R’ [42s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(heemod)
  > 
  > ## the Sys.setenv fixes a problem running tests
  > ##   with parallel processing; related to
  > ##   https://github.com/hadley/testthat/issues/86 and
  > ##   https://github.com/hadley/testthat/issues/144
  > 
  > Sys.setenv("R_TESTS" = "")
  > test_check("heemod")
  ── 1. Error: Running model from files works. (@test_tabular_input.R#772)  ──────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: run_model_tabular(location = file.path(tempdir(), "tabular", "thr"), run_psa = TRUE, 
         run_demo = TRUE, save = TRUE, overwrite = TRUE) at testthat/test_tabular_input.R:772
  2: save_outputs(outputs, output_dir, overwrite)
  3: save_graph(this_plot, output_dir, this_file)
  4: print(plot)
  5: print.ggplot(plot)
  6: ggplot_gtable(data)
  7: ggplot_gtable.ggplot_built(data)
  8: layout$render(geom_grobs, data, theme, plot$labels)
  9: f(..., self = self)
  10: self$facet$draw_panels(panels, self$layout, self$panel_scales_x, self$panel_scales_y, 
         self$panel_params, self$coord, data, theme, self$facet_params)
  11: f(...)
  12: render_strips(col_vars, row_vars, params$labeller, theme)
  13: build_strip(y, labeller, theme, FALSE)
  14: ggstrip(grobs_right, theme, element, gp, horizontal, clip = "on")
  15: Summary.unit(structure(c(4.4, 4.4), unit = 8L, class = c("margin", "unit")), na.rm = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 471 SKIPPED: 0 FAILED: 1
  1. Error: Running model from files works. (@test_tabular_input.R#772) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘helixvis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw_wenxiang
> ### Title: Create Wenxiang diagrams to visualize alpha helical sequences.
> ### Aliases: draw_wenxiang
> 
> ### ** Examples
> 
> draw_wenxiang("GIGAVLKVLTTGLPALIS")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 52-57 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘FRB’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ctstm.Rmd’ using rmarkdown
Loading required package: survival
Quitting from lines 189-206 (ctstm.Rmd) 
Error: processing vignette 'ctstm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ctstm.Rmd’

--- re-building ‘icea.Rmd’ using rmarkdown
Quitting from lines 169-177 (icea.Rmd) 
Error: processing vignette 'icea.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘icea.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Loading required package: survival
Quitting from lines 262-269 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

--- re-building ‘psm.Rmd’ using rmarkdown
Loading required package: survival
Quitting from lines 179-198 (psm.Rmd) 
Error: processing vignette 'psm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘psm.Rmd’

SUMMARY: processing the following files failed:
  ‘ctstm.Rmd’ ‘icea.Rmd’ ‘intro.Rmd’ ‘psm.Rmd’

Error: Vignette re-building failed.
Execution halted
Warning: no function found corresponding to methods exports from ‘het.test’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  ‘methods’ ‘vars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
whites.htest: no visible global function definition for ‘residuals’
whites.htest: no visible global function definition for ‘lm’
whites.htest: no visible global function definition for ‘pchisq’
whites.htest: no visible global function definition for ‘new’
Undefined global functions or variables:
  lm new pchisq residuals
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "lm", "pchisq", "residuals")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error(s) in re-building vignettes:
  ...
--- re-building ‘detect_idiosyncratic_vignette.Rmd’ using rmarkdown
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 59-68 (detect_idiosyncratic_vignette.Rmd) 
Error: processing vignette 'detect_idiosyncratic_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘detect_idiosyncratic_vignette.Rmd’

--- re-building ‘estimate_systematic_vignette.Rmd’ using rmarkdown
--- finished re-building ‘estimate_systematic_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘detect_idiosyncratic_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘README.Rmd’ using rmarkdown
--- finished re-building ‘README.Rmd’

--- re-building ‘confusion-matrix.Rmd’ using rmarkdown
--- finished re-building ‘confusion-matrix.Rmd’

--- re-building ‘cross-validation.Rmd’ using rmarkdown
Quitting from lines 96-105 (cross-validation.Rmd) 
Error: processing vignette 'cross-validation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cross-validation.Rmd’

--- re-building ‘how-to-make-heuristic.Rmd’ using rmarkdown
--- finished re-building ‘how-to-make-heuristic.Rmd’

--- re-building ‘reproducing-results.Rmd’ using rmarkdown
--- finished re-building ‘reproducing-results.Rmd’

SUMMARY: processing the following file failed:
  ‘cross-validation.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘hexbin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ColorRamps
> ### Title: Color Ramps on Perceptually Linear Scales
> ### Aliases: ColorRamps LinGray BTC BTY LinOCS heat.ob magent plinrain
> ### Keywords: color
> 
> ### ** Examples
> 
> h <- hexbin(rnorm(10000),rnorm(10000))
> plot(h, colramp= BTY)
Error in (function (cl, name, valueClass)  : 
  c("assignment of an object of class “simpleUnit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE", "assignment of an object of class “unit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE")
Calls: plot -> plot -> .local -> hexViewport -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hexagon_binning.Rnw’ using Sweave

Error: processing vignette 'hexagon_binning.Rnw' failed with diagnostics:
 chunk 1 (label = comphexsq) 
Error in (function (cl, name, valueClass)  : 
  c("assignment of an object of class “simpleUnit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE", "assignment of an object of class “unit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE")

--- failed re-building ‘hexagon_binning.Rnw’

SUMMARY: processing the following file failed:
  ‘hexagon_binning.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘hexSticker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sticker
> ### Title: sticker
> ### Aliases: sticker
> 
> ### ** Examples
> 
> library(ggplot2)
> p <- ggplot(aes(x = mpg, y = wt), data = mtcars) + geom_point()
> p <- p + theme_void() + theme_transparent()
> sticker(p, package="hexSticker")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: sticker ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘grplasso’ ‘lattice’ ‘rgl’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HubNetwork: no visible global function definition for ‘rbinom’
HubNetwork: no visible global function definition for ‘runif’
HubNetwork: no visible global function definition for ‘cov2cor’
binaryMCMC: no visible global function definition for ‘rbinom’
image.hbn: no visible global function definition for ‘col2rgb’
image.hbn: no visible global function definition for ‘rgb’
image.hbn: no visible global function definition for ‘dev.new’
image.hbn: no visible global function definition for ‘par’
image.hbn: no visible global function definition for ‘image’
image.hcov: no visible global function definition for ‘col2rgb’
image.hcov: no visible global function definition for ‘rgb’
image.hcov: no visible global function definition for ‘dev.new’
image.hcov: no visible global function definition for ‘par’
image.hcov: no visible global function definition for ‘image’
image.hglasso: no visible global function definition for ‘col2rgb’
image.hglasso: no visible global function definition for ‘rgb’
image.hglasso: no visible global function definition for ‘dev.new’
image.hglasso: no visible global function definition for ‘par’
image.hglasso: no visible global function definition for ‘image’
plot.hbn: no visible global function definition for ‘rgb’
plot.hbn: no visible global function definition for ‘plot’
plot.hcov: no visible global function definition for ‘rgb’
plot.hcov: no visible global function definition for ‘plot’
plot.hglasso: no visible global function definition for ‘rgb’
plot.hglasso: no visible global function definition for ‘plot’
Undefined global functions or variables:
  col2rgb cov2cor dev.new image par plot rbinom rgb runif
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rgb")
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov2cor", "rbinom", "runif")
to your NAMESPACE file.
Running examples in ‘hhi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_hhi
> ### Title: Plots a Herfindahl-Hirschman Index Time Series
> ### Aliases: plot_hhi
> 
> ### ** Examples
> 
> hhi <- c(45,60,50,100,94,15,88,200,215,68,
+ 47,62,52,102,96,17,90,202,217,70)
> year <- c(1990,1991,1992,1993,1994,1995,1996,1997,1998,1999,
+ 2000,2001,2002,2003,2004,2005,2006,2007,2008,2009)
> data <- data.frame(hhi, year)
> plot_hhi(data, "year", "hhi")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘HH-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hovBF
> ### Title: Homogeneity of Variance: Brown-Forsyth method
> ### Aliases: hovBF hovplotBF
> ### Keywords: dplot
> 
> ### ** Examples
> 
> data(batch)
> batch1.aov <- aov(Calcium ~ Batch, data=batch)
> anova(batch1.aov)
Analysis of Variance Table

Response: Calcium
          Df   Sum Sq  Mean Sq F value   Pr(>F)   
Batch      4 0.096976 0.024244  5.5352 0.003626 **
Residuals 20 0.087600 0.004380                    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> hovBF(Calcium ~ Batch, data=batch)

	hov: Brown-Forsyth

data:  Calcium
F = 0.032193, df:Batch = 4, df:Residuals = 20, p-value = 0.9978
alternative hypothesis: variances are not identical

> hovplotBF(Calcium ~ Batch, data=batch)
Warning in formals(fun) : argument is not a function
Warning in formals(fun) : argument is not a function
Error in unit(0.5 * showr, "strwidth", list(right)) : 
  no string supplied for 'strwidth/height' unit
Calls: <Anonymous> ... strip -> do.call -> strip.default -> paste.and.draw -> unit
Execution halted
Unexported objects imported by ':::' calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::guide_axis’
  ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
Running examples in ‘hierarchicalSets-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_outlier_distribution
> ### Title: Plot the outlying elements of a HierarchicalSet object
> ### Aliases: plot_outlier_distribution
> 
> ### ** Examples
> 
> data('twitter')
> 
> twitSet <- create_hierarchy(twitter)
> plot_outlier_distribution(twitSet)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
banded: no visible global function definition for ‘toeplitz’
gpband: no visible global function definition for ‘toeplitz’
hierband.cv: no visible global function definition for ‘cov’
hierband.cv: no visible binding for global variable ‘sd’
subdiag.thresh: no visible global function definition for ‘uniroot’
subdiag.thresh: no visible global function definition for ‘toeplitz’
Undefined global functions or variables:
  cov sd toeplitz uniroot
Consider adding
  importFrom("stats", "cov", "sd", "toeplitz", "uniroot")
to your NAMESPACE file.
booties: no visible binding for global variable ‘sd’
booties: no visible binding for global variable ‘quantile’
hierDiversity: no visible global function definition for
  ‘txtProgressBar’
hierDiversity: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  quantile sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running examples in ‘HierDpart-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DeltaDcorplot
> ### Title: Plot correlation matrix for pairwise Delta D
> ### Aliases: DeltaDcorplot
> ### Keywords: Correlation plot Plot genetic differentiation
> 
> ### ** Examples
> 
> # example genepop file
> f <- system.file('extdata',package='HierDpart')
> infile <- file.path(f, "Island.gen")
> DeltaDcorplot(infile,ncode=3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘HierDpart.Rmd’ using rmarkdown
Quitting from lines 59-60 (HierDpart.Rmd) 
Error: processing vignette 'HierDpart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘HierDpart.Rmd’

SUMMARY: processing the following file failed:
  ‘HierDpart.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘XMLRPC’
calcPower: no visible global function definition for ‘pchisq’
calcPower: no visible global function definition for ‘qchisq’
delta2 : K1: no visible global function definition for ‘qnorm’
delta2: no visible global function definition for ‘qnorm’
delta2: no visible global function definition for ‘pnorm’
delta2: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hier.part.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘gtools’ which was already attached by Depends.
  Please remove these calls from your code.
all.regs: no visible global function definition for ‘glm’
all.regs: no visible global function definition for ‘logLik’
combos: no visible global function definition for ‘menu’
current.model: no visible global function definition for ‘formula’
current.model: no visible global function definition for ‘glm’
current.model: no visible global function definition for ‘logLik’
current.model: no visible global function definition for ‘lm’
rand.hp: no visible global function definition for ‘runif’
rand.hp: no visible global function definition for ‘sd’
Undefined global functions or variables:
  formula glm lm logLik menu runif sd
Consider adding
  importFrom("stats", "formula", "glm", "lm", "logLik", "runif", "sd")
  importFrom("utils", "menu")
to your NAMESPACE file.
compute.contrasts: no visible binding for global variable ‘sd’
compute.contrasts: no visible global function definition for ‘cor’
compute.contrasts: no visible global function definition for ‘sd’
plot.estfdr: no visible global function definition for ‘plot’
plot.hiertest: no visible global function definition for ‘plot’
plot.hiertest: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cor legend plot sd
Consider adding
  importFrom("graphics", "legend", "plot")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘nnet’ ‘stats’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘nnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CLX.sim.Covtest: no visible global function definition for ‘cov’
CLX.sim.equalcov: no visible global function definition for ‘cov’
CLX.sim.unequalcov: no visible global function definition for ‘cov’
CLX.test.equalcov: no visible global function definition for ‘cov’
CLX.test.unequalcov: no visible global function definition for ‘cov’
ChenQin.sim: no visible global function definition for ‘pnorm’
ChenQin.test: no visible global function definition for ‘pnorm’
GCT.sim: no visible binding for global variable ‘var’
GCT.sim: no visible global function definition for ‘acf’
GCT.sim: no visible global function definition for ‘pnorm’
GCT.test: no visible binding for global variable ‘var’
GCT.test: no visible global function definition for ‘acf’
GCT.test: no visible global function definition for ‘pnorm’
GCT.test.missing: no visible binding for global variable ‘var’
GCT.test.missing: no visible global function definition for ‘acf’
GCT.test.missing: no visible global function definition for ‘pnorm’
SK.sim: no visible global function definition for ‘cov’
SK.sim: no visible global function definition for ‘pnorm’
SK.test: no visible global function definition for ‘cov’
SK.test: no visible global function definition for ‘pnorm’
build2popData : <anonymous>: no visible global function definition for
  ‘rnorm’
build2popData: no visible global function definition for ‘arima.sim’
build2popData_muYafunction : <anonymous>: no visible global function
  definition for ‘rnorm’
build2popData_muYafunction: no visible global function definition for
  ‘arima.sim’
innovate: no visible binding for global variable ‘rnorm’
rdblepareto: no visible global function definition for ‘runif’
rgammashift: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  acf arima.sim cov pnorm rgamma rnorm runif var
Consider adding
  importFrom("stats", "acf", "arima.sim", "cov", "pnorm", "rgamma",
             "rnorm", "runif", "var")
to your NAMESPACE file.
Func.ABOD: no visible global function definition for ‘combn’
Func.ABOD: no visible global function definition for ‘var’
Func.SOD: no visible global function definition for ‘var’
Func.trans : erf: no visible global function definition for ‘pnorm’
Func.trans: no visible global function definition for ‘sd’
Undefined global functions or variables:
  combn pnorm sd var
Consider adding
  importFrom("stats", "pnorm", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running examples in ‘HighDimOut-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Func.ABOD
> ### Title: Angle-based outlier detection (ABOD) algorithm
> ### Aliases: Func.ABOD
> 
> ### ** Examples
> 
> library(ggplot2)
> res.ABOD <- Func.ABOD(data=TestData[,1:2], basic=FALSE, perc=0.2)
Warning: executing %dopar% sequentially: no parallel backend registered
> data.temp <- TestData[,1:2]
> data.temp$Ind <- NA
> data.temp[order(res.ABOD, decreasing = FALSE)[1:10],"Ind"] <- "Outlier"
> data.temp[is.na(data.temp$Ind),"Ind"] <- "Inlier"
> data.temp$Ind <- factor(data.temp$Ind)
> ggplot(data = data.temp) + geom_point(aes(x = x, y = y, color=Ind, shape=Ind))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
BenjaminiHochberg: no visible global function definition for ‘p.adjust’
CaoKosorok : CKfunc: no visible global function definition for ‘pnorm’
CaoKosorok : <anonymous>: no visible global function definition for
  ‘pnorm’
StoreyTibshirani: no visible global function definition for
  ‘smooth.spline’
plotI_Lines: no visible global function definition for ‘par’
plotI_Lines: no visible global function definition for ‘lines’
plotI_Lines: no visible global function definition for ‘legend’
plotI_Points: no visible global function definition for ‘points’
plotI_Points: no visible global function definition for ‘legend’
tStatistic : <anonymous>: no visible global function definition for
  ‘t.test’
venn2: no visible global function definition for ‘plot.new’
venn3: no visible global function definition for ‘plot.new’
Undefined global functions or variables:
  legend lines p.adjust par plot.new pnorm points smooth.spline t.test
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot.new", "points")
  importFrom("stats", "p.adjust", "pnorm", "smooth.spline", "t.test")
to your NAMESPACE file.
occupancy: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
data_simu: no visible global function definition for ‘runif’
data_simu: no visible global function definition for ‘rbinom’
data_simu: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rbinom rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rnorm", "runif")
to your NAMESPACE file.
overlay.sim: no visible global function definition for ‘points’
plotDistr: no visible global function definition for ‘dev.hold’
plotDistr: no visible global function definition for ‘dev.flush’
plotDistr: no visible global function definition for ‘plot’
plotDistr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  dev.flush dev.hold plot points segments
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold")
  importFrom("graphics", "plot", "points", "segments")
to your NAMESPACE file.
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘hiPOD/R/predictPoolNCP.R’:
  data(ncp.pool.pred)
See section ‘Good practice’ in ‘?data’.
arms: no visible global function definition for ‘rnorm’
rballunif: no visible global function definition for ‘rnorm’
rballunif: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Running examples in ‘hIRT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: latent_scores
> ### Title: Estimates of Latent Preferences/Abilities
> ### Aliases: latent_scores
> 
> ### ** Examples
> 
> y <- nes_econ2008[, -(1:3)]
> x <- model.matrix( ~ party * educ, nes_econ2008)
> z <- model.matrix( ~ party, nes_econ2008)
> nes_m1 <- hgrm(y, x, z)
...................
 converged at iteration 19 
> pref <- latent_scores(nes_m1)
> require(ggplot2)
Loading required package: ggplot2
> ggplot(data = nes_econ2008) +
+ geom_density(aes(x = pref$est, col = party))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘HistData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bowley
> ### Title: Bowley's data on values of British and Irish trade, 1855-1899
> ### Aliases: Bowley
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Bowley)
> 
> # plot the data 
> with(Bowley,plot(Year, Value, type='b', 
+ 	ylab="Value of British and Irish Exports",
+ 	main="Bowley's example of the method of smoothing curves"))
> 
> # find moving averages-- use center alignment (requires width=ODD)
> require(gtools, warn.conflicts=FALSE)
Loading required package: gtools
> mav3<-running(Bowley$Value, width=3, align="center")
> mav5<-running(Bowley$Value, width=5, align="center")
> mav9<-running(Bowley$Value, width=9, align="center")
> lines(Bowley$Year[2:44], mav3, col='blue', lty=2)
> lines(Bowley$Year[3:43], mav5, col='green3', lty=3)
> lines(Bowley$Year[5:41], mav9, col='brown', lty=4)
> 
> # add lowess smooth
> lines(lowess(Bowley), col='red', lwd=2)
> 
> require(ggplot2, warn.conflicts=FALSE)
Loading required package: ggplot2
> qplot(Year,Value, data=Bowley)+geom_smooth()
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘HistDAWass-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: data2hist
> ### Title: From real data to distributionH.
> ### Aliases: data2hist
> 
> ### ** Examples
> 
> data=rnorm(n = 1000,mean = 2,sd = 3)
> mydist=data2hist(data)
> plot(mydist)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘historydata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: early_colleges
> ### Title: Early colleges in the United States
> ### Aliases: early_colleges
> ### Keywords: datasets
> 
> ### ** Examples
> 
> head(early_colleges)
                 college         original_name         city state established
1                Harvard                  <NA>    Cambridge    MA        1636
2       William and Mary                  <NA> Williamsburg    VA        1693
3                   Yale                  <NA>    New Haven    CT        1701
4 Pennsylvania, Univ. of                  <NA> Philadelphia    PA        1740
5              Princeton College of New Jersey    Princeton    NJ        1746
6               Columbia        King's College     New York    NY        1754
                           sponsorship
1 Congregational; after 1805 Unitarian
2                             Anglican
3                       Congregational
4                    Nondenominational
5                         Presbyterian
6                             Anglican
> if(require(ggplot2)) {
+   ggplot(early_colleges, aes(x = established)) + geom_bar(binwidth = 5) +
+   ggtitle("Founding Dates of Early American Colleges")
+ }
Loading required package: ggplot2
Warning: `geom_bar()` no longer has a `binwidth` parameter. Please use `geom_histogram()` instead.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package suggested but not available for checking: ‘FGN’
Running examples in ‘HLMdiag-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare_eb_ls
> ### Title: Visually comparing shrinkage and LS estimates
> ### Aliases: compare_eb_ls
> 
> ### ** Examples
> 
> library(lme4)
Loading required package: Matrix
> wages.fm1 <- lmer(lnw ~ exper + (exper | id), data = wages)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00609024 (tol = 0.002, component 1)
> wages.sepLM <- adjust_lmList(lnw ~ exper | id, data = wages)
> rancoef.eb <- coef(wages.fm1)$id
> rancoef.ols <- coef(wages.sepLM) # note diff. length than rancoef.eb
> compare_eb_ls(eb = rancoef.eb[rownames(rancoef.ols),], ols = rancoef.ols, identify = 0.01)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: compare_eb_ls ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Hmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggfreqScatter
> ### Title: Frequency Scatterplot
> ### Aliases: ggfreqScatter
> ### Keywords: hplot
> 
> ### ** Examples
> 
> set.seed(1)
> x <- rnorm(1000)
> y <- rnorm(1000)
> count <- sample(1:100, 1000, TRUE)
> x <- rep(x, count)
> y <- rep(y, count)
> # color=alpha=NULL below makes loess smooth over all points
> g <- ggfreqScatter(x, y) +   # might add g=0 if using plotly
+       geom_smooth(aes(color=NULL, alpha=NULL), se=FALSE) +
+       ggtitle("Using Deciles of Frequency Counts, 2500 Bins")
> g
Warning: Using alpha for a discrete variable is not advised.
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
baumwelchcont: no visible global function definition for ‘dnorm’
hmmcontSimul: no visible global function definition for ‘rnorm’
hmmcontSimul: no visible global function definition for ‘rbinom’
plot.ContObservHMM: no visible global function definition for ‘plot’
plot.ContObservHMM: no visible global function definition for ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘dnorm’
statesDistributionsPlot: no visible global function definition for ‘sd’
statesDistributionsPlot: no visible global function definition for
  ‘plot’
statesDistributionsPlot: no visible global function definition for
  ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘legend’
summary.ContObservHMM: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm legend lines plot rbinom rnorm sd
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "dnorm", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
dishonestCasino: no visible global function definition for ‘plot’
dishonestCasino: no visible global function definition for ‘axis’
dishonestCasino: no visible global function definition for ‘text’
dishonestCasino: no visible global function definition for ‘rect’
dishonestCasino: no visible global function definition for ‘rgb’
dishonestCasino: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis plot points rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "plot", "points", "rect", "text")
to your NAMESPACE file.
PlotBasic: no visible global function definition for ‘dev.new’
PlotBasic: no visible global function definition for ‘par’
PlotBasic: no visible global function definition for ‘plot’
PlotBasic: no visible global function definition for ‘grid’
PlotBasic: no visible global function definition for ‘lines’
PlotChoice : plotgraph: no visible global function definition for ‘par’
PlotChoice : plotgraph: no visible global function definition for
  ‘plot’
PlotChoice : plotgraph: no visible global function definition for
  ‘grid’
PlotChoice : plotgraph: no visible global function definition for
  ‘points’
PlotChoice : plotgraph: no visible global function definition for
  ‘lines’
PlotChoice : plotgraph: no visible global function definition for
  ‘axis’
PlotChoice : plotgraph: no visible global function definition for
  ‘mtext’
Undefined global functions or variables:
  axis dev.new grid lines mtext par plot points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "grid", "lines", "mtext", "par", "plot",
             "points")
to your NAMESPACE file.
Running examples in ‘HoRM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: regressogram
> ### Title: Regressogram
> ### Aliases: regressogram
> ### Keywords: file
> 
> ### ** Examples
>  
> ## Regressogram for the natural gas dataset.
> 
> data(gas)
> 
> regressogram(x = gas$LA, y = gas$OK, nbins = 6, x.lab = "LA",
+              y.lab = "OK", main = "Regressogram")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
hornpa: no visible global function definition for ‘rnorm’
hornpa: no visible global function definition for ‘cor’
hornpa: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cor quantile rnorm
Consider adding
  importFrom("stats", "cor", "quantile", "rnorm")
to your NAMESPACE file.
hpbayes.plot: no visible global function definition for ‘par’
hpbayes.plot: no visible global function definition for ‘plot’
hpbayes.plot: no visible global function definition for ‘points’
postpri.plot: no visible global function definition for ‘par’
postpri.plot: no visible global function definition for ‘plot’
postpri.plot: no visible global function definition for ‘points’
postpri.plot: no visible global function definition for ‘segments’
postpri.plot: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot par plot points segments
Consider adding
  importFrom("graphics", "boxplot", "par", "plot", "points", "segments")
to your NAMESPACE file.
ApproxC: no visible global function definition for ‘convolve’
DMC: no visible global function definition for ‘median’
DMC: no visible global function definition for ‘ecdf’
ToSWF: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  convolve ecdf median write.table
Consider adding
  importFrom("stats", "convolve", "ecdf", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in ‘hpiR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.hpi
> ### Title: Plot method for 'hpi' object
> ### Aliases: plot.hpi
> 
> ### ** Examples
> 
> 
>  # Load data
>  data(ex_sales)
> 
>  # Create index with raw transaction data
>  rt_index <- rtIndex(trans_df = ex_sales,
+                      periodicity = 'monthly',
+                      min_date = '2010-06-01',
+                      max_date = '2015-11-30',
+                      adj_type = 'clip',
+                      date = 'sale_date',
+                      price = 'sale_price',
+                      trans_id = 'sale_id',
+                      prop_id = 'pinx',
+                      estimator = 'robust',
+                      log_dep = TRUE,
+                      trim_model = TRUE,
+                      max_period = 48,
+                      smooth = FALSE)
Supplied "min_date" date is greater than minimum of transactions. Clipping transactions.

Supplied "max_date" is less than maximum of transactions. Clipping transactions.

> 
>  # Plot data
>  plot(rt_index)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘classstructure.Rmd’ using rmarkdown
--- finished re-building ‘classstructure.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 228-230 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
bracket: no visible global function definition for ‘segments’
Undefined global functions or variables:
  segments
Consider adding
  importFrom("graphics", "segments")
to your NAMESPACE file.
Running examples in ‘hrbrthemes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_check
> ### Title: Spell check ggplot2 plot labels
> ### Aliases: gg_check
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> df <- data.frame(x=c(20, 25, 30), y=c(4, 4, 4), txt=c("One", "Two", "Three"))
> 
> # not piping
> ggplot(mtcars, aes(mpg, wt)) +
+   geom_point() +
+   labs(x="This is some txt", y="This is more text",
+        title="Thisy is a titlle",
+        subtitle="This is a subtitley",
+        caption="This is a captien") -> gg
> 
> gg_check(gg)
Possible misspelled words in [title]: (Thisy, titlle)
Possible misspelled words in [subtitle]: (subtitley)
Possible misspelled words in [caption]: (captien)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘why_hrbrthemes.Rmd’ using rmarkdown
Quitting from lines 36-51 (why_hrbrthemes.Rmd) 
Error: processing vignette 'why_hrbrthemes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘why_hrbrthemes.Rmd’

SUMMARY: processing the following file failed:
  ‘why_hrbrthemes.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘HRM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hrm.plot
> ### Title: Plots profiles of the groups in case of one whole- and one
> ###   subplot-factor.
> ### Aliases: hrm.plot
> ### Keywords: internal
> 
> ### ** Examples
> 
> data(EEG)
> head(EEG)
  group    value sex subject variable region dimension
1  SCC+ 2.804180   W       1        1      1         1
2  SCC+ 2.285004   W       1        1      2         2
3  SCC+ 1.473094   W       1        1      3         3
4  SCC+ 1.548939   W       1        1      4         4
5  SCC+ 2.160346   W       1        1      5         5
6  SCC+ 2.143525   W       1        1      6         6
> 
> # plots profiles according to groups with
> # subplot-factor called dimension
> 
> # first create an HRM object
> object_hrm <- hrm_test(value ~ group*dimension, subject = "subject", data = EEG)
> 
> # plot the HRM object, here we use the additional argument 'theme_bw()' for ggplot2
> plot(object_hrm, legend = TRUE, legend.title = "Group", ... =  theme_bw() )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
File ‘hSDM/libs/hSDM.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
hsicCCA: no visible global function definition for ‘median’
hsicCCA: no visible global function definition for ‘dist’
hsicCCAfunc: no visible global function definition for ‘rnorm’
hsicCCAfunc: no visible global function definition for ‘runif’
hsicCCAfunc: no visible global function definition for ‘optim’
ktaCCA: no visible global function definition for ‘median’
ktaCCA: no visible global function definition for ‘dist’
ktaCCAfunc: no visible global function definition for ‘rnorm’
ktaCCAfunc: no visible global function definition for ‘runif’
ktaCCAfunc: no visible global function definition for ‘optim’
Undefined global functions or variables:
  dist median optim rnorm runif
Consider adding
  importFrom("stats", "dist", "median", "optim", "rnorm", "runif")
to your NAMESPACE file.
get.d: no visible global function definition for ‘dgeom’
get.d: no visible global function definition for ‘dnbinom’
get.d: no visible global function definition for ‘dpois’
get.pdf: no visible global function definition for ‘dnorm’
get.pdf: no visible global function definition for ‘dpois’
get.pdf: no visible global function definition for ‘dmvnorm’
hsmm: no visible global function definition for ‘uniroot’
hsmm.sim: no visible global function definition for ‘rbinom’
hsmm.sim: no visible global function definition for ‘rnorm’
hsmm.sim: no visible global function definition for ‘rpois’
hsmm.sim: no visible global function definition for ‘rmvnorm’
loggeom.update: no visible global function definition for ‘plogis’
rmt: no visible global function definition for ‘rt’
rmt: no visible global function definition for ‘rnorm’
rmt: no visible global function definition for ‘rchisq’
rvm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dgeom dmvnorm dnbinom dnorm dpois plogis rbinom rchisq rmvnorm rnorm
  rpois rt runif uniroot
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dnorm", "dpois", "plogis",
             "rbinom", "rchisq", "rnorm", "rpois", "rt", "runif",
             "uniroot")
to your NAMESPACE file.
Huber: no visible global function definition for ‘quantile’
SSVD.iter.thresh: no visible global function definition for ‘mad’
error.est.full: no visible global function definition for ‘mad’
error.est.full : <anonymous>: no visible global function definition for
  ‘median’
low_rank: no visible global function definition for ‘median’
low_rank: no visible global function definition for ‘mad’
low_rank: no visible global function definition for ‘sd’
select.indices: no visible global function definition for ‘mad’
select.indices: no visible global function definition for ‘median’
select.indices: no visible global function definition for ‘pnorm’
select.indices: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  mad median p.adjust pnorm quantile sd
Consider adding
  importFrom("stats", "mad", "median", "p.adjust", "pnorm", "quantile",
             "sd")
to your NAMESPACE file.
BasicHTML: no visible global function definition for ‘png’
BasicHTML: no visible global function definition for ‘dev.list’
BasicHTML: no visible global function definition for ‘dev.off’
FramedHTML: no visible global function definition for ‘graphics.off’
Undefined global functions or variables:
  dev.list dev.off graphics.off png
Consider adding
  importFrom("grDevices", "dev.list", "dev.off", "graphics.off", "png")
to your NAMESPACE file.
getToHost: no visible global function definition for ‘make.socket’
getToHost: no visible global function definition for ‘write.socket’
getToHost: no visible global function definition for ‘read.socket’
getToHost: no visible global function definition for ‘close.socket’
postToHost: no visible global function definition for ‘runif’
simplePostToHost: no visible global function definition for
  ‘make.socket’
simplePostToHost: no visible global function definition for
  ‘write.socket’
simplePostToHost: no visible global function definition for
  ‘read.socket’
simplePostToHost: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket make.socket read.socket runif write.socket
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "close.socket", "make.socket", "read.socket",
             "write.socket")
to your NAMESPACE file.
Package in Depends field not imported from: ‘testthat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Calculate3D: no visible global function definition for ‘persp’
CalculateHUM_Ex: no visible global function definition for ‘combn’
CalculateHUM_Plot: no visible global function definition for ‘plot’
CalculateHUM_Plot: no visible global function definition for ‘polygon’
CalculateHUM_Plot: no visible global function definition for ‘text’
CalculateHUM_Plot: no visible global function definition for ‘points’
CalculateHUM_Plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘hutils.Rmd’ using rmarkdown
Quitting from lines 396-404 (hutils.Rmd) 
Error: processing vignette 'hutils.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘hutils.Rmd’

SUMMARY: processing the following file failed:
  ‘hutils.Rmd’

Error: Vignette re-building failed.
Execution halted
HWEImportSamp: no visible global function definition for ‘dnorm’
HWEImportSamp: no visible global function definition for ‘rnorm’
HWEmodelsMLE: no visible global function definition for ‘optim’
HWEsimdat: no visible global function definition for ‘rmultinom’
LambdaOptim: no visible global function definition for ‘rnorm’
LambdaOptim : LambdaPriorChoice: no visible global function definition
  for ‘quantile’
LambdaOptim: no visible global function definition for ‘optim’
SinglefPrior: no visible global function definition for ‘rnorm’
SinglefReject: no visible global function definition for ‘runif’
TriangNormHWE: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  dnorm optim pbeta quantile rmultinom rnorm runif
Consider adding
  importFrom("stats", "dnorm", "optim", "pbeta", "quantile", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
HW.plain: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
getHwriterVersion: no visible global function definition for
  ‘sessionInfo’
hmapRowCol: no visible global function definition for ‘na.omit’
hwriteImage: no visible global function definition for ‘dev.print’
hwriteImage: no visible binding for global variable ‘png’
showExample: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL dev.print na.omit png sessionInfo
Consider adding
  importFrom("grDevices", "dev.print", "png")
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "sessionInfo")
to your NAMESPACE file.
Running examples in ‘HWxtest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hwx.test
> ### Title: Test for HW by either full enumeration or Monte Carlo.
> ### Aliases: hwx.test
> 
> ### ** Examples
> 
> # Data from Louis and Dempster 1987 Table 2 and Guo and Thompson 1992 Figure 2:
> c <- c(0,3,1,5,18,1,3,7,5,2)
> hwx.test(c)

*****    Sample of 45 diploids with 4 alleles
Full enumeration of 162365 tables to test for HW

P value (LLR)   = 0.012945
P value (Prob)  = 0.017442
P value (U)     = 0.003343 (test for heterozygote excess)
P value (Chisq) = 0.020170
> # To see a histogram of the LLR statistic:
> hwx.test(c, histobins=TRUE)

*****    Sample of 45 diploids with 4 alleles
Full enumeration of 162365 tables to test for HW

P value (LLR)   = 0.012945
P value (Prob)  = 0.017442
P value (U)     = 0.003343 (test for heterozygote excess)
P value (Chisq) = 0.020170
Loading required namespace: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘HWxtest.Rmd’ using rmarkdown
Quitting from lines 146-147 (HWxtest.Rmd) 
Error: processing vignette 'HWxtest.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘HWxtest.Rmd’

SUMMARY: processing the following file failed:
  ‘HWxtest.Rmd’

Error: Vignette re-building failed.
Execution halted
hybridMC: no visible global function definition for ‘txtProgressBar’
hybridMC : pbFun: no visible global function definition for
  ‘setTxtProgressBar’
hybridMC: no visible global function definition for ‘mcmc’
Undefined global functions or variables:
  mcmc setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
ARPIEM2012.Lmom.sample: no visible global function definition for ‘var’
ARPIEM2012.freq: no visible binding for global variable ‘quantile’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.Qind_camp: no visible global
  function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.Qind_reg_moltiplicativo: no
  visible global function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.LCV_camp.LCA_camp: no visible
  global function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.LCV_camp.LCA_reg_additivo: no
  visible global function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments :
  ARPIEM2012.sim.LCV_reg_moltiplicativo.LCA_reg_additivo: no visible
  global function definition for ‘rnorm’
Undefined global functions or variables:
  quantile rnorm var
Consider adding
  importFrom("stats", "quantile", "rnorm", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘minpack.lm’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Dstart: no visible global function definition for ‘coef’
Dstart: no visible global function definition for ‘lm’
SSkosugi: no visible global function definition for ‘pnorm’
SSkosugi: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  coef dnorm lm pnorm
Consider adding
  importFrom("stats", "coef", "dnorm", "lm", "pnorm")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_hydroscoper.Rmd’ using rmarkdown
Quitting from lines 115-125 (intro_hydroscoper.Rmd) 
Error: processing vignette 'intro_hydroscoper.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro_hydroscoper.Rmd’

--- re-building ‘stations_with_data.Rmd’ using rmarkdown
Quitting from lines 50-61 (stations_with_data.Rmd) 
Error: processing vignette 'stations_with_data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘stations_with_data.Rmd’

SUMMARY: processing the following files failed:
  ‘intro_hydroscoper.Rmd’ ‘stations_with_data.Rmd’

Error: Vignette re-building failed.
Execution halted
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS but not in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Packages in Depends field not imported from:
  ‘R.utils’ ‘ape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
requiprobable: no visible global function definition for ‘extract’
requiprobable : make.tree: no visible global function definition for
  ‘extract’
requiprobable : make.tree: no visible global function definition for
  ‘runif’
rgenetree: no visible global function definition for ‘dbinom’
rgenetree: no visible global function definition for ‘dnbinom’
rgenetree: no visible global function definition for ‘runif’
rgenetree: no visible global function definition for ‘rbinom’
rgenetree: no visible global function definition for ‘rnbinom’
Undefined global functions or variables:
  dbinom dnbinom extract rbinom rnbinom runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "rbinom", "rnbinom", "runif")
to your NAMESPACE file.
conint: no visible global function definition for ‘sd’
findroot: no visible global function definition for ‘integrate’
hypothesis: no visible global function definition for ‘sd’
hypothesis: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate sd
Consider adding
  importFrom("stats", "integrate", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MCMCpack’ ‘coda’ ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error(s) in re-building vignettes:
  ...
--- re-building ‘IAPWS95.Rmd’ using rmarkdown
Quitting from lines 121-144 (IAPWS95.Rmd) 
Error: processing vignette 'IAPWS95.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘IAPWS95.Rmd’

SUMMARY: processing the following file failed:
  ‘IAPWS95.Rmd’

Error: Vignette re-building failed.
Execution halted
ibdhap.barplot: no visible global function definition for ‘plot’
ibdhap.barplot: no visible global function definition for ‘rect’
ibdhap.compare.loci: no visible global function definition for ‘hist’
ibdhap.compare.segs: no visible global function definition for ‘tail’
ibdhap.make.calls: no visible global function definition for
  ‘count.fields’
ibdhap.make.calls: no visible global function definition for
  ‘read.table’
ibdhap.make.true: no visible global function definition for
  ‘read.table’
ibdhap.names: no visible global function definition for ‘count.fields’
ibdhap.names: no visible global function definition for ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  count.fields hist plot read.table rect tail write.table
Consider adding
  importFrom("graphics", "hist", "plot", "rect")
  importFrom("utils", "count.fields", "read.table", "tail",
             "write.table")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘perl’
create.ibd.dat: no visible global function definition for ‘read.table’
create.pairs.frame: no visible global function definition for ‘terms’
ibd.moments: no visible global function definition for ‘var’
ibdreg: no visible global function definition for ‘terms’
ibdreg: no visible global function definition for ‘as.formula’
linkage.tests: no visible global function definition for ‘pchisq’
pchibar: no visible global function definition for ‘pchisq’
plot.linkage.all: no visible global function definition for ‘plot’
plot.linkage.all: no visible global function definition for ‘title’
plotpval: no visible global function definition for ‘plot’
plotpval: no visible global function definition for ‘lines’
sim.ibd.var: no visible global function definition for ‘read.table’
sim.mark.prop: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as.formula lines pchisq plot read.table runif terms title var
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("stats", "as.formula", "pchisq", "runif", "terms", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in ‘IBDsim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: oneLocusIBD
> ### Title: Estimating pairwise IBD coefficients
> ### Aliases: oneLocusIBD
> ### Keywords: math
> 
> ### ** Examples
> 
> ### Example 1: Full siblings
> x <- nuclearPed(2) 
> Nsim <- 100 # Should be increased substantially
> 
> # Autosomal kappa: Estimate vs exact 
> k_est = oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim, seed=123)
---------------
Performing unconditional simulation
Mode: autosomal 
Recombination model: haldane (poisson process) 
Number of simulations: 100 
Simulation finished. Time used: 0.026 seconds
---------------
IBD analysis finished. Total time used: 0.029 seconds.
> k_exact = c(0.25, 0.5, 0.25)
> stopifnot(all(round(k_est - k_exact, 1) == 0))
Error: all(round(k_est - k_exact, 1) == 0) is not TRUE
Execution halted
CreateVoronoi: no visible global function definition for ‘slot’
CreateVoronoi : <anonymous>: no visible global function definition for
  ‘slot’
CreateVoronoi: no visible global function definition for ‘chull’
ExtractIMFi2D: no visible global function definition for ‘par’
LocatedAtBoundary: no visible global function definition for
  ‘txtProgressBar’
LocatedAtBoundary: no visible global function definition for
  ‘setTxtProgressBar’
PlotFit: no visible global function definition for ‘par’
iBEEMD: no visible global function definition for ‘is’
iBEEMD: no visible global function definition for ‘sd’
iBEEMD: no visible global function definition for ‘txtProgressBar’
iBEEMD: no visible global function definition for ‘rnorm’
iBEEMD: no visible global function definition for ‘setTxtProgressBar’
iBEEMD: no visible global function definition for ‘terrain.colors’
rbfcreate: no visible global function definition for ‘is’
rbfcreate : rbfAssemble: no visible global function definition for
  ‘dist’
rbfinterp: no visible global function definition for ‘is’
rbfinterp: no visible global function definition for ‘dist’
Undefined global functions or variables:
  chull dist is par rnorm sd setTxtProgressBar slot terrain.colors
  txtProgressBar
Consider adding
  importFrom("grDevices", "chull", "terrain.colors")
  importFrom("graphics", "par")
  importFrom("methods", "is", "slot")
  importFrom("stats", "dist", "rnorm", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘SparkR’
Iboot: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
..placeOrder: no visible global function definition for ‘str’
.reqMktData.vignette: no visible global function definition for
  ‘flush.console’
e_portfolio_value: no visible global function definition for ‘str’
print.eventPortfolioValue: no visible global function definition for
  ‘str’
print.twsContract: no visible global function definition for ‘str’
print.twsContractDetails: no visible global function definition for
  ‘str’
print.twsOrder: no visible global function definition for ‘str’
print.twsOrderState: no visible global function definition for ‘str’
print.twsScannerSubscription: no visible global function definition for
  ‘str’
reqAccountUpdates: no visible binding for global variable ‘timestamp’
reqContractDetails: no visible binding for global variable ‘timestamp’
reqHistoricalData: no visible global function definition for
  ‘flush.console’
reqHistoricalData: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  flush.console str timestamp write.table
Consider adding
  importFrom("utils", "flush.console", "str", "timestamp", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ICA: no visible global function definition for ‘runif’
plot.ICA: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
ICCbare: no visible global function definition for ‘na.omit’
ICCbare: no visible global function definition for ‘formula’
ICCbare: no visible global function definition for ‘replications’
ICCbare: no visible global function definition for ‘aggregate’
ICCbare: no visible global function definition for ‘anova’
ICCbare: no visible global function definition for ‘aov’
ICCbareF: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘na.omit’
ICCest: no visible global function definition for ‘anova’
ICCest: no visible global function definition for ‘aov’
ICCest: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘qf’
ICCest: no visible global function definition for ‘qnorm’
Nest: no visible global function definition for ‘qnorm’
effort : CIW: no visible global function definition for ‘qf’
effort: no visible global function definition for ‘plot’
effort: no visible global function definition for ‘axis’
effort: no visible global function definition for ‘lines’
effort: no visible global function definition for ‘legend’
Undefined global functions or variables:
  aggregate anova aov axis formula legend lines na.omit plot qf qnorm
  replications
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "aggregate", "anova", "aov", "formula", "na.omit",
             "qf", "qnorm", "replications")
to your NAMESPACE file.
'library' or 'require' call to ‘KernSmooth’ which was already attached by Depends.
  Please remove these calls from your code.
bickde: no visible global function definition for ‘optimize’
iclocpoly: no visible global function definition for ‘approx’
iclocpoly: no visible global function definition for ‘sd’
iclocpoly: no visible global function definition for ‘dnorm’
iclocpoly: no visible global function definition for ‘pnorm’
iclocpoly: no visible global function definition for ‘var’
inmost: no visible global function definition for ‘stack’
Undefined global functions or variables:
  approx dnorm optimize pnorm sd stack var
Consider adding
  importFrom("stats", "approx", "dnorm", "optimize", "pnorm", "sd",
             "var")
  importFrom("utils", "stack")
to your NAMESPACE file.
INCAncinner : dian: no visible global function definition for ‘cutree’
INCAncinner : bestela: no visible global function definition for
  ‘cutree’
center: no visible global function definition for ‘var’
dbhatta: no visible global function definition for ‘as.dist’
dcor: no visible global function definition for ‘cor’
dcor: no visible global function definition for ‘as.dist’
dgower: no visible global function definition for ‘as.dist’
dmahal: no visible global function definition for ‘as.dist’
dproc2: no visible global function definition for ‘as.dist’
plot.incaix: no visible global function definition for ‘barplot’
plot.incanc: no visible global function definition for ‘plot’
plot.incanc: no visible global function definition for ‘lines’
plot.incanc: no visible global function definition for ‘legend’
selectioncluster : dian: no visible global function definition for
  ‘cutree’
selectioncluster : bestela: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  as.dist barplot cor cutree legend lines plot var
Consider adding
  importFrom("graphics", "barplot", "legend", "lines", "plot")
  importFrom("stats", "as.dist", "cor", "cutree", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘caTools’ ‘gdata’ ‘gplots’ ‘gtools’ ‘lattice’ ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
PH.ICsurv.EM: no visible global function definition for ‘quantile’
PH.ICsurv.EM: no visible global function definition for ‘optim’
fast.PH.ICsurv.EM: no visible global function definition for ‘quantile’
fast.PH.ICsurv.EM: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim quantile
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
Running examples in ‘ICtest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggladleplot
> ### Title: Ladle Plot for an Object of Class ladle Using ggplot2
> ### Aliases: ggladleplot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> n <- 1000
> X <- cbind(rexp(n), rt(n,5), rnorm(n), rnorm(n), rnorm(n), rnorm(n))
> test <- FOBIladle(X)
> ggladleplot(test)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ICA.Rmd’ using rmarkdown
Loading required package: JADE
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: ggplot2
--- finished re-building ‘ICA.Rmd’

--- re-building ‘PCA.Rmd’ using rmarkdown
Loading required package: JADE
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: ggplot2
Quitting from lines 66-71 (PCA.Rmd) 
Error: processing vignette 'PCA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PCA.Rmd’

--- re-building ‘SIR.Rmd’ using rmarkdown
Loading required package: JADE
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: ggplot2
--- finished re-building ‘SIR.Rmd’

SUMMARY: processing the following file failed:
  ‘PCA.Rmd’

Error: Vignette re-building failed.
Execution halted
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

idbg.interact: no visible global function definition for
  ‘capture.output’
idbg.interact: no visible global function definition for ‘timestamp’
idbg.print_breakpoints: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output timestamp
Consider adding
  importFrom("utils", "capture.output", "timestamp")
to your NAMESPACE file.
Running examples in ‘ideamdb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TimeSeries
> ### Title: Graphical exploratory charts
> ### Aliases: TimeSeries
> 
> ### ** Examples
> 
> Example_IDEAM <- system.file("extdata", "Example_IDEAM", package = "ideamdb")
> TimeSeries(Example_IDEAM, station = "LUCERO")
Warning: Removed 33 rows containing missing values (geom_path).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: TimeSeries ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 128-130 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘README.Idcoefs2b1.txt’
comp.uri: no visible global function definition for ‘quantile’
est.IDR: no visible global function definition for ‘ecdf’
get.pseudo.mix: no visible global function definition for ‘pnorm’
get.uri.2d: no visible global function definition for ‘smooth.spline’
get.uri.2d: no visible global function definition for ‘predict’
Undefined global functions or variables:
  ecdf pnorm predict quantile smooth.spline
Consider adding
  importFrom("stats", "ecdf", "pnorm", "predict", "quantile",
             "smooth.spline")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘XML’ ‘vegan’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘ie2miscdata’
Package suggested but not available for checking: ‘financial’
ROC_plot: no visible global function definition for ‘pdf’
ROC_plot: no visible global function definition for ‘par’
ROC_plot: no visible global function definition for ‘dev.off’
Ymean_compare: no visible binding for global variable ‘sd’
Ymean_compare: no visible global function definition for ‘pdf’
Ymean_compare: no visible global function definition for ‘par’
Ymean_compare: no visible global function definition for ‘dev.off’
data_simulation: no visible global function definition for ‘rnorm’
gibbs_sampling: no visible global function definition for ‘rnorm’
mcmc_trace_plot: no visible global function definition for ‘pdf’
mcmc_trace_plot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par pdf rnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "rnorm", "sd")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

ifa.em: no visible global function definition for ‘runif’
ifa.init.pca: no visible global function definition for ‘var’
ifa.init.pca: no visible global function definition for ‘cor’
ifa.init.pca: no visible global function definition for ‘runif’
ifa.init.random: no visible global function definition for ‘runif’
ifa.init.random: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor runif var
Consider adding
  importFrom("stats", "cor", "runif", "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘pritikin-schmidt.Rnw’ using knitr
Quitting from lines 220-244 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pritikin-schmidt.Rnw’

SUMMARY: processing the following file failed:
  ‘pritikin-schmidt.Rnw’

Error: Vignette re-building failed.
Execution halted
Found the following assignments to the global environment:
File ‘IgorR/R/ReadIgorBinary.R’:
  assign(WaveName, rval, envir = .GlobalEnv)
ihs.mle: no visible global function definition for ‘as.formula’
pihs: no visible global function definition for ‘pnorm’
qihs: no visible global function definition for ‘qnorm’
rihs: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  as.formula pnorm qnorm rnorm
Consider adding
  importFrom("stats", "as.formula", "pnorm", "qnorm", "rnorm")
to your NAMESPACE file.
Running examples in ‘imageData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anomPlot
> ### Title: Identifies anomalous individuals and produces longitudinal plots
> ###   without them and with just them
> ### Aliases: anomPlot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(exampleData)
> anomalous <- anomPlot(longi.dat, response="Area.smooth.AGR", 
+                       lower=2.5, start.time=40, 
+                       x = "xDays+35.42857143", vertical.line=29, 
+                       breaks=seq(28, 42, by=2), 
+                       whichPrint=c("innerPlot"), 
+                       y.title="Area.smooth.AGR")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: anomPlot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gettingstarted.Rmd’ using rmarkdown
Loading required package: magrittr

Attaching package: 'imager'

The following object is masked from 'package:magrittr':

    add

The following objects are masked from 'package:stats':

    convolve, spectrum

The following object is masked from 'package:graphics':

    frame

The following object is masked from 'package:base':

    save.image


Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 152-158 (gettingstarted.Rmd) 
Error: processing vignette 'gettingstarted.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gettingstarted.Rmd’

--- re-building ‘pixsets.Rmd’ using rmarkdown
Loading required package: magrittr

Attaching package: 'imager'

The following object is masked from 'package:magrittr':

    add

The following objects are masked from 'package:stats':

    convolve, spectrum

The following object is masked from 'package:graphics':

    frame

The following object is masked from 'package:base':

    save.image


Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘pixsets.Rmd’

SUMMARY: processing the following file failed:
  ‘gettingstarted.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘imbalance-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotComparison
> ### Title: Plots comparison between the original and the new balanced
> ###   dataset.
> ### Aliases: plotComparison
> 
> ### ** Examples
> 
> data(iris0)
> set.seed(12345)
> 
> rwoSamples <- rwo(iris0, numInstances = 100)
> rwoBalanced <- rbind(iris0, rwoSamples)
> plotComparison(iris0, rwoBalanced, names(iris0), cols = 2, classAttr = "Class")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotComparison ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘imbalance.Rmd’ using rmarkdown
Quitting from lines 70-75 (imbalance.Rmd) 
Error: processing vignette 'imbalance.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘imbalance.Rmd’

SUMMARY: processing the following file failed:
  ‘imbalance.Rmd’

Error: Vignette re-building failed.
Execution halted
IMIS: no visible global function definition for ‘sample.prior’
IMIS: no visible global function definition for ‘var’
IMIS: no visible global function definition for ‘cov’
IMIS: no visible global function definition for ‘prior’
IMIS: no visible global function definition for ‘likelihood’
IMIS : posterior: no visible global function definition for ‘prior’
IMIS : posterior: no visible global function definition for
  ‘likelihood’
IMIS: no visible global function definition for ‘optim’
IMIS: no visible global function definition for ‘rnorm’
IMIS: no visible global function definition for ‘mahalanobis’
IMIS: no visible global function definition for ‘cov.wt’
IMIS: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  cov cov.wt dnorm likelihood mahalanobis optim prior rnorm
  sample.prior var
Consider adding
  importFrom("stats", "cov", "cov.wt", "dnorm", "mahalanobis", "optim",
             "rnorm", "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Quitting from lines 73-76 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

--- re-building ‘parallel.Rmd’ using rmarkdown
Quitting from lines 51-53 (parallel.Rmd) 
Error: processing vignette 'parallel.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘parallel.Rmd’

SUMMARY: processing the following files failed:
  ‘intro.Rmd’ ‘parallel.Rmd’

Error: Vignette re-building failed.
Execution halted
heter_IV2: no visible global function definition for ‘poly’
heter_IV2: no visible global function definition for ‘lm’
heter_IV2: no visible global function definition for ‘step’
heter_IV2: no visible global function definition for ‘pnorm’
heter_IV2: no visible global function definition for ‘qnorm’
homo_IV1: no visible global function definition for ‘coef’
homo_IV1: no visible global function definition for ‘pnorm’
homo_IV1: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  coef lm pnorm poly qnorm step
Consider adding
  importFrom("stats", "coef", "lm", "pnorm", "poly", "qnorm", "step")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘inline’ ‘lpSolve’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘inline’ ‘lpSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
FctReducedNodevalues: no visible global function definition for
  ‘signature’
FctReducedNodevalues: no visible global function definition for
  ‘cfunction’
TotalVar: no visible global function definition for ‘lp’
Undefined global functions or variables:
  cfunction lp signature
Consider adding
  importFrom("methods", "signature")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
generate.ExpressionData: no visible global function definition for
  ‘rnorm’
impute.MinDet: no visible binding for global variable ‘quantile’
impute.MinProb: no visible binding for global variable ‘quantile’
impute.MinProb: no visible binding for global variable ‘sd’
impute.MinProb: no visible global function definition for ‘median’
impute.MinProb: no visible global function definition for ‘rnorm’
impute.QRILC: no visible global function definition for ‘qnorm’
impute.QRILC: no visible global function definition for ‘quantile’
impute.QRILC: no visible global function definition for ‘lm’
insertMVs: no visible global function definition for ‘rnorm’
model.Selector: no visible global function definition for ‘qnorm’
model.Selector: no visible global function definition for ‘quantile’
model.Selector: no visible global function definition for ‘lm’
model.Selector: no visible global function definition for ‘ecdf’
model.Selector: no visible global function definition for ‘pnorm’
pep2prot: no visible binding for global variable ‘median’
Undefined global functions or variables:
  ecdf lm median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "ecdf", "lm", "median", "pnorm", "qnorm",
             "quantile", "rnorm", "sd")
to your NAMESPACE file.
impute.mdr: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
heal_data: no visible global function definition for ‘optimum_k’
heal_data: no visible global function definition for ‘optimum_w’
heal_data: no visible global function definition for ‘pred_for_w’
Undefined global functions or variables:
  optimum_k optimum_w pred_for_w
Running examples in ‘imputeTestbench-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_errors
> ### Title: Function to plot the Error Comparison
> ### Aliases: plot_errors plot_errors.errprof
> 
> ### ** Examples
> 
> aa <- impute_errors(dataIn = nottem)
Warning in predict.lm(fit, newdata = data.frame(X)) :
  prediction from a rank-deficient fit may be misleading
Warning in predict.lm(fit, newdata = data.frame(X)) :
  prediction from a rank-deficient fit may be misleading
Warning in predict.lm(fit, newdata = data.frame(X)) :
  prediction from a rank-deficient fit may be misleading
> 
> # default plot
> plot_errors(aa)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Warning: no function found corresponding to methods exports from ‘IM’ for: ‘initialize’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  ‘bmp’ ‘jpeg’ ‘methods’ ‘png’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘imsig-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_abundance
> ### Title: Plot relative abundance of immune cells
> ### Aliases: plot_abundance
> 
> ### ** Examples
> 
> plot_abundance (exp = example_data, r = 0.7)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_abundance ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
GenerateMixData: no visible global function definition for ‘rnbinom’
GenerateMixData: no visible global function definition for ‘rbeta’
GenerateMixData: no visible global function definition for ‘rbinom’
GenerateMixData: no visible global function definition for ‘rpois’
InitializePars: no visible global function definition for ‘aggregate’
InitializePars: no visible global function definition for ‘rnorm’
MultiStart: no visible global function definition for ‘rnorm’
MultiStart: no visible global function definition for ‘runif’
inarmix: no visible global function definition for ‘terms’
inarmix: no visible global function definition for ‘model.frame’
inarmix: no visible global function definition for ‘model.response’
inarmix: no visible global function definition for ‘model.matrix’
print.diagnose.inarmix: no visible global function definition for
  ‘plot’
print.diagnose.inarmix: no visible global function definition for
  ‘lines’
print.summary.inarmix: no visible global function definition for
  ‘printCoefmat’
summary.inarmix: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  aggregate lines model.frame model.matrix model.response plot pnorm
  printCoefmat rbeta rbinom rnbinom rnorm rpois runif terms
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "aggregate", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "rbeta",
             "rbinom", "rnbinom", "rnorm", "rpois", "runif", "terms")
to your NAMESPACE file.
Running examples in ‘IncDTW-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dtw_partial
> ### Title: Partial Dynamic Time Warping
> ### Aliases: dtw_partial
> ### Keywords: cluster ts
> 
> ### ** Examples
> 
> # open-end alignment for multivariate time series
> # first simulate a 2-dim time series Q
> Q <- matrix(cumsum(rnorm(100)), ncol=2)
> 
> # simulate C as noisy and warped version of Q, and append noise at the end
> C <- Q[sort(sample(50, 40, replace=FALSE)), ] + rnorm(80)
> C <- rbind(C, matrix(rnorm(30), ncol=2))
> 
> tmp <- dtw(Q = Q, C = C, ws = 30, return_QC = TRUE, return_wp = TRUE)
> par <- dtw_partial(tmp, partial_C = TRUE)
> par
$rangeQ
[1]  1 50

$rangeC
[1]  1 38

$normalized_distance
[1] 1.344722

> plot(tmp, partial = par, type = "QC")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Incremental_Dynamic_Time_Warping.Rmd’ using rmarkdown

Attaching package: 'IncDTW'

The following object is masked from 'package:grDevices':

    cm

The following object is masked from 'package:base':

    norm

Loading required package: proxy

Attaching package: 'proxy'

The following objects are masked from 'package:stats':

    as.dist, dist

The following object is masked from 'package:base':

    as.matrix

Loaded dtw v1.20-1. See ?dtw for help, citation("dtw") for use in publication.


Attaching package: 'dtw'

The following object is masked from 'package:IncDTW':

    dtw

Quitting from lines 73-74 (Incremental_Dynamic_Time_Warping.Rmd) 
Error: processing vignette 'Incremental_Dynamic_Time_Warping.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Incremental_Dynamic_Time_Warping.Rmd’

--- re-building ‘Runtime_Comparison.Rmd’ using rmarkdown
Quitting from lines 102-108 (Runtime_Comparison.Rmd) 
Error: processing vignette 'Runtime_Comparison.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Runtime_Comparison.Rmd’

SUMMARY: processing the following files failed:
  ‘Incremental_Dynamic_Time_Warping.Rmd’ ‘Runtime_Comparison.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘incidence-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bootstrap
> ### Title: Bootstrap incidence time series
> ### Aliases: bootstrap
> 
> ### ** Examples
> 
> 
> if (require(outbreaks) && require(ggplot2)) { withAutoprint({
+   i <- incidence(fluH7N9_china_2013$date_of_onset)
+   i
+   plot(i)
+ 
+   ## one simple bootstrap
+   x <- bootstrap(i)
+   x
+   plot(x)
+ 
+ })}
Loading required package: outbreaks
Loading required package: ggplot2
> i <- incidence(fluH7N9_china_2013$date_of_onset)
10 missing observations were removed.
> i
<incidence object>
[126 cases from days 2013-02-19 to 2013-07-27]

$counts: matrix with 159 rows and 1 columns
$n: 126 cases in total
$dates: 159 dates marking the left-side of bins
$interval: 1 day
$timespan: 159 days
$cumulative: FALSE

> plot(i)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: withAutoprint ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘conversions.Rmd’ using rmarkdown
Quitting from lines 49-55 (conversions.Rmd) 
Error: processing vignette 'conversions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘conversions.Rmd’

--- re-building ‘customize_plot.Rmd’ using rmarkdown
Quitting from lines 78-81 (customize_plot.Rmd) 
Error: processing vignette 'customize_plot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘customize_plot.Rmd’

--- re-building ‘incidence_class.Rmd’ using rmarkdown
Quitting from lines 47-50 (incidence_class.Rmd) 
Error: processing vignette 'incidence_class.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘incidence_class.Rmd’

--- re-building ‘incidence_fit_class.Rmd’ using rmarkdown
Quitting from lines 55-63 (incidence_fit_class.Rmd) 
Error: processing vignette 'incidence_fit_class.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘incidence_fit_class.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 132-135 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following files failed:
  ‘conversions.Rmd’ ‘customize_plot.Rmd’ ‘incidence_class.Rmd’
  ‘incidence_fit_class.Rmd’ ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘incR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: incRplot
> ### Title: Quick visualisation of incubation temperatures, on-bouts and
> ###   off-bouts
> ### Aliases: incRplot
> 
> ### ** Examples
> 
> # loading example data
> data(incR_procdata)
> my_plot <- incRplot(data = incR_procdata[complete.cases(incR_procdata$temperature),], 
+                     time.var = "dec_time", 
+                     day.var = "date", 
+                     inc.temperature.var = "temperature", 
+                     env.temperature.var = "env_temp",
+                     vector.incubation = "incR_score")
>                     
> # see your plot
> my_plot
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘incR_pipeline.Rmd’ using rmarkdown
Quitting from lines 116-125 (incR_pipeline.Rmd) 
Error: processing vignette 'incR_pipeline.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘incR_pipeline.Rmd’

SUMMARY: processing the following file failed:
  ‘incR_pipeline.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EstimatingIncidence.Rmd’ using rmarkdown
--- finished re-building ‘EstimatingIncidence.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘SurveyDesign.Rmd’ using rmarkdown
--- finished re-building ‘SurveyDesign.Rmd’

--- re-building ‘TestCalibration.Rmd’ using rmarkdown
Quitting from lines 96-97 (TestCalibration.Rmd) 
Error: processing vignette 'TestCalibration.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TestCalibration.Rmd’

SUMMARY: processing the following file failed:
  ‘TestCalibration.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘IncucyteDRC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculateCutTimeForGrowthCurve
> ### Title: calculateCutTimeForGrowthCurve
> ### Aliases: calculateCutTimeForGrowthCurve
> 
> ### ** Examples
> 
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/IncucyteDRC/extdata/example_data.txt
> 
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
> 
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object> 
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> plotIncucyteDRCSet(test_idrc_set, grouped=TRUE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘IncucyteZoomExport.Rmd’ using rmarkdown
--- finished re-building ‘IncucyteZoomExport.Rmd’

--- re-building ‘Overview.Rmd’ using rmarkdown
Quitting from lines 35-36 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following file failed:
  ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘rsprng’
'library' or 'require' call to ‘xtable’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Rmpi’ ‘rsprng’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
A.dep.tests: no visible global function definition for ‘combn’
A.dep.tests: no visible global function definition for ‘pchisq’
dependogram: no visible global function definition for ‘makeCluster’
dependogram: no visible global function definition for
  ‘clusterSetupSPRNG’
dependogram: no visible global function definition for ‘clusterCall’
dependogram: no visible global function definition for ‘stopCluster’
dependogram: no visible global function definition for ‘combn’
dependogram: no visible global function definition for ‘plot’
dependogram: no visible global function definition for ‘points’
dependogram: no visible global function definition for ‘segments’
Undefined global functions or variables:
  clusterCall clusterSetupSPRNG combn makeCluster pchisq plot points
  segments stopCluster
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "pchisq")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running examples in ‘INDperform-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_clust_sc
> ### Title: Dendrogram of the cluster analysis.
> ### Aliases: plot_clust_sc
> 
> ### ** Examples
> 
> # Using the Baltic Sea demo data
> scores_tbl <- scoring(trend_tbl = model_trend_ex,
+   mod_tbl = all_results_ex, press_type = press_type_ex)
> scores_mat <- summary_sc(scores_tbl)$scores_matrix
> dist_matrix <- dist_sc(scores_mat, method_dist = "euclidean")
> clust_analysis <- clust_sc(dist_matrix, method_clust = "complete")
With the selected agglomeration method (complete), the cophonetic correlation coeffient is 0.842 and the Gower distance is 417.41.
> plot_clust_sc(clust_analysis)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘iNextPD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggiNEXT
> ### Title: ggplot2 extension for an iNextPD object
> ### Aliases: ggiNEXT ggiNEXT.default ggiNEXT.iNextPD
> 
> ### ** Examples
> 
> # single-assemblage abundance data
> data(bird)
> bird.phy <- ade4::newick2phylog(bird$tre)
> bird.lab <- rownames(bird$abun)
> out1 <- iNextPD(bird$abun$North.site, bird.lab, bird.phy, 
+         q=1, datatype="abundance", endpoint=400, se=TRUE)
> ggiNEXT(x=out1, type=1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Attaching package: 'iNextPD'

The following object is masked from 'package:iNEXT':

    ggiNEXT

Quitting from lines 294-297 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘iNEXT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bird
> ### Title: Bird abundance-based data
> ### Aliases: bird
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> data(bird)
> out <- iNEXT(bird, datatype="abundance")
> ggiNEXT(out)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 253-255 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
IDM.bootCI: no visible global function definition for ‘cov’
IDM.bootCI: no visible global function definition for ‘cor’
IDM.bootCI: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cor cov quantile
Consider adding
  importFrom("stats", "cor", "cov", "quantile")
to your NAMESPACE file.
Package in Depends field not imported from: ‘sandwich’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
infer,coxph: no visible global function definition for ‘coef’
infer,coxph: no visible global function definition for ‘vcov’
infer,coxph: no visible global function definition for ‘sandwich’
infer,coxph: no visible global function definition for ‘pnorm’
infer,coxph: no visible global function definition for ‘qnorm’
infer,gee: no visible global function definition for ‘coef’
infer,gee: no visible global function definition for ‘pnorm’
infer,gee: no visible global function definition for ‘qnorm’
infer,glm: no visible global function definition for ‘coef’
infer,glm: no visible global function definition for ‘sandwich’
infer,glm: no visible global function definition for ‘vcov’
infer,glm: no visible global function definition for ‘pnorm’
infer,glm: no visible global function definition for ‘qnorm’
infer,lm: no visible global function definition for ‘coef’
infer,lm: no visible global function definition for ‘sandwich’
infer,lm: no visible global function definition for ‘vcov’
infer,lm: no visible global function definition for ‘pnorm’
infer,lm: no visible global function definition for ‘qnorm’
infer,lme: no visible global function definition for ‘coef’
infer,lme: no visible global function definition for ‘fixed.effects’
infer,lme: no visible global function definition for ‘vcov’
infer,lme: no visible global function definition for ‘pnorm’
infer,lme: no visible global function definition for ‘qnorm’
infer,mer: no visible global function definition for ‘coef’
infer,mer: no visible global function definition for ‘vcov’
infer,mer: no visible global function definition for ‘pnorm’
infer,mer: no visible global function definition for ‘qnorm’
infer,mer: no visible binding for global variable ‘fm1’
Undefined global functions or variables:
  coef fixed.effects fm1 pnorm qnorm sandwich vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "vcov")
to your NAMESPACE file.
contrib: no visible global function definition for ‘aggregate’
est.expDeath : surv_p: no visible global function definition for
  ‘survfit’
est.expDeath : surv_p: no visible global function definition for
  ‘approx’
function1: no visible global function definition for ‘coxph.detail’
inference.SMR: no visible global function definition for ‘qnorm’
var.expDeath : surv_p: no visible global function definition for
  ‘survfit’
var.expDeath : surv_p: no visible global function definition for
  ‘approx’
Undefined global functions or variables:
  aggregate approx coxph.detail qnorm survfit
Consider adding
  importFrom("stats", "aggregate", "approx", "qnorm")
to your NAMESPACE file.
Running ‘testthat.R’ [10s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(infer)
  > 
  > test_check("infer")
  Setting `type = "permute"` in `generate()`.
  ── 1. Failure: conf_int argument works (@test-wrappers.R#141)  ─────────────────
  no_var_equal == var_equal isn't false.
  
  ── 2. Failure: conf_int argument works (@test-wrappers.R#153)  ─────────────────
  shortcut_no_var_equal == shortcut_var_equal isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 347 SKIPPED: 0 FAILED: 2
  1. Failure: conf_int argument works (@test-wrappers.R#141) 
  2. Failure: conf_int argument works (@test-wrappers.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘Information-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Information
> ### Title: Data exploration with information theory (weight-of-evidence and
> ###   information value)
> ### Aliases: Information Information-package
> ### Keywords: IV, NIV, NWOE, WOE, classification, uplift
> ###   weight-of-evidence,
> 
> ### ** Examples
> 
> ##------------------------------------------------------------
> ## WOE analysis, no validation
> ##------------------------------------------------------------
> library(Information)
> 
> data(train, package="Information")
> train <- subset(train, TREATMENT==1)
> IV <- Information::create_infotables(data=train, y="PURCHASE", parallel=FALSE)
[1] "Variable TREATMENT was removed because it has only 1 unique level"
> 
> print(head(IV$Summary), row.names=FALSE)
                    Variable        IV
             N_OPEN_REV_ACTS 1.0107695
        TOT_HI_CRDT_CRDT_LMT 0.9345902
        RATIO_BAL_TO_HI_CRDT 0.8232539
 D_NA_M_SNC_MST_RCNT_ACT_OPN 0.6355466
  M_SNC_OLDST_RETAIL_ACT_OPN 0.5573438
      M_SNC_MST_RCNT_ACT_OPN 0.5026402
> print(IV$Tables$N_OPEN_REV_ACTS, row.names=FALSE)
 N_OPEN_REV_ACTS    N    Percent        WOE        IV
           [0,0] 1469 0.29545455 -2.0465968 0.6401443
           [1,2]  958 0.19267900 -0.5900120 0.6958705
           [3,3]  310 0.06234916  0.2033085 0.6986029
           [4,5]  583 0.11725664  0.4419768 0.7244762
           [6,8]  632 0.12711183  0.6148243 0.7810611
          [9,11]  453 0.09111022  0.8815772 0.8692672
         [12,48]  567 0.11403862  0.9883818 1.0107695
> 
> # Plotting a single variable
> Information::plot_infotables(IV, "N_OPEN_REV_ACTS")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Information-vignette.Rmd’ using rmarkdown_notangle
Quitting from lines 223-224 (Information-vignette.Rmd) 
Error: processing vignette 'Information-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Information-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Information-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘InformationValue-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ks_plot
> ### Title: ks_plot
> ### Aliases: ks_plot
> 
> ### ** Examples
> 
> data('ActualsAndScores')
> ks_plot(actuals=ActualsAndScores$Actuals, predictedScores=ActualsAndScores$PredictedScores)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ks_plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘InformationValue.Rmd’ using rmarkdown
Quitting from lines 65-67 (InformationValue.Rmd) 
Error: processing vignette 'InformationValue.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘InformationValue.Rmd’

SUMMARY: processing the following file failed:
  ‘InformationValue.Rmd’

Error: Vignette re-building failed.
Execution halted
gen.intercepts: no visible global function definition for ‘contr.SAS’
Undefined global functions or variables:
  contr.SAS
Consider adding
  importFrom("stats", "contr.SAS")
to your NAMESPACE file.
entropy: no visible global function definition for ‘na.omit’
interinformation: no visible global function definition for ‘na.omit’
multiinformation: no visible global function definition for ‘na.omit’
mutinformation: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
getInfra: no visible global function definition for ‘txtProgressBar’
getInfra: no visible global function definition for ‘download.file’
getInfra: no visible global function definition for ‘setTxtProgressBar’
getInfra : <anonymous>: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "download.file", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Unexported object imported by a ':::' call: ‘ltm:::crf.GPCM’
  See the note in ?`:::` about the use of this operator.
Jeffreys: no visible global function definition for ‘integrate’
Jeffreys: no visible global function definition for ‘splinefun’
count.rows: no visible global function definition for ‘tail’
count.rows: no visible global function definition for ‘head’
cprobs : <anonymous>: no visible global function definition for
  ‘plogis’
inf.func.ltm : f: no visible global function definition for ‘plogis’
iota: no visible global function definition for ‘integrate’
iota: no visible global function definition for ‘optimize’
iota: no visible global function definition for ‘pchisq’
iota.c : rirm: no visible global function definition for ‘coef’
iota.c: no visible global function definition for ‘integrate’
iota.c: no visible global function definition for ‘sd’
iota.u: no visible global function definition for ‘integrate’
iprobs : <anonymous>: no visible global function definition for
  ‘plogis’
logL.ltm : logL: no visible global function definition for ‘dbinom’
logL.ltm : logL: no visible global function definition for ‘plogis’
logL.ltm : logL : <anonymous>: no visible global function definition
  for ‘plogis’
rJeffreys : Jpinv.min: no visible global function definition for
  ‘integrate’
rJeffreys : Jpinv: no visible global function definition for ‘nlminb’
rJeffreys : Jpinv: no visible global function definition for ‘qnorm’
rJeffreys: no visible global function definition for ‘runif’
Undefined global functions or variables:
  coef dbinom head integrate nlminb optimize pchisq plogis qnorm runif
  sd splinefun tail
Consider adding
  importFrom("stats", "coef", "dbinom", "integrate", "nlminb",
             "optimize", "pchisq", "plogis", "qnorm", "runif", "sd",
             "splinefun")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: ‘INLA’
Running examples in ‘inlabru-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg
> ### Title: ggplot2 geomes for inlabru related objects
> ### Aliases: gg
> 
> ### ** Examples
> 
> 
> # Load Gorilla data
> 
> data(gorillas, package = "inlabru")
> 
> # Invoke ggplot and add geomes for the Gorilla nests and the survey boundary
> 
> ggplot() + gg(gorillas$boundary) + gg(gorillas$nests)
Regions defined for each Polygons
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘compiler’ ‘deSolve’ ‘lattice’ ‘nlme’
  Please remove these calls from your code.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘insideRODE/R/zzz.r’:
  .First.lib calls:
    require(nlme)
    require(lattice)
    require(deSolve)
    require(compiler)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

cfLSODE: no visible global function definition for ‘deriv’
cfODE: no visible global function definition for ‘deriv’
cfVODE: no visible global function definition for ‘deriv’
cpLSODE: no visible global function definition for ‘deriv’
cpODE: no visible global function definition for ‘deriv’
cpVODE: no visible global function definition for ‘deriv’
nlmLSODE: no visible global function definition for ‘deriv’
nlmLSODEcp: no visible global function definition for ‘deriv’
nlmODE: no visible global function definition for ‘deriv’
nlmODEcp: no visible global function definition for ‘deriv’
nlmVODE: no visible global function definition for ‘deriv’
nlmVODEcp: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Running examples in ‘insurancerating-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.insurancerating
> ### Title: Automatically create a ggplot for objects obtained from
> ###   construct_tariff_classes()
> ### Aliases: autoplot.insurancerating
> 
> ### ** Examples
> 
> library(ggplot2)
> x <- construct_tariff_classes(MTPL, nclaims, age_policyholder, exposure)
> autoplot(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘IntegratedMRF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CombPredict
> ### Title: Integrated Prediction of Testing samples using Combination
> ###   Weights from integrated RF or MRF model
> ### Aliases: CombPredict
> 
> ### ** Examples
> 
> library(IntegratedMRF)
> data(Dream_Dataset)
> Tree=1
> Feature=1
> Leaf=10
> Confidence=80
> finalX=Dream_Dataset[[1]]
> Cell=Dream_Dataset[[2]]
> Y_train_Dream=Dream_Dataset[[3]]
> Y_train_cell=Dream_Dataset[[4]]
> Y_test=Dream_Dataset[[5]]
> Y_test_cell=Dream_Dataset[[6]]
> Drug=1
> Y_train_Drug=matrix(Y_train_Dream[,Drug],ncol=length(Drug))
> Result=Combination(finalX,Y_train_Drug,Cell,Y_train_cell,Tree,Feature,Leaf,Confidence)
Warning in stats::cor(final_genome_BSP1 %*% BSP_temp_coeff1, finalY_bsp_pred[,  :
  the standard deviation is zero
Warning in stats::cor(final_genome_BSP1 %*% BSP_temp_coeff1, finalY_bsp_pred[,  :
  the standard deviation is zero
Elapsed Time for Bootstrap Error Estimation is 0.368
Elapsed Time for Resubstitution Error Estimation is 0.034
Elapsed Time for 0.632+ Bootstrap Error Estimation is 0.0170000000000001
Elapsed Time for Jackknife Confidence Interval Calculation is 0.002
Elapsed Time for Leave-one-out Error Estimation is 0.163
Elapsed Time for N-fold cross validation Error Estimation is 0.0759999999999998
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Combination ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘interactions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cat_plot
> ### Title: Plot interaction effects between categorical predictors.
> ### Aliases: cat_plot
> 
> ### ** Examples
> 
> 
> library(ggplot2)
> fit <- lm(price ~ cut * color, data = diamonds)
> cat_plot(fit, pred = color, modx = cut, interval = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘categorical.Rmd’ using rmarkdown
Quitting from lines 70-71 (categorical.Rmd) 
Error: processing vignette 'categorical.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘categorical.Rmd’

--- re-building ‘interactions.Rmd’ using rmarkdown
Quitting from lines 56-57 (interactions.Rmd) 
Error: processing vignette 'interactions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘interactions.Rmd’

SUMMARY: processing the following files failed:
  ‘categorical.Rmd’ ‘interactions.Rmd’

Error: Vignette re-building failed.
Execution halted
ClearBottomMenuPlot: no visible global function definition for ‘rect’
InteractiveIGraph : mousedown: no visible global function definition
  for ‘grconvertX’
InteractiveIGraph : mousedown: no visible global function definition
  for ‘grconvertY’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘grconvertX’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘grconvertY’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘polygon’
InteractiveIGraph : mouseup: no visible global function definition for
  ‘grconvertX’
InteractiveIGraph : mouseup: no visible global function definition for
  ‘grconvertY’
InteractiveIGraph : keybd: no visible global function definition for
  ‘par’
PlotRegionGeneral: no visible global function definition for ‘polygon’
plot.InteractiveIGraph: no visible global function definition for
  ‘plot’
plot.InteractiveIGraph: no visible global function definition for ‘par’
plot.Menu: no visible global function definition for ‘par’
plot.Menu: no visible binding for global variable ‘rect’
plot.MenuItem: no visible binding for global variable ‘strwidth’
plot.MenuItem: no visible binding for global variable ‘strheight’
plot.MenuItem: no visible binding for global variable ‘rect’
plot.MenuItem: no visible binding for global variable ‘text’
plot.MenuLine: no visible binding for global variable ‘rect’
Undefined global functions or variables:
  grconvertX grconvertY par plot polygon rect strheight strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
to your NAMESPACE file.
interact: no visible global function definition for ‘cor’
plot.interact: no visible global function definition for ‘plot’
standardize.matrix: no visible binding for global variable ‘var’
standardize.matrix: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor plot sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "sd", "var")
to your NAMESPACE file.
HH: no visible global function definition for ‘var’
HH: no visible global function definition for ‘qnorm’
exactCI: no visible global function definition for ‘quantile’
sample.n: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  qnorm quantile rbinom var
Consider adding
  importFrom("stats", "qnorm", "quantile", "rbinom", "var")
to your NAMESPACE file.
Running examples in ‘interflex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: inter.binning
> ### Title: The Binning Estimator
> ### Aliases: inter.binning
> ### Keywords: graphics
> 
> ### ** Examples
> 
> library(interflex)
> data(interflex)
> inter.binning(Y = "Y", D = "D", X = "X", Z = "Z1",
+                   data = s1, nbins = 3, vartype = "homoscedastic",
+                   Ylabel = "Y", Dlabel = "Tr", Xlabel="X")
$est.binning
                     x0    coef     se CI_lower CI_upper
X: [-0.396,2.48] 2.0467 -3.0545 0.5001  -4.0411  -2.0679
X: (2.48,3.42]   2.9599  0.5706 0.4823  -0.3808   1.5220
X: (3.42,6.2]    4.1025  3.1651 0.4770   2.2242   4.1061

$binary.treatment
[1] 1

$bin.size
    1     2     3 
0.335 0.330 0.335 

$treat.variation.byGroup
[1] 1.0459 1.2955 0.9281

$X.Lkurtosis
[1] 0.1241

$correctOrder
[1] TRUE

$p.twosided
p.1v2 p.2v3 p.1v3 
0e+00 2e-04 0e+00 

$p.wald
[1] 0.5054

$graph
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘interplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: interplot
> ### Title: Plot Conditional Coefficients of a Variable in an Interaction
> ###   Term
> ### Aliases: interplot
> 
> ### ** Examples
> 
> data(mtcars)
> m_cyl <- lm(mpg ~ wt * cyl, data = mtcars)
> library(interplot)
> 
> # Plot interactions with a continous conditioning variable
> interplot(m = m_cyl, var1 = 'cyl', var2 = 'wt') +
+ xlab('Automobile Weight (thousands lbs)') +
+ ylab('Estimated Coefficient for Number of Cylinders') +
+ ggtitle('Estimated Coefficient of Engine Cylinders\non Mileage by Automobile Weight') +
+ theme(plot.title = element_text(face='bold'))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘interplot-vignette.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: abind
Loading required package: arm
Loading required package: MASS
Loading required package: Matrix
Loading required package: lme4

arm (Version 1.10-1, built: 2018-4-12)

Working directory is /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/interplot.Rcheck/vign_test/interplot/vignettes

Quitting from lines 78-81 (interplot-vignette.Rmd) 
Error: processing vignette 'interplot-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘interplot-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘interplot-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘Interpol/R/AAdescriptor.R’:
  data(AAindex)
See section ‘Good practice’ in ‘?data’.
Packages in Depends field not imported from:
  ‘chron’ ‘date’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Mo.Th.Ra.: no visible global function definition for ‘aggregate’
daily_mean: no visible global function definition for ‘aggregate’
date.time: no visible global function definition for ‘chron’
date.time: no visible global function definition for ‘years’
date.time: no visible global function definition for ‘days’
date.time: no visible global function definition for ‘hours’
par_calibration: no visible global function definition for ‘date.mdy’
par_calibration: no visible global function definition for ‘as.date’
par_calibration: no visible global function definition for ‘aggregate’
plot_meas_sim: no visible global function definition for ‘as.date’
plot_meas_sim: no visible global function definition for ‘date.mdy’
plot_meas_sim: no visible global function definition for ‘plot’
plot_meas_sim: no visible global function definition for ‘par’
plot_meas_sim: no visible global function definition for ‘legend’
shape_calibration: no visible global function definition for ‘date.mdy’
shape_calibration: no visible global function definition for ‘as.date’
shape_calibration: no visible global function definition for
  ‘aggregate’
Undefined global functions or variables:
  aggregate as.date chron date.mdy days hours legend par plot years
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "aggregate")
to your NAMESPACE file.
icScoreTest: no visible global function definition for ‘pnorm’
icScoreTest: no visible global function definition for ‘pchisq’
icfit.formula: no visible global function definition for ‘terms’
icfit.formula: no visible global function definition for
  ‘model.extract’
icfitBootCI: no visible global function definition for ‘binom.test’
ictest.formula: no visible global function definition for
  ‘model.extract’
plot.icfit: no visible global function definition for ‘gray’
plot.icfit: no visible global function definition for ‘plot’
plot.icfit: no visible global function definition for ‘axis’
plot.icfit : polygon.icfit: no visible global function definition for
  ‘polygon’
scoresFromFit: no visible global function definition for ‘dnorm’
scoresFromFit: no visible global function definition for ‘qnorm’
wsrHLYpclt: no visible global function definition for ‘model.matrix’
wsrHLYpclt: no visible global function definition for ‘pchisq’
wsrHLYpclt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis binom.test dnorm gray model.extract model.matrix pchisq plot
  pnorm polygon qnorm terms
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis", "plot", "polygon")
  importFrom("stats", "binom.test", "dnorm", "model.extract",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
interventionEffects: no visible binding for global variable ‘sd’
interventionEffects: no visible global function definition for ‘pt’
interventionEffects: no visible global function definition for ‘sd’
interventionalInference: no visible global function definition for ‘sd’
interventionalInferenceAdvanced: no visible global function definition
  for ‘sd’
linesROC: no visible global function definition for ‘segments’
plotMaxML: no visible global function definition for ‘plot’
plotMaxML: no visible global function definition for ‘segments’
Undefined global functions or variables:
  plot pt sd segments
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "pt", "sd")
to your NAMESPACE file.
'library' or 'require' call to ‘maxLik’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘maxLik’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ILik : rbern: no visible global function definition for ‘runif’
ILik : q: no visible global function definition for ‘dnorm’
ILik : SlambdaG: no visible global function definition for ‘rnorm’
ILik : Pi_hat: no visible global function definition for ‘rnorm’
ILik : q: no visible global function definition for ‘dgamma’
ILik : SlambdaG: no visible global function definition for ‘rgamma’
ILik : Pi_hat: no visible global function definition for ‘rgamma’
ILik: no visible global function definition for ‘maxLik’
ILik: no visible global function definition for ‘coef’
ILik: no visible global function definition for ‘hessian’
ILik: no visible global function definition for ‘plot’
Undefined global functions or variables:
  coef dgamma dnorm hessian maxLik plot rgamma rnorm runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dgamma", "dnorm", "rgamma", "rnorm",
             "runif")
to your NAMESPACE file.
Running examples in ‘IntNMF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ConsensusMatPlot
> ### Title: A function to create image plot of the consensus matrix
> ### Aliases: ConsensusMatPlot
> 
> ### ** Examples
> 
> prop <- c(0.20,0.30,0.27,0.23)
> effect <- 2.5
> sim.D <- InterSIM(n.sample=100,cluster.sample.prop=prop,delta.methyl=effect,
+ delta.expr=effect,delta.protein=effect,p.DMP=0.25,p.DEG=NULL,p.DEP=NULL,
+ do.plot=FALSE, sample.cluster=TRUE, feature.cluster=TRUE)
> dat1 <- sim.D$dat.methyl
> dat2 <- sim.D$dat.expr
> dat3 <- sim.D$dat.protein
> true.cluster.assignment <- sim.D$clustering.assignment
> 
> ## Make all data positive by shifting to positive direction.
> ## Also rescale the datasets so that they are comparable.
> if (!all(dat1>=0)) dat1 <- pmax(dat1 + abs(min(dat1)), .Machine$double.eps)
> dat1 <- dat1/max(dat1)
> if (!all(dat2>=0)) dat2 <- pmax(dat2 + abs(min(dat2)), .Machine$double.eps)
> dat2 <- dat2/max(dat2)
> if (!all(dat3>=0)) dat3 <- pmax(dat3 + abs(min(dat3)), .Machine$double.eps)
> dat3 <- dat3/max(dat3)
> 
> # The function nmf.mnnals requires the samples to be on rows and variables on columns.
> dat <- list(dat1,dat2,dat3)
> fit <- nmf.mnnals(dat=dat,k=length(prop),maxiter=200,st.count=20,n.ini=15,ini.nndsvd=TRUE,
+ seed=TRUE)
> ConsensusMatPlot(fit,rowLab=TRUE,colLab=TRUE)
Error in Ops.unit(m, unit(1, "grobwidth", textGrob(coln[i <- which.max(nchar(coln))],  : 
  REAL() can only be applied to a 'numeric', not a 'integer'
Calls: ConsensusMatPlot ... aheatmap -> heatmap_motor -> draw_colnames -> Ops.unit
Execution halted
intReg: no visible binding for global variable ‘plogis’
intReg: no visible binding for global variable ‘pnorm’
intReg: no visible binding for global variable ‘pcauchy’
intReg: no visible binding for global variable ‘dlogis’
intReg: no visible binding for global variable ‘dnorm’
intReg: no visible binding for global variable ‘dcauchy’
intReg: no visible global function definition for ‘model.matrix’
intReg: no visible global function definition for ‘model.weights’
intReg: no visible global function definition for ‘model.offset’
intReg: no visible global function definition for ‘model.response’
intReg: no visible global function definition for ‘glm.fit’
intReg: no visible global function definition for ‘binomial’
intReg: no visible binding for global variable ‘coef’
intReg: no visible global function definition for ‘lm’
intReg: no visible global function definition for ‘coef’
intReg: no visible global function definition for ‘var’
model.matrix.intReg: no visible global function definition for
  ‘model.frame’
print.intReg: no visible global function definition for ‘coef’
print.summary.intReg: no visible global function definition for
  ‘logLik’
print.summary.intReg: no visible global function definition for
  ‘printCoefmat’
summary.intReg: no visible global function definition for ‘coef’
Undefined global functions or variables:
  binomial coef dcauchy dlogis dnorm glm.fit lm logLik model.frame
  model.matrix model.offset model.response model.weights pcauchy plogis
  pnorm printCoefmat var
Consider adding
  importFrom("stats", "binomial", "coef", "dcauchy", "dlogis", "dnorm",
             "glm.fit", "lm", "logLik", "model.frame", "model.matrix",
             "model.offset", "model.response", "model.weights",
             "pcauchy", "plogis", "pnorm", "printCoefmat", "var")
to your NAMESPACE file.
Running examples in ‘inventorize-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ABC
> ### Title: ABC
> ### Aliases: ABC
> 
> ### ** Examples
> 
> ABC(data.frame(SKU= seq(1:1000),demand=runif(1000,1,1000)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ABC ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
f.B: no visible global function definition for ‘pnorm’
f.B.neglog.deriv: no visible global function definition for ‘pnorm’
f.B.neglog.deriv: no visible global function definition for ‘dnorm’
f.grovest3 : f.est: no visible global function definition for ‘survfit’
f.grovest3 : f.est: no visible global function definition for ‘plot’
f.grovest3 : f.est: no visible global function definition for ‘lines’
f.grovest3: no visible global function definition for ‘model.frame’
f.grovest3: no visible global function definition for ‘model.extract’
invGauss: no visible global function definition for ‘model.frame’
invGauss: no visible global function definition for ‘model.extract’
invGauss: no visible global function definition for ‘model.matrix’
predict.invGauss: no visible global function definition for
  ‘model.frame’
predict.invGauss: no visible global function definition for
  ‘model.extract’
predict.invGauss: no visible global function definition for
  ‘model.matrix’
predict.invGauss: no visible binding for global variable ‘formula’
predict.invGauss: no visible binding for global variable ‘data’
summary.invGauss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  data dnorm formula lines model.extract model.frame model.matrix plot
  pnorm survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "dnorm", "formula", "model.extract", "model.frame",
             "model.matrix", "pnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
flowsRandom: no visible global function definition for ‘dmultinom’
readBed: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dmultinom read.table
Consider adding
  importFrom("stats", "dmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘beta’
Warning: no function found corresponding to methods exports from ‘ipdmeta’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
ipd.meta.power.base.function : power: no visible global function
  definition for ‘qnorm’
ipd.meta.power.base.function : power: no visible global function
  definition for ‘pnorm’
ipd.meta.power.base.function: no visible global function definition for
  ‘qnorm’
ipdlme.hetero: no visible global function definition for ‘new’
ipdlme.homo: no visible global function definition for ‘new’
plot_ipdlme: no visible global function definition for ‘par’
plot_ipdlme: no visible global function definition for ‘abline’
plot_ipdlme: no visible global function definition for ‘axis’
plot_ipdlme: no visible global function definition for ‘segments’
confint,ipdlme: no visible global function definition for ‘qt’
plot,ipdlme: no visible global function definition for ‘par’
plot,ipdlme: no visible global function definition for ‘abline’
plot,ipdlme: no visible global function definition for ‘axis’
plot,ipdlme: no visible global function definition for ‘segments’
summary,ipdlme: no visible global function definition for ‘pt’
Undefined global functions or variables:
  abline axis new par pnorm pt qnorm qt segments
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "pt", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘ipft-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ipfPlotEcdf
> ### Title: Plots the cumulative distribution function of the estimated
> ###   error
> ### Aliases: ipfPlotEcdf
> 
> ### ** Examples
> 
> 
>     model <- ipfKnn(ipftrain[, 1:168], ipftrain[, 169:170])
>     estimation <- ipfEstimate(model, ipftest[, 1:168], ipftest[, 169:170])
>     ipfPlotEcdf(estimation)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Non-standard file/directory found at top level:
  ‘version’
'library' or 'require' calls in package code:
  ‘MCMCpack’ ‘mvtnorm’ ‘truncnorm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
code.simple.gaps: no visible global function definition for ‘tail’
multistateMCMC: no visible global function definition for ‘write.table’
multistateMCMC: no visible global function definition for ‘read.table’
multistateMCMC: no visible global function definition for ‘tail’
multistateML: no visible global function definition for ‘tail’
multistateML: no visible global function definition for ‘write.table’
multistateML: no visible global function definition for ‘read.table’
phylo2mafft: no visible global function definition for ‘write.table’
read.beast : foo: no visible global function definition for ‘head’
read.beast: no visible global function definition for ‘tail’
read.starbeast: no visible global function definition for ‘head’
trimEnds : replaceWithN : getIndex: no visible global function
  definition for ‘head’
unresolve.clade: no visible global function definition for ‘tail’
unresolve.clade: no visible global function definition for ‘head’
write.fas: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head read.table tail write.table
Consider adding
  importFrom("utils", "head", "read.table", "tail", "write.table")
to your NAMESPACE file.
Running examples in ‘IPtoCountry-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IP_plot
> ### Title: Convert IPs to countries and plot on world map
> ### Aliases: IP_plot
> 
> ### ** Examples
> 
> IP_plot(IPs)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘RBGL’ ‘graph’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
convert_MITAB_to_edgeList: no visible global function definition for
  ‘combn’
convert_edgeList_to_graph: no visible global function definition for
  ‘ftM2graphNEL’
convert_edgeList_to_graph: no visible global function definition for
  ‘graph.data.frame’
convert_graph_to_edgeList: no visible global function definition for
  ‘edgeWeights’
convert_graph_to_edgeList: no visible global function definition for
  ‘get.edgelist’
convert_graph_to_edgeList: no visible global function definition for
  ‘E’
create_id_conversion_table: no visible global function definition for
  ‘write.table’
get_irefindex: no visible global function definition for ‘read.table’
get_irefindex: no visible global function definition for
  ‘download.file’
get_irefindex: no visible global function definition for ‘unzip’
summary_graph: no visible global function definition for
  ‘connectedComp’
summary_graph: no visible global function definition for ‘subGraph’
summary_graph: no visible global function definition for ‘clusters’
summary_graph: no visible global function definition for ‘subgraph’
summary_graph: no visible global function definition for ‘plot’
summary_graph: no visible binding for global variable
  ‘layout.fruchterman.reingold’
Undefined global functions or variables:
  E clusters combn connectedComp download.file edgeWeights ftM2graphNEL
  get.edgelist graph.data.frame layout.fruchterman.reingold plot
  read.table subGraph subgraph unzip write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "combn", "download.file", "read.table", "unzip",
             "write.table")
to your NAMESPACE file.
dendrify: no visible binding for global variable ‘item’
dendrify: no visible binding for global variable ‘node’
dendrify: no visible binding for global variable ‘value’
exogenize: no visible binding for global variable ‘item’
Undefined global functions or variables:
  item node value
isbf: no visible global function definition for ‘var’
isbf: no visible global function definition for ‘qnorm’
isbfReg: no visible global function definition for ‘var’
isbfReg: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
residualplot: no visible global function definition for ‘predict’
residualplot: no visible global function definition for ‘rstandard’
residualplot: no visible global function definition for
  ‘complete.cases’
residualplot: no visible global function definition for ‘plot’
residualplot: no visible global function definition for ‘points’
residualplot: no visible global function definition for ‘lines’
residualplot: no visible global function definition for ‘smooth.spline’
residualplot: no visible global function definition for ‘sd’
residualplot: no visible global function definition for ‘rgb’
residualplot: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  complete.cases lines plot points polygon predict rgb rstandard sd
  smooth.spline
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "complete.cases", "predict", "rstandard", "sd",
             "smooth.spline")
to your NAMESPACE file.
EstimateIsingLL: no visible global function definition for ‘combn’
EstimateIsingLL: no visible global function definition for ‘loglin’
EstimateIsingPL: no visible global function definition for ‘nlm’
EstimateIsingUni : <anonymous>: no visible global function definition
  for ‘glm’
EstimateIsingUni : <anonymous>: no visible binding for global variable
  ‘binomial’
EstimateIsingUni: no visible binding for global variable ‘coef’
Undefined global functions or variables:
  binomial coef combn glm loglin nlm
Consider adding
  importFrom("stats", "binomial", "coef", "glm", "loglin", "nlm")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running examples in ‘isoband-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iso_to_sfg
> ### Title: Convert isolines or isobands to sfg object
> ### Aliases: iso_to_sfg
> 
> ### ** Examples
> 
> library(sf)
Linking to GEOS 3.7.1, GDAL 2.4.0, PROJ 5.2.0
> library(ggplot2)
> 
> m <- matrix(c(0, 2, 2, 2, 0,
+               0, 1, 0, 1, 0,
+               0, 1, 0, 0, 0,
+               0, 1, 0, 1, 0,
+               0, 0, 0, 0, 0), 5, 5, byrow = TRUE)
> 
> z <- isolines(1:ncol(m), nrow(m):1, m, c(0.5, 1.5))
> lines <- iso_to_sfg(z)
> x <- st_sf(level = names(lines), geometry = st_sfc(lines))
> ggplot(x) + geom_sf(aes(color = level))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
C.cal: no visible global function definition for ‘as.stepfun’
bandwidth.choose.cv: no visible global function definition for ‘isoreg’
g.density: no visible global function definition for ‘as.stepfun’
g.density: no visible global function definition for ‘dnorm’
h.density: no visible global function definition for ‘dnorm’
iso.bt.unit: no visible global function definition for ‘quantile’
iso.bt.unit.sub: no visible global function definition for ‘isoreg’
iso.bt.unit.sub: no visible global function definition for ‘as.stepfun’
iso.bt.wald.unit: no visible global function definition for ‘var’
iso.ci: no visible global function definition for ‘isoreg’
iso.ci.transform.unit: no visible global function definition for
  ‘as.stepfun’
Undefined global functions or variables:
  as.stepfun dnorm isoreg quantile var
Consider adding
  importFrom("stats", "as.stepfun", "dnorm", "isoreg", "quantile", "var")
to your NAMESPACE file.
ACO : bordacircular: no visible global function definition for
  ‘medianCircular’
Undefined global functions or variables:
  medianCircular
'library' or 'require' call to ‘proxy’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
isopam : core: no visible global function definition for ‘dist’
isopam : core: no visible global function definition for ‘write.table’
isopam : core: no visible global function definition for ‘as.dist’
isopam : core: no visible global function definition for
  ‘txtProgressBar’
isopam : core: no visible global function definition for
  ‘setTxtProgressBar’
isopam : core: no visible global function definition for ‘aggregate’
isopam: no visible binding for global variable ‘var’
isopam: no visible global function definition for ‘na.omit’
isopam: no visible global function definition for ‘write.table’
isopam: no visible global function definition for ‘bmp’
isopam: no visible global function definition for ‘dev.off’
isotab: no visible global function definition for ‘aggregate’
isotab : fshtest: no visible global function definition for ‘dhyper’
isotab : fshtest : pnhyper: no visible global function definition for
  ‘phyper’
Undefined global functions or variables:
  aggregate as.dist bmp dev.off dhyper dist na.omit phyper
  setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.off")
  importFrom("stats", "aggregate", "as.dist", "dhyper", "dist",
             "na.omit", "phyper", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
ufit: no visible global function definition for ‘stepfun’
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
Running examples in ‘itan-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: agi
> ### Title: Analisis grafico de items.
> ### Aliases: agi
> 
> ### ** Examples
> 
> data(datos)
> data(clave)
> respuestas <- subset(datos, select=-id)
> plots <- agi(respuestas, clave, nGrupos=ncol(respuestas)/2)
> plots[[1]][[1]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘MASS’ ‘VGAM’ ‘apTreeshape’ ‘ape’ ‘geiger’ ‘gtools’ ‘partitions’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘ITNr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_degree_distribution
> ### Title: Plot Degree Distribution
> ### Aliases: plot_degree_distribution
> 
> ### ** Examples
> 
> require(igraph)
Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:network’:

    %c%, %s%, add.edges, add.vertices, delete.edges, delete.vertices,
    get.edge.attribute, get.edges, get.vertex.attribute, is.bipartite,
    is.directed, list.edge.attributes, list.vertex.attributes,
    set.edge.attribute, set.vertex.attribute

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

> ##Create random International Trade Network (igraph object)
> ITN<-erdos.renyi.game(75,0.05,directed = TRUE)
> 
> ##Plot out degree distribution
> plot_degree_distribution(ITN,"in")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:base':

    isFALSE

Loading required package: rngtools
Loading required package: cluster
# NOTE - CRAN check detected: limiting maximum number of cores [2/32]
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
Quitting from lines 45-47 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
REAL() can only be applied to a 'numeric', not a 'integer'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘Readme’
Packages in Depends field not imported from:
  ‘Matching’ ‘R2jags’ ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bpsm: no visible global function definition for ‘glm’
bpsm: no visible global function definition for ‘binomial’
bpsm: no visible global function definition for ‘Match’
bpsm: no visible global function definition for ‘cov’
bpsm: no visible global function definition for ‘vcov’
bpsm : inits: no visible global function definition for ‘runif’
bpsm: no visible global function definition for ‘jags’
bpsr: no visible global function definition for ‘glm’
bpsr: no visible global function definition for ‘binomial’
bpsr: no visible global function definition for ‘lm’
bpsr : inits: no visible global function definition for ‘runif’
bpsr: no visible global function definition for ‘jags’
modelpsm: no visible binding for global variable ‘D’
modelpsr: no visible binding for global variable ‘D’
Undefined global functions or variables:
  D Match binomial cov glm jags lm runif vcov
Consider adding
  importFrom("stats", "D", "binomial", "cov", "glm", "lm", "runif",
             "vcov")
to your NAMESPACE file.
ivFixed.formula: no visible global function definition for
  ‘model.matrix’
ivFixed.formula: no visible global function definition for
  ‘model.response’
summary.ivFixed: no visible global function definition for ‘coef’
summary.ivFixed: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gurobi’
ARsensitivity.ci: no visible global function definition for ‘residuals’
ARsensitivity.ci: no visible global function definition for ‘lm’
ARsensitivity.ci: no visible global function definition for ‘qf’
ARsensitivity.ci: no visible global function definition for ‘fitted’
ARsensitivity.power: no visible global function definition for ‘qf’
ARsensitivity.power: no visible global function definition for ‘pf’
ARsensitivity.size: no visible global function definition for ‘qf’
ARsensitivity.size: no visible global function definition for ‘pf’
anderson.rubin.ci: no visible global function definition for ‘qf’
anderson.rubin.ci: no visible global function definition for ‘fitted’
anderson.rubin.ci: no visible global function definition for ‘lm’
power.iv: no visible global function definition for ‘qf’
power.iv: no visible global function definition for ‘pf’
Undefined global functions or variables:
  fitted lm pf qf residuals
Consider adding
  importFrom("stats", "fitted", "lm", "pf", "qf", "residuals")
to your NAMESPACE file.
hausman: no visible global function definition for ‘pchisq’
ivbe: no visible global function definition for ‘cor’
ivbe: no visible global function definition for ‘pt’
ivfixed: no visible global function definition for ‘cor’
ivfixed: no visible global function definition for ‘pt’
ivpan.formula: no visible global function definition for ‘model.matrix’
ivpan.formula: no visible global function definition for
  ‘model.response’
ivrandom: no visible global function definition for ‘cor’
ivrandom: no visible global function definition for ‘pt’
summary.ivpan: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response", "pchisq",
             "printCoefmat", "pt")
to your NAMESPACE file.
histw: no visible global function definition for ‘plot.new’
histw: no visible global function definition for ‘plot.window’
histw: no visible global function definition for ‘axis’
histw: no visible global function definition for ‘rect’
histw: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis lines plot.new plot.window rect
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
to your NAMESPACE file.
boxplot.james: no visible global function definition for ‘mtext’
getBestSolutionValues.james : <anonymous>: no visible global function
  definition for ‘tail’
isMinimizing: no visible global function definition for ‘head’
isMinimizing: no visible global function definition for ‘tail’
mergeJAMES.james: no visible global function definition for ‘glob2rx’
plotConvergence.james : <anonymous> : <anonymous>: no visible global
  function definition for ‘tail’
plotConvergence.james: no visible global function definition for ‘tail’
plotConvergence.james: no visible global function definition for ‘head’
plotConvergence.james : <anonymous>: no visible global function
  definition for ‘tail’
plotConvergence.james: no visible global function definition for
  ‘matplot’
plotConvergence.james: no visible global function definition for
  ‘mtext’
summary.james: no visible global function definition for ‘sd’
summary.james: no visible global function definition for ‘median’
summary.james: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR glob2rx head matplot median mtext sd tail
Consider adding
  importFrom("graphics", "matplot", "mtext")
  importFrom("stats", "IQR", "median", "sd")
  importFrom("utils", "glob2rx", "head", "tail")
to your NAMESPACE file.
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(janitor)
  > 
  > test_check("janitor")
  ── 1. Failure: users can supply own Ns (@test-adorn-ns.R#129)  ─────────────────
  `%>%`(...) not equal to data.frame(...).
  Component "big": 2 string mismatches
  Component "small": 2 string mismatches
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 438 SKIPPED: 0 FAILED: 1
  1. Failure: users can supply own Ns (@test-adorn-ns.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
Package in Depends field not imported from: ‘gtools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

make_template: no visible global function definition for ‘invalid’
Undefined global functions or variables:
  invalid
Output from running autoreconf:
  configure.ac:103: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
  configure.ac:103: the top level
  configure.ac:103: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
  configure.ac:103: the top level
  configure.ac:103: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
  configure.ac:103: the top level
  configure.ac:103: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from...
  configure.ac:103: the top level
Non-standard files/directories found at top level:
  ‘getsp.class’ ‘getsp.java’ ‘version’
.getJavaGDObject: no visible global function definition for ‘.jmkref’
.javaGD.copy.device: no visible global function definition for
  ‘dev.cur’
.javaGD.copy.device: no visible binding for global variable ‘pdf’
.javaGD.copy.device: no visible global function definition for
  ‘dev.set’
.javaGD.copy.device: no visible global function definition for
  ‘dev.copy’
.javaGD.copy.device: no visible global function definition for ‘par’
.javaGD.copy.device: no visible global function definition for
  ‘dev.off’
.javaGD.get.size: no visible global function definition for ‘dev.cur’
.javaGD.resize: no visible global function definition for ‘dev.cur’
JavaGD: no visible global function definition for ‘.jinit’
Undefined global functions or variables:
  .jinit .jmkref dev.copy dev.cur dev.off dev.set par pdf
Consider adding
  importFrom("grDevices", "dev.copy", "dev.cur", "dev.off", "dev.set",
             "pdf")
  importFrom("graphics", "par")
to your NAMESPACE file.
getSysinfo: no visible global function definition for ‘sessionInfo’
getVecInfo: no visible global function definition for ‘sd’
isSeriesConstant: no visible global function definition for ‘median’
labelMargins: no visible global function definition for ‘mtext’
plotBG: no visible global function definition for ‘plot’
plotBG: no visible global function definition for ‘polygon’
plotBG: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘text’
plotImageRotated: no visible global function definition for
  ‘heat.colors’
plotImageRotated: no visible global function definition for ‘par’
plotImageRotated: no visible global function definition for ‘plot’
plotImageRotated: no visible global function definition for ‘image’
plotImageRotated: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘par’
plotNLines: no visible global function definition for ‘plot’
plotNLines: no visible global function definition for ‘mtext’
plotNLines: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘points’
plotNLines: no visible global function definition for ‘sd’
userCoords: no visible global function definition for ‘par’
Undefined global functions or variables:
  axis heat.colors image median mtext par plot points polygon sd
  sessionInfo text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "image", "mtext", "par", "plot",
             "points", "polygon", "text")
  importFrom("stats", "median", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Running examples in ‘jcolors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_color_jcolors_contin
> ### Title: continuous jcolors color scales
> ### Aliases: scale_color_jcolors_contin scale_colour_jcolors_contin
> ###   scale_fill_jcolors_contin scale_color_jcolors scale_colour_jcolors
> ###   scale_fill_jcolors
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> plt <- ggplot(data.frame(x = rnorm(10000), y = rexp(10000, 1.5)), aes(x = x, y = y)) +
+    geom_hex() + coord_fixed()
> 
> plt + scale_fill_jcolors_contin() + theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_the_jcolors_package.Rmd’ using rmarkdown
Quitting from lines 62-96 (using_the_jcolors_package.Rmd) 
Error: processing vignette 'using_the_jcolors_package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using_the_jcolors_package.Rmd’

SUMMARY: processing the following file failed:
  ‘using_the_jcolors_package.Rmd’

Error: Vignette re-building failed.
Execution halted
powerLongSurv: no visible global function definition for ‘qnorm’
powerLongSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
JBTest: no visible global function definition for ‘pchisq’
generateSignificance: no visible global function definition for ‘pnorm’
packages: no visible global function definition for ‘install.packages’
shift: no visible global function definition for ‘tail’
shift: no visible global function definition for ‘head’
splitBy: no visible global function definition for ‘head’
Undefined global functions or variables:
  head install.packages pchisq pnorm tail
Consider adding
  importFrom("stats", "pchisq", "pnorm")
  importFrom("utils", "head", "install.packages", "tail")
to your NAMESPACE file.
':::' calls which should be '::':
  ‘jmvcore:::decomposeFormula’ ‘jmvcore:::enquo’
  ‘jmvcore:::marshalData’ ‘jmvcore:::marshalFormula’
  ‘jmvcore:::resolveQuo’
  See the note in ?`:::` about the use of this operator.
RE.ADT: no visible global function definition for ‘sd’
RE.ADT: no visible global function definition for ‘pnorm’
RE.Johnson: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm sd
Consider adding
  importFrom("stats", "pnorm", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘joineRmeta.Rmd’ using rmarkdown
Quitting from lines 227-229 (joineRmeta.Rmd) 
Error: processing vignette 'joineRmeta.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘joineRmeta.Rmd’

SUMMARY: processing the following file failed:
  ‘joineRmeta.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘JointAI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: densplot
> ### Title: Plot posterior density from JointAI model
> ### Aliases: densplot densplot.mcmc.list densplot.JointAI
> 
> ### ** Examples
> 
> 
> # fit a JointAI object:
> mod <- lm_imp(y ~ C1 + C2 + M2, data = wideDF, n.iter = 100)
This is new software. Please report any bugs to the package maintainer.
> 
> # Example 1: basic densityplot
> densplot(mod)
> 
> 
> # Example 2: use vlines to mark zero
> densplot(mod, col = c("darkred", "darkblue", "darkgreen"),
+          vlines = list(list(v = rep(0, nrow(summary(mod)$stats)),
+                             col = grey(0.8))))
> 
> 
> # Example 3: use vlines to visualize the posterior mean and 2.5% and 97.5% quantiles
> densplot(mod, vlines = list(list(v = summary(mod)$stats[, "Mean"], lty = 1, lwd = 2),
+                             list(v = summary(mod)$stats[, "2.5%"], lty = 2),
+                             list(v = summary(mod)$stats[, "97.5%"], lty = 2)))
> 
> 
> # Example 4: ggplot version
> densplot(mod, use_ggplot = TRUE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
binteg: no visible global function definition for ‘contourLines’
binteg: no visible global function definition for ‘approx’
binteg: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘plot’
plot1: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘rect’
plot1: no visible global function definition for ‘axis’
plot1: no visible global function definition for ‘contour’
plot1: no visible global function definition for ‘contourLines’
plot1: no visible binding for global variable ‘approx’
plot1: no visible global function definition for ‘lines’
plot1: no visible global function definition for ‘text’
plot2: no visible global function definition for ‘plot’
plot2: no visible global function definition for ‘abline’
plot2: no visible global function definition for ‘lines’
plot2: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline approx axis contour contourLines legend lines par plot rect
  text
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "abline", "axis", "contour", "legend", "lines",
             "par", "plot", "rect", "text")
  importFrom("stats", "approx")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Rsolnp’ ‘dglm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘jrt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: info.plot
> ### Title: Plot the information function for a judge or for the entire set
> ###   of judges.
> ### Aliases: info.plot
> 
> ### ** Examples
> 
> 
> # Simulate data with package mirt
> # (6 judges, 300 productions, ordinal ratings from 1 to 5)
> set.seed(123)
> N <- 300
> judges <- 6
> diffs <- t(apply(matrix(runif(judges*4, .4, 5), judges), 1, cumsum))
> d <- -(diffs - rowMeans(diffs)) + stats::rnorm(judges, mean = 0, sd= 1)
> data <- mirt::simdata(matrix(rlnorm(judges,1,0)), d, N,
+ itemtype = 'graded') + 1
> colnames(data) <- paste("Judge_", 1:dim(data)[2], sep = "")
> data <- as.data.frame(data)
> ### --> See mirt documentation for details
> 
> # Fit model
> fit <- jrt(data, irt.model = "PCM")
The possible responses detected are: 1-2-3-4-5

 -== General Summary ==-
- 6 Judges
- 300 Products
- 5 response categories (1-2-3-4-5)
- Mean judgment = 2.977 | SD = 0.862

-== IRT Summary ==-
- Model: Partial Credit Model (Masters, 1982) | doi: 10.1007/BF02296272
- Estimation package: mirt (Chalmers, 2012) | doi: 10.18637/jss.v048.i06
- Estimation algorithm: Expectation-Maximization (EM; Bock & Atkin, 1981) | doi: 10.1007/BF02293801
- Method of factor scoring: Expected A Posteriori (EAP)
- AIC = 4022.955 | AICc = 4027.7 | BIC = 4115.55 | SABIC = 4022.955

-== Model-based reliability ==-
- Empirical reliability | Average in the sample: .889
- Expected reliability | Assumes a Normal(0,1) prior density: .758

Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: jrt ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 85-86 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘jskm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: jskm
> ### Title: Creates a Kaplan-Meier plot for survfit object.
> ### Aliases: jskm
> 
> ### ** Examples
> 
>  library(survival)
>  data(colon)
>  fit <- survfit(Surv(time,status)~rx, data=colon)
>  jskm(fit, timeby=500)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘jskm.Rmd’ using rmarkdown
Quitting from lines 35-45 (jskm.Rmd) 
Error: processing vignette 'jskm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘jskm.Rmd’

SUMMARY: processing the following file failed:
  ‘jskm.Rmd’

Error: Vignette re-building failed.
Execution halted
sonarCSV: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Running examples in ‘jtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: effect_plot
> ### Title: Plot simple effects in regression models
> ### Aliases: effect_plot
> 
> ### ** Examples
> 
> # Using a fitted lm model
> states <- as.data.frame(state.x77)
> states$HSGrad <- states$`HS Grad`
> fit <- lm(Income ~ HSGrad + Murder,
+   data = states)
> effect_plot(model = fit, pred = Murder)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘effect_plot.Rmd’ using rmarkdown
Quitting from lines 49-50 (effect_plot.Rmd) 
Error: processing vignette 'effect_plot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘effect_plot.Rmd’

--- re-building ‘summ.Rmd’ using rmarkdown
Loading required package: Matrix
Quitting from lines 250-251 (summ.Rmd) 
Error: processing vignette 'summ.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘summ.Rmd’

--- re-building ‘svycor.Rmd’ using rmarkdown
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

The following object is masked from 'package:graphics':

    dotchart

--- finished re-building ‘svycor.Rmd’

SUMMARY: processing the following files failed:
  ‘effect_plot.Rmd’ ‘summ.Rmd’

Error: Vignette re-building failed.
Execution halted
qtls: no visible global function definition for ‘quantile’
qtls: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm quantile
Consider adding
  importFrom("stats", "pnorm", "quantile")
to your NAMESPACE file.
Running examples in ‘JWileymisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TukeyHSDgg
> ### Title: Tukey HSD Plot
> ### Aliases: TukeyHSDgg
> ### Keywords: plot
> 
> ### ** Examples
> 
> 
> ## examples using it with single level data
> ## differences based on an ANOVA and follow up contrasts
> TukeyHSDgg("cyl", "mpg", mtcars)
Warning in TukeyHSDgg("cyl", "mpg", mtcars) :
  x was not a factor, attempting to coerce
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
expression_up : <anonymous>: no visible global function definition for
  ‘quantile’
expression_up : <anonymous>: no visible global function definition for
  ‘IQR’
expression_up : <anonymous>: no visible global function definition for
  ‘median’
expression_up : <anonymous>: no visible global function definition for
  ‘sd’
plot_up: no visible global function definition for ‘plot’
plot_up: no visible global function definition for ‘text’
Undefined global functions or variables:
  IQR median plot quantile sd text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "IQR", "median", "quantile", "sd")
to your NAMESPACE file.
Running examples in ‘kaos-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cgr
> ### Title: Chaos Game Representation Object
> ### Aliases: cgr
> 
> ### ** Examples
> 
> ###HIV data
> data("HIV")
> 
> ### encoding the sequence
> HIV.cgr = cgr(HIV, res = 100)
> 
> ###plot the sequence
> cgr.plot(HIV.cgr, mode = "points")
> 
> ###plot the FCGR
> cgr.plot(HIV.cgr, mode = "matrix")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
KappaV: no visible global function definition for ‘over’
KappaV: no visible global function definition for ‘layout’
KappaV: no visible global function definition for ‘terrain.colors’
KappaV: no visible global function definition for ‘as’
Undefined global functions or variables:
  as layout over terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "layout")
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘kayadata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_fuel_mix
> ### Title: Plot fuel mix
> ### Aliases: plot_fuel_mix
> 
> ### ** Examples
> 
> usa_fuel <- get_fuel_mix("United States", collapse_renewables = FALSE)
> plot_fuel_mix(usa_fuel)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘policy_analysis.Rmd’ using rmarkdown
Quitting from lines 88-90 (policy_analysis.Rmd) 
Error: processing vignette 'policy_analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘policy_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘policy_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
ikcirt.fun.mss.eta: no visible global function definition for ‘var’
ikcirt.fun.mss.eta: no visible global function definition for ‘pnorm’
ikcirt.fun.mss.lambda: no visible global function definition for ‘var’
ikcirt.fun.mss.lambda: no visible global function definition for
  ‘pnorm’
ikcirt.fun.mss.mu: no visible global function definition for ‘pnorm’
kcirt.fitEE: no visible binding for global variable ‘sd’
kcirt.fitEE: no visible global function definition for ‘var’
kcirt.fitEE: no visible global function definition for ‘cor’
kcirt.fitMSS: no visible global function definition for ‘var’
kcirt.fitMSS: no visible global function definition for ‘pnorm’
kcirt.fitMSS: no visible global function definition for ‘sfInit’
kcirt.fitMSS: no visible global function definition for ‘sfExport’
kcirt.fitMSS: no visible global function definition for ‘rnorm’
kcirt.fitMSS: no visible global function definition for
  ‘txtProgressBar’
kcirt.fitMSS: no visible global function definition for ‘sfIsRunning’
kcirt.fitMSS: no visible global function definition for ‘sfStop’
kcirt.fitMSS: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor pnorm rnorm sd sfExport sfInit sfIsRunning sfStop txtProgressBar
  var
Consider adding
  importFrom("stats", "cor", "pnorm", "rnorm", "sd", "var")
  importFrom("utils", "txtProgressBar")
to your NAMESPACE file.
as.matrix.multiPhylo : tip2tip: no visible global function definition
  for ‘cophenetic’
bw.nn : <anonymous>: no visible global function definition for
  ‘quantile’
dist.diss: no visible binding for global variable ‘median’
dist.diss: no visible global function definition for ‘dist’
hist.kdetrees: no visible binding for global variable ‘density’
kdetrees : cutoff: no visible global function definition for ‘quantile’
kdetrees.complete: no visible global function definition for ‘plot’
kdetrees.complete: no visible global function definition for ‘hist’
kdetrees.complete: no visible global function definition for
  ‘write.csv’
plot.kdetrees: no visible binding for global variable ‘density’
Undefined global functions or variables:
  cophenetic density dist hist median plot quantile write.csv
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "cophenetic", "density", "dist", "median",
             "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Running examples in ‘kdetrees-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hist.kdetrees
> ### Title: Create a histogram of tree density estimates
> ### Aliases: hist.kdetrees
> 
> ### ** Examples
> 
> result <- kdetrees(apicomplexa)
> hist(result)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kdetrees.Rnw’ using Sweave
Error: processing vignette 'kdetrees.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘kdetrees.Rnw’

--- re-building ‘simulation.Rnw’ using Sweave
Loading required package: ade4
Loading required package: lattice
--- finished re-building ‘simulation.Rnw’

SUMMARY: processing the following file failed:
  ‘kdetrees.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kdtools.Rmd’ using rmarkdown
--- finished re-building ‘kdtools.Rmd’

--- re-building ‘methods.Rmd’ using rmarkdown
Quitting from lines 82-95 (methods.Rmd) 
Error: processing vignette 'methods.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘methods.Rmd’

SUMMARY: processing the following file failed:
  ‘methods.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘kendallRandomWalks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: transform_kendall_rw
> ### Title: Transforming (scaling and shifting) Kendall random walks
> ### Aliases: transform_kendall_rw
> 
> ### ** Examples
> 
> kendall_simulations <- simulate_kendall_rw(10, 1000, runif, 0.5)
> scaled_kendall <- transform_kendall_rw(kendall_simulations, (1:1000)^(-2))
> scaled_kendall # kendall random walked scaled by the sequence n^(-1/alpha)
Simulations of Kendall random walk 
Number of simulations:  10 
Length of a single simulation:  1000 
Step distribution:  runif 
Alpha parameter:  0.5> scaled_data <- scaled_kendall$simulation # simulated values
> plot(scaled_kendall)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘behaviour.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 36-38 (behaviour.Rmd) 
Error: processing vignette 'behaviour.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘behaviour.Rmd’

--- re-building ‘kendall_rws.Rmd’ using rmarkdown
Quitting from lines 23-29 (kendall_rws.Rmd) 
Error: processing vignette 'kendall_rws.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘kendall_rws.Rmd’

SUMMARY: processing the following files failed:
  ‘behaviour.Rmd’ ‘kendall_rws.Rmd’

Error: Vignette re-building failed.
Execution halted
SeasonalMannKendall: no visible global function definition for ‘is.ts’
SeasonalMannKendall: no visible global function definition for
  ‘frequency’
SeasonalMannKendall: no visible global function definition for ‘cycle’
SeasonalMannKendall: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cycle frequency is.ts pnorm
Consider adding
  importFrom("stats", "cycle", "frequency", "is.ts", "pnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Checking should be performed on sources prepared by ‘R CMD build’.
Packages in Depends field not imported from:
  ‘chron’ ‘date’ ‘evir’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ALbw: no visible global function definition for ‘sd’
ALbw: no visible global function definition for ‘quantile’
CVbw: no visible global function definition for ‘quantile’
PBbw: no visible global function definition for ‘sd’
PBbw: no visible global function definition for ‘IQR’
kernel_function: no visible global function definition for ‘dnorm’
kernel_function_distribution: no visible global function definition for
  ‘pnorm’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  IQR approx dnorm pnorm quantile sd
Consider adding
  importFrom("stats", "IQR", "approx", "dnorm", "pnorm", "quantile",
             "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using knitr
Loading required package: knitr
Loading required package: kfigr
knitr hook "anchor" is now available
Loading required package: ggplot2
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 26-28 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘khroma-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_colour_soil
> ### Title: FAO Soil Reference Groups Colour Scheme for ggplot2
> ### Aliases: scale_colour_soil scale_color_soil scale_fill_soil
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> soil <- data.frame(
+   name = c("Acrisol", "Albeluvisol", "Andosol", "Anthrosol", "Arenosol",
+            "Calcisol", "Cambisol", "Chernozem", "Cryosol", "Fluvisol",
+            "Kastanozem", "Gleysol", "Gypsisol", "Histosol", "Leptosol",
+            "Luvisol", "Phaeozem", "Planosol", "Podzol", "Regosol", "Solonchak",
+            "Solonetz", "Umbrisol", "Vertisol")
+ )
> 
> ggplot(soil, aes(fill = name)) +
+   geom_rect(aes(xmin = rep(0, 24), xmax = rep(1, 24),
+                 ymin = 1:24, ymax = 1:24+1)) +
+   scale_y_reverse() +
+   scale_fill_soil(name = "Soil")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
kissmigDummyS: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
distrct.analysis : <anonymous> : <anonymous>: no visible global
  function definition for ‘cor’
grand.table: no visible global function definition for ‘write.csv2’
grand.table: no visible global function definition for ‘write.csv’
klausur: no visible global function definition for ‘sd’
klausur: no visible global function definition for ‘na.omit’
klausur.gen.marks : suggestion : <anonymous>: no visible global
  function definition for ‘qnorm’
klausur.mufo: no visible global function definition for ‘sd’
klausur.report: no visible global function definition for ‘dev.off’
klausur.report : tabellenbau: no visible global function definition for
  ‘capture.output’
plot,klausuR-missing: no visible global function definition for
  ‘na.omit’
plot,klausuR-missing: no visible global function definition for ‘sd’
plot,klausuR-missing : <anonymous>: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  capture.output cor dev.off dnorm na.omit qnorm sd write.csv
  write.csv2
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "cor", "dnorm", "na.omit", "qnorm", "sd")
  importFrom("utils", "capture.output", "write.csv", "write.csv2")
to your NAMESPACE file.
klin.solve : <anonymous>: no visible global function definition for
  ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘km.ci/R/epband.fun.R’:
  data(critical.value.nair.90, critical.value.nair.95, critical.value.nair.99)
File ‘km.ci/R/hall.wellner.fun.R’:
  data(critical.value.hall.90, critical.value.hall.95, critical.value.hall.99)
See section ‘Good practice’ in ‘?data’.
noe.compute.pv: no visible global function definition for ‘punif’
Undefined global functions or variables:
  punif
Consider adding
  importFrom("stats", "punif")
to your NAMESPACE file.
dscore: no visible global function definition for ‘glm’
dscore: no visible binding for global variable ‘binomial’
dscore: no visible global function definition for ‘pnorm’
pearson.group: no visible global function definition for ‘cor’
spearman.group: no visible global function definition for ‘cor’
sscore: no visible global function definition for ‘glm’
sscore: no visible binding for global variable ‘binomial’
sscore: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binomial cor glm pnorm
Consider adding
  importFrom("stats", "binomial", "cor", "glm", "pnorm")
to your NAMESPACE file.
Running examples in ‘kmed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: barplotnum
> ### Title: Barplot of each cluster for numerical variables data set.
> ### Aliases: barplotnum
> 
> ### ** Examples
> 
> dat <- iris[,1:4]
> memb <- cutree(hclust(dist(dat)),3)
> barplotnum(dat, memb)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kmedoid.Rmd’ using rmarkdown
Quitting from lines 143-147 (kmedoid.Rmd) 
Error: processing vignette 'kmedoid.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘kmedoid.Rmd’

SUMMARY: processing the following file failed:
  ‘kmedoid.Rmd’

Error: Vignette re-building failed.
Execution halted
Warning: no function found corresponding to methods exports from ‘kmlcov’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
C_zero : <anonymous>: no visible global function definition for ‘runif’
get_extra_centroid_index: no visible global function definition for
  ‘head’
get_within_cluster_ss: no visible global function definition for
  ‘aggregate’
kmod: no visible global function definition for ‘head’
kmod: no visible global function definition for ‘tail’
Undefined global functions or variables:
  aggregate head runif tail
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
knncat: no visible global function definition for ‘quantile’
plot.knncat: no visible global function definition for ‘plot’
plot.knncat: no visible global function definition for ‘box’
plot.knncat: no visible global function definition for ‘axis’
plot.knncat: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box plot quantile text
Consider adding
  importFrom("graphics", "axis", "box", "plot", "text")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dataFiller : central.value: no visible global function definition for
  ‘median’
dataFiller: no visible global function definition for ‘daisy’
dataFiller: no visible global function definition for ‘complete.cases’
knnMCN: no visible global function definition for ‘cov’
knnVCN: no visible global function definition for ‘dist’
Undefined global functions or variables:
  complete.cases cov daisy dist median
Consider adding
  importFrom("stats", "complete.cases", "cov", "dist", "median")
to your NAMESPACE file.
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘rbeta’
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘runif’
calculate.power : <anonymous>: no visible binding for global variable
  ‘quantile’
generate.benchmark.data: no visible global function definition for
  ‘runif’
generate.benchmark.data: no visible global function definition for
  ‘rnorm’
generate.benchmark.data: no visible global function definition for
  ‘rbinom’
generate.patchwork.copula: no visible global function definition for
  ‘rbeta’
generate.patchwork.copula: no visible global function definition for
  ‘runif’
novelTest.chisq: no visible global function definition for ‘pchisq’
novelTest.chisq4nn: no visible global function definition for ‘pchisq’
optimise.copula.mi : <anonymous>: no visible global function definition
  for ‘optimize’
power.plot: no visible global function definition for ‘plot’
power.plot: no visible global function definition for ‘axis’
power.plot : <anonymous>: no visible global function definition for
  ‘points’
power.plot: no visible global function definition for ‘legend’
roc.plot: no visible global function definition for ‘colorRampPalette’
roc.plot : <anonymous>: no visible global function definition for
  ‘plot’
roc.plot : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
run.tests : <anonymous> : <anonymous>: no visible global function
  definition for ‘runif’
Undefined global functions or variables:
  axis colorRampPalette legend optimize pchisq plot points quantile
  rbeta rbinom rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "legend", "plot", "points")
  importFrom("stats", "optimize", "pchisq", "quantile", "rbeta",
             "rbinom", "rnorm", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-konfound.Rmd’ using rmarkdown
Quitting from lines 83-84 (introduction-to-konfound.Rmd) 
Error: processing vignette 'introduction-to-konfound.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction-to-konfound.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-konfound.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
assign_clustpp: no visible global function definition for ‘kmeans’
kpod: no visible global function definition for ‘kmeans’
makeData: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
Running examples in ‘KraljicMatrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SAVF_plot
> ### Title: Plot the single attribute value curve
> ### Aliases: SAVF_plot
> 
> ### ** Examples
> 
> 
> # Given the single attribute x is bounded between 1 and 5 and the subject matter experts
> # prefer x values of 3, 4, & 5 provide a utility score of .75, .90 & 1.0 respectively,
> # the preferred rho is 0.54. We can visualize this value function:
> 
> SAVF_plot(desired_x = c(3, 4, 5),
+           desired_v = c(.75, .9, 1),
+           x_low = 1,
+           x_high = 5,
+           rho = 0.54)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kraljic.Rmd’ using rmarkdown
Quitting from lines 145-152 (kraljic.Rmd) 
Error: processing vignette 'kraljic.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘kraljic.Rmd’

SUMMARY: processing the following file failed:
  ‘kraljic.Rmd’

Error: Vignette re-building failed.
Execution halted
image.kriging: no visible global function definition for ‘heat.colors’
image.kriging: no visible global function definition for ‘image’
kriging: no visible global function definition for ‘lm’
plot.kriging: no visible global function definition for ‘plot’
plot.kriging: no visible global function definition for ‘curve’
Undefined global functions or variables:
  curve heat.colors image lm plot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "curve", "image", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars.win: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
kselection: no visible global function definition for ‘txtProgressBar’
kselection: no visible global function definition for
  ‘setTxtProgressBar’
plot.Kselection: no visible global function definition for ‘plot’
plot.Kselection: no visible global function definition for ‘lines’
plot.Kselection: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines plot setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rbuildindex.10034
  .Rbuildindex.31551
  .Rbuildindex.31678
  .Rbuildindex.9995
  inst/doc/.fr-hy2VZf
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘Biobase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
S3 methods shown with full name in documentation object 'predict.ktsp':
  ‘predict.ktsp’

S3 methods shown with full name in documentation object 'print.ktsp':
  ‘print.ktsp’

S3 methods shown with full name in documentation object 'summary.ktsp':
  ‘summary.ktsp’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'library' or 'require' call to ‘XML’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
auc: no visible global function definition for ‘approx’
kulife.colors: no visible global function definition for ‘palette’
rootonorm: no visible global function definition for ‘sd’
rootonorm: no visible global function definition for ‘hist’
rootonorm: no visible global function definition for ‘pnorm’
rootonorm: no visible global function definition for ‘dnorm’
rootonorm: no visible global function definition for ‘plot’
rootonorm: no visible global function definition for ‘rect’
rootonorm: no visible global function definition for ‘lines’
rootonorm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approx dnorm hist lines palette plot pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "plot", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE file.
compareModelResults: no visible global function definition for
  ‘reshape’
erf: no visible global function definition for ‘pnorm’
getModelComparisonTable: no visible global function definition for
  ‘read.csv’
hantushSstar: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate pnorm read.csv reshape
Consider adding
  importFrom("stats", "integrate", "pnorm", "reshape")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘readme.txt’
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  ‘dim’ to ‘dims’
Error(s) in re-building vignettes:
  ...
--- re-building ‘L0Learn-vignette.Rmd’ using rmarkdown
Quitting from lines 129-130 (L0Learn-vignette.Rmd) 
Error: processing vignette 'L0Learn-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘L0Learn-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘L0Learn-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘l1kdeconv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gmmplot
> ### Title: Plot the Fit Results of 2-Component Gaussian Mixture Model
> ### Aliases: gmmplot
> ### Keywords: distribution
> 
> ### ** Examples
> 
> set.seed(0)
> x=list(c(
+   rnorm(150, mean=0)
+   , rnorm(50, mean=10)
+   ))
> fit_res=multigmmsamedistribu(x)
number of iterations= 7 
> 
> with(
+   as.list(fit_res$par_conv)
+   , gmmplot(x[[1]]
+     , mu1=mu1
+     , mu2=mu2
+     , sigma=sigma
+     , lambda=lambda
+     , xlim=range(unlist(x))
+     )
+   )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following hidden files and directories:
  .Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
extended.figures: no visible global function definition for ‘par’
extended.figures: no visible global function definition for ‘runif’
extended.figures : figure2: no visible global function definition for
  ‘hist’
extended.figures : figure2: no visible global function definition for
  ‘axis’
extended.figures : figure3 : <anonymous>: no visible global function
  definition for ‘median’
extended.figures : figure3: no visible global function definition for
  ‘barplot’
Undefined global functions or variables:
  axis barplot hist median par runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "median", "runif")
to your NAMESPACE file.
LDuncan.aov : prob: no visible global function definition for ‘qtukey’
LDuncan.aov: no visible global function definition for ‘qtukey’
LScottKnott.aov : sk: no visible global function definition for
  ‘pchisq’
LScottKnott.aov: no visible global function definition for ‘read.table’
LTukey.aov: no visible global function definition for ‘qtukey’
Undefined global functions or variables:
  pchisq qtukey read.table
Consider adding
  importFrom("stats", "pchisq", "qtukey")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘GPArotation’ ‘mice’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
angoff: no visible global function definition for ‘cov2cor’
angoff: no visible global function definition for ‘runif’
cov.lambda4: no visible global function definition for ‘cov2cor’
cov.lambda4: no visible global function definition for ‘median’
guttman: no visible global function definition for ‘cov2cor’
impute.cov: no visible global function definition for ‘cov’
impute.cov: no visible global function definition for ‘complete’
impute.cov: no visible global function definition for ‘mice’
kristof: no visible global function definition for ‘cov2cor’
kristof: no visible global function definition for ‘runif’
lambda1: no visible global function definition for ‘cov2cor’
lambda2: no visible global function definition for ‘cov2cor’
lambda3: no visible global function definition for ‘cov2cor’
lambda3: no visible binding for global variable ‘sd’
lambda5: no visible global function definition for ‘cov2cor’
lambda6: no visible global function definition for ‘cov2cor’
omega.tot: no visible global function definition for ‘cov2cor’
omega.tot: no visible global function definition for ‘factanal’
quant.lambda4: no visible global function definition for ‘cov2cor’
quant.lambda4: no visible global function definition for ‘runif’
quant.lambda4: no visible global function definition for ‘quantile’
raju: no visible global function definition for ‘cov2cor’
raju: no visible global function definition for ‘runif’
user.lambda4: no visible global function definition for ‘runif’
user.lambda4: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  complete cov cov2cor factanal median mice quantile runif sd
Consider adding
  importFrom("stats", "cov", "cov2cor", "factanal", "median", "quantile",
             "runif", "sd")
to your NAMESPACE file.
getGO: no visible global function definition for ‘new’
getGO: no visible global function definition for ‘getGeneric’
graph.kd: no visible global function definition for ‘as’
Undefined global functions or variables:
  as getGeneric new
Consider adding
  importFrom("methods", "as", "getGeneric", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Kern.FUN: no visible global function definition for ‘dnorm’
Prob.Covariate.ShortEvent: no visible global function definition for
  ‘bw.nrd’
optimize.mse.BW: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  bw.nrd dnorm optimize
Consider adding
  importFrom("stats", "bw.nrd", "dnorm", "optimize")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘rgdal’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BSL: no visible global function definition for ‘read.asciigrid’
BSL: no visible global function definition for ‘quantile’
PIF: no visible global function definition for ‘read.asciigrid’
PIF: no visible global function definition for ‘quantile’
RCS: no visible global function definition for ‘quantile’
clouds: no visible global function definition for ‘read.asciigrid’
geoshift: no visible global function definition for ‘bbox’
histmatch: no visible global function definition for ‘hist’
minnaert: no visible global function definition for ‘coefficients’
minnaert: no visible global function definition for ‘lm’
minnaert: no visible global function definition for ‘predict’
topocorr: no visible global function definition for ‘lm’
topocorr: no visible global function definition for ‘coefficients’
Undefined global functions or variables:
  bbox coefficients hist lm predict quantile read.asciigrid
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coefficients", "lm", "predict", "quantile")
to your NAMESPACE file.
Running examples in ‘landscapemetrics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: show_cores
> ### Title: Show core area
> ### Aliases: show_cores show_cores.RasterLayer show_cores.RasterStack
> ###   show_cores.RasterBrick show_cores.stars show_cores.list
> 
> ### ** Examples
> 
> # show "global" core area
> show_cores(landscape, class = "global", labels = FALSE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘landscapetools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: util_merge
> ### Title: util_merge
> ### Aliases: util_merge util_merge.RasterLayer
> 
> ### ** Examples
> 
> x <- util_merge(gradient_landscape, random_landscape)
> show_landscape(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Loading required package: raster
Loading required package: sp
Quitting from lines 31-46 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lans2r-calculate.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 102-109 (lans2r-calculate.Rmd) 
Error: processing vignette 'lans2r-calculate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lans2r-calculate.Rmd’

--- re-building ‘lans2r-hmr.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 33-39 (lans2r-hmr.Rmd) 
Error: processing vignette 'lans2r-hmr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lans2r-hmr.Rmd’

--- re-building ‘lans2r.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 92-103 (lans2r.Rmd) 
Error: processing vignette 'lans2r.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lans2r.Rmd’

SUMMARY: processing the following files failed:
  ‘lans2r-calculate.Rmd’ ‘lans2r-hmr.Rmd’ ‘lans2r.Rmd’

Error: Vignette re-building failed.
Execution halted
betabreaker: no visible global function definition for ‘predict’
coef.lars: no visible global function definition for ‘predict’
cv.lars: no visible global function definition for ‘predict’
cv.lars: no visible binding for global variable ‘var’
error.bars: no visible global function definition for ‘segments’
plot.lars: no visible global function definition for ‘plot’
plot.lars: no visible global function definition for ‘matplot’
plot.lars: no visible global function definition for ‘title’
plot.lars: no visible global function definition for ‘abline’
plot.lars: no visible global function definition for ‘axis’
plotCVLars: no visible global function definition for ‘plot’
predict.lars: no visible global function definition for ‘approx’
Undefined global functions or variables:
  abline approx axis matplot plot predict segments title var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "plot", "segments",
             "title")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘covTest’
glassoscore: no visible global function definition for ‘var’
glassoscore: no visible global function definition for ‘pchisq’
lassoscore: no visible global function definition for ‘txtProgressBar’
lassoscore: no visible global function definition for
  ‘setTxtProgressBar’
lassoscore: no visible global function definition for ‘pchisq’
plot.glassoscore: no visible global function definition for ‘legend’
plot.lassoscore: no visible global function definition for ‘legend’
plot.mbscore: no visible global function definition for ‘legend’
qqpval: no visible global function definition for ‘ppoints’
qqpval: no visible global function definition for ‘qbeta’
qqpval: no visible global function definition for ‘points’
qqpval: no visible global function definition for ‘plot’
qqpval: no visible global function definition for ‘abline’
qqpval: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline legend pchisq plot points polygon ppoints qbeta
  setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points", "polygon")
  importFrom("stats", "pchisq", "ppoints", "qbeta", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-latex2exp.Rmd’ using rmarkdown
Quitting from lines 55-71 (using-latex2exp.Rmd) 
Error: processing vignette 'using-latex2exp.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-latex2exp.Rmd’

SUMMARY: processing the following file failed:
  ‘using-latex2exp.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘lavaSearch2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: intDensTri
> ### Title: Integrate a Gaussian/Student Density over a Triangle
> ### Aliases: intDensTri
> 
> ### ** Examples
> 
> library(mvtnorm)
> 
> p <- 2
> Sigma <- diag(p)
> mu <- rep(0, p)
> 
> ## bivariate normal distribution
> z2 <- qmvt(0.975, mean = mu, sigma = Sigma, df = 1e3)$quantile
> 
> # compute integral
> intDensTri(mu = mu, Sigma = Sigma, n=5, x.min=0, type = "fine")$value-1/2
[1] -5.73303e-07
> intDensTri(mu = mu, Sigma = Sigma, n=30, x.min=0, type = "raw")$value-1/2
[1] -0.04696203
> intDensTri(mu = mu, Sigma = Sigma, n=50, x.min=0, type = "raw")$value-1/2
[1] -0.0281983
> 
> intDensTri(mu = mu, Sigma = Sigma, df = 5, n=5, x.min=0, distribution = "pmvt")$value-1/2
[1] -1.814574e-06
> res <- intDensTri(mu = mu, Sigma = Sigma, df = 5, n=10, x.min=0, distribution = "pmvt")
> res$value-1/2
[1] -1.814574e-06
> ggplot2::autoplot(res)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
plotcorr.lba.3d: warning in pch3d(colcoordi[, dim], pch = pch.budget,
  col = col.budget, ...): partial argument match of ‘col’ to ‘color’
lbfgs: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
  hasArg
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘LBSPR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSim
> ### Title: General plotting function for simulated data
> ### Aliases: plotSim
> 
> ### ** Examples
> 
>  LB_pars <- new("LB_pars")
A blank LB_pars object created
Default values have been set for some parameters
>  LB_pars@MK <- 1.5
>  LB_pars@Linf <- 100
>  LB_pars@L50 <- 50
>  LB_pars@L95 <- 55
>  LB_pars@SL50 <- 60
>  LB_pars@SL95 <- 65
>  LB_pars@FM <- 1
>  Sim <- LBSPRsim(LB_pars)
BinMax not set. Using default of 1.3 Linf
BinMin not set. Using default value of 0
BinWidth not set. Using default value of 1/20 Linf
>  plotSim(Sim)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotSim ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LBSPR.Rmd’ using rmarkdown
Quitting from lines 233-234 (LBSPR.Rmd) 
Error: processing vignette 'LBSPR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘LBSPR.Rmd’

SUMMARY: processing the following file failed:
  ‘LBSPR.Rmd’

Error: Vignette re-building failed.
Execution halted
LCA: no visible global function definition for ‘dist’
LCA: no visible global function definition for ‘combn’
LCA: no visible global function definition for ‘p.adjust’
LCA: no visible global function definition for ‘pchisq’
LCA : <anonymous>: no visible global function definition for ‘pchisq’
LCD: no visible global function definition for ‘ecdf’
estimateB: no visible global function definition for ‘median’
evaluateDiffSignificance: no visible global function definition for
  ‘ecdf’
fitPTLmodel: no visible global function definition for ‘lm’
getPTLparams: no visible global function definition for ‘nls’
getPTLparams: no visible global function definition for ‘coef’
predictPTLparams: no visible global function definition for
  ‘predict.lm’
Undefined global functions or variables:
  coef combn dist ecdf lm median nls p.adjust pchisq predict.lm
Consider adding
  importFrom("stats", "coef", "dist", "ecdf", "lm", "median", "nls",
             "p.adjust", "pchisq", "predict.lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running examples in ‘LCA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LCA
> ### Title: Localised Co-dependency Analysis
> ### Aliases: LCA
> 
> ### ** Examples
> 
> ## create a data matrix
> 
> x <- array(runif(1200),dim=c(40,12))
> 
> ## implant similarity across a 'clique'
> 
> clique.cols <- sample(ncol(x),4)
> x[,clique.cols] <- x[,clique.cols] + rnorm(nrow(x))
> 
> ## scale x to (0,1)
> 
> x[x<0] <- 0
> x[x>1] <- 1
> 
> ## choose a 'seed' feature and some partner
> 
> seed.row <- sample(nrow(x),1)
> partner.row <- sample(setdiff(c(1:nrow(x)),seed.row),1)
> 
> x[c(seed.row,partner.row),clique.cols] <- x[c(seed.row,partner.row),clique.cols] + 
+ rep(rnorm(length(clique.cols)),each=2)
> 
> ## calibrate PTL models to dataset
> 
> PTL.fit <- fitPTLmodel(x,nPairs=15)
1 models successfully fitted out of 12 
Error in fitPTLmodel(x, nPairs = 15) : 
  Rerun model calibration (possibly with higher nPairs), no successful fits this time.
Execution halted
cclcda.default: no visible global function definition for ‘as.formula’
cclcda.default: no visible global function definition for ‘chisq.test’
cclcda.formula: no visible global function definition for ‘model.frame’
cclcda2.default: no visible global function definition for ‘runif’
cclcda2.default: no visible global function definition for ‘chisq.test’
cclcda2.formula: no visible global function definition for
  ‘model.frame’
lcda.default: no visible global function definition for ‘as.formula’
lcda.formula: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  as.formula chisq.test model.frame runif
Consider adding
  importFrom("stats", "as.formula", "chisq.test", "model.frame", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘topics.Rmd’ using rmarkdown
Quitting from lines 84-85 (topics.Rmd) 
Error: processing vignette 'topics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘topics.Rmd’

SUMMARY: processing the following file failed:
  ‘topics.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LDheatmap.Rnw’ using Sweave
Loading required package: grid
--- finished re-building ‘LDheatmap.Rnw’

--- re-building ‘addTracks.Rnw’ using Sweave
Loading required package: survival
Loading required package: Matrix

Error: processing vignette 'addTracks.Rnw' failed with diagnostics:
 chunk 7 (label = fig2) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘addTracks.Rnw’

SUMMARY: processing the following file failed:
  ‘addTracks.Rnw’

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘LDOD.Rproj’
multistart : <anonymous>: no visible global function definition for
  ‘runif’
plot.FreD.x: no visible global function definition for ‘modifyList’
plot.FreD.x: no visible global function definition for ‘abline’
plot.FreD.x: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline modifyList points runif
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "runif")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
ARConfIntEst: no visible global function definition for ‘sd’
PTLinkFunc: no visible global function definition for ‘pnorm’
PTLinkFunc: no visible global function definition for ‘qnorm’
PTMultiPeriodPD: no visible global function definition for ‘uniroot’
PTOnePeriodPD : f: no visible global function definition for ‘pbinom’
PTOnePeriodPD: no visible global function definition for ‘uniroot’
QMMGetRLogitPD: no visible global function definition for ‘ecdf’
QMMPDlinkFunc: no visible global function definition for ‘qnorm’
QMMPlot: no visible global function definition for ‘plot’
QMMPlot: no visible global function definition for ‘lines’
QMMPlot: no visible global function definition for ‘legend’
VDBCalibratePD: no visible global function definition for ‘ecdf’
VDBGetK: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  ecdf legend lines pbinom plot pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "ecdf", "pbinom", "pnorm", "qnorm", "sd",
             "uniroot")
to your NAMESPACE file.
BEAPFrOG: no visible global function definition for ‘jags.model’
BEAPFrOG: no visible global function definition for ‘coda.samples’
LEAPFrOG_EM: no visible global function definition for ‘write.table’
LEAPFrOG_EM: no visible global function definition for ‘constrOptim’
LEAPFrOG_plot: no visible global function definition for ‘par’
LEAPFrOG_plot: no visible global function definition for ‘barplot’
LEAPFrOG_plot: no visible global function definition for ‘legend’
constrOptim2: no visible global function definition for ‘optim’
Undefined global functions or variables:
  barplot coda.samples constrOptim jags.model legend optim par
  write.table
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "constrOptim", "optim")
  importFrom("utils", "write.table")
to your NAMESPACE file.
AlternateSVD: no visible binding for global variable ‘sd’
IPOD: no visible global function definition for ‘mad’
IPOD: no visible global function definition for ‘pnorm’
Pvalue: no visible global function definition for ‘pf’
ROCplot: no visible global function definition for ‘png’
ROCplot: no visible global function definition for ‘matplot’
ROCplot: no visible global function definition for ‘legend’
ROCplot: no visible global function definition for ‘dev.off’
leapp: no visible global function definition for ‘png’
leapp: no visible global function definition for ‘plot’
leapp: no visible global function definition for ‘dev.off’
ridge: no visible global function definition for ‘sd’
ridge: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dev.off legend mad matplot pf plot png pnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "matplot", "plot")
  importFrom("stats", "mad", "pf", "pnorm", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘LEAP_Vignette.Rnw’ using Sweave
Error: processing vignette 'LEAP_Vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘LEAP_Vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘LEAP_Vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
File ‘leaps/libs/leaps.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘learningCurve-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_block_summary
> ### Title: Block Summary Plot
> ### Aliases: plot_block_summary
> 
> ### ** Examples
> 
>  
> # A production block runs from unit 201 to unit 500 inclusive.
> # The 201st unit had a required time of 125 hours with a 75% 
> # learning curve. Plot the block summary?
> 
> plot_block_summary(t = 125, m = 201, n = 500, r = .75)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘learningCurve.Rmd’ using rmarkdown
Quitting from lines 170-171 (learningCurve.Rmd) 
Error: processing vignette 'learningCurve.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘learningCurve.Rmd’

SUMMARY: processing the following file failed:
  ‘learningCurve.Rmd’

Error: Vignette re-building failed.
Execution halted
Fmntd.a : Fmntd.a.sub: no visible global function definition for
  ‘weighted.mean’
Fmpd : Fmpd.sub: no visible global function definition for ‘as.dist’
Fmpd.a : Fmpd.a.sub: no visible global function definition for
  ‘weighted.mean’
Fsntd : Fsntd.sub: no visible global function definition for ‘sd’
com.trait.moments : skewness: no visible global function definition for
  ‘var’
com.trait.moments : kurtosis: no visible global function definition for
  ‘var’
com.trait.moments : sd.funk: no visible global function definition for
  ‘sd’
com.trait.weighted : weight.mean.funk: no visible global function
  definition for ‘weighted.mean’
Undefined global functions or variables:
  as.dist sd var weighted.mean
Consider adding
  importFrom("stats", "as.dist", "sd", "var", "weighted.mean")
to your NAMESPACE file.
Running examples in ‘lemon-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate_y_axis
> ### Title: Annotations in the axis
> ### Aliases: annotate_y_axis annotate_x_axis
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> p <- ggplot(mtcars, aes(mpg, hp, colour=disp)) + geom_point()
> 
> l <- p + annotate_y_axis('mark at', y=200, tick=TRUE)
> l
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘capped-axes.Rmd’ using rmarkdown
Quitting from lines 28-43 (capped-axes.Rmd) 
Error: processing vignette 'capped-axes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘capped-axes.Rmd’

--- re-building ‘facet-rep-labels.Rmd’ using rmarkdown
Quitting from lines 27-29 (facet-rep-labels.Rmd) 
Error: processing vignette 'facet-rep-labels.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘facet-rep-labels.Rmd’

--- re-building ‘geoms.Rmd’ using rmarkdown
Quitting from lines 30-41 (geoms.Rmd) 
Error: processing vignette 'geoms.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘geoms.Rmd’

--- re-building ‘gtable_show_lemonade.Rmd’ using rmarkdown
Quitting from lines 22-38 (gtable_show_lemonade.Rmd) 
Error: processing vignette 'gtable_show_lemonade.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gtable_show_lemonade.Rmd’

--- re-building ‘legends.Rmd’ using rmarkdown
Quitting from lines 37-45 (legends.Rmd) 
Error: processing vignette 'legends.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘legends.Rmd’

--- re-building ‘lemon_print.Rmd’ using rmarkdown
--- finished re-building ‘lemon_print.Rmd’

SUMMARY: processing the following files failed:
  ‘capped-axes.Rmd’ ‘facet-rep-labels.Rmd’ ‘geoms.Rmd’
  ‘gtable_show_lemonade.Rmd’ ‘legends.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘LexisPlotR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lexis.cohort
> ### Title: Emphasize a certain cohort in a Lexis grid
> ### Aliases: lexis.cohort
> 
> ### ** Examples
> 
> library(LexisPlotR)
> lg <- lexis.grid(year.start = 1900, year.end = 1905, age.start = 0, age.end = 5)
> lexis.cohort(lg = lg, cohort = 1901)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LexisPlotR.rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 27-29 (LexisPlotR.rmd) 
Error: processing vignette 'LexisPlotR.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘LexisPlotR.rmd’

SUMMARY: processing the following file failed:
  ‘LexisPlotR.rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘snow’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘liayson-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterCells
> ### Title: Grouping cells into clones.
> ### Aliases: clusterCells
> 
> ### ** Examples
> 
> data(cnps)
> set.seed(2)
> rcells = sample(colnames(cnps), 120)
> outc = clusterCells(cnps[apply(cnps, 1, var)>0, rcells])
[1] "Neither k nor h is set."
[1] "Using Akaike information criterion to decide number of clusters..."
Error in kmeans(t(cnps), centers = x) : 
  more cluster centers than distinct data points.
Calls: clusterCells ... sapply -> lapply -> FUN -> .kmeansAIC -> ncol -> kmeans
Execution halted
Running examples in ‘lidR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: grid_hexametrics
> ### Title: Area-Based Approach in hexagonal cells.
> ### Aliases: grid_hexametrics
> 
> ### ** Examples
> 
> LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
> lidar = readLAS(LASfile)
> 
> col = grDevices::colorRampPalette(c("blue", "cyan2", "yellow", "red"))
> 
> # Maximum elevation with a resolution of 8 m
> hm = grid_hexametrics(lidar, max(Z), 8)
> hexbin::plot(hm, colramp = col, main = "Max Z")
Error in (function (cl, name, valueClass)  : 
  c("assignment of an object of class “simpleUnit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE", "assignment of an object of class “unit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE")
Calls: <Anonymous> ... <Anonymous> -> .local -> hexViewport -> <Anonymous>
Execution halted
Running examples in ‘lifelogr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: experiment
> ### Title: Do the specified analysis of the impact of the variables on the
> ###   measure
> ### Aliases: experiment
> 
> ### ** Examples
> 
> data(EX)
> experiment(person = EX, variables = list("fitbit_daily" = c("sleepDuration"),
+                                          "util" = c("day_of_week")),
+                         measures = list("fitbit_daily" = 
+                                           c("restingHeartRate")),
+                         analysis = c("plot"), time_var = c("date"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: experiment ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘summary.Rmd’ using rmarkdown
Quitting from lines 129-130 (summary.Rmd) 
Error: processing vignette 'summary.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘summary.Rmd’

--- re-building ‘vignette_viz.Rmd’ using rmarkdown
Quitting from lines 32-33 (vignette_viz.Rmd) 
Error: processing vignette 'vignette_viz.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette_viz.Rmd’

SUMMARY: processing the following files failed:
  ‘summary.Rmd’ ‘vignette_viz.Rmd’

Error: Vignette re-building failed.
Execution halted
Non-standard files/directories found at top level:
  ‘LIHNPSD-manual.pdf’ ‘PSD-Paper.pdf’ ‘Rplots.pdf’
Packages in Depends field not imported from:
  ‘BB’ ‘Bolstad2’ ‘Rmpfr’ ‘moments’ ‘optimx’ ‘sn’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘likert-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: likert
> ### Title: Analyze Likert type items.
> ### Aliases: likert
> 
> ### ** Examples
> 
> data(pisaitems)
> items29 <- pisaitems[,substr(names(pisaitems), 1,5) == 'ST25Q']
> names(items29) <- c("Magazines", "Comic books", "Fiction", 
+                    "Non-fiction books", "Newspapers")
> l29 <- likert(items29)
> summary(l29)
               Item      low  neutral     high     mean       sd
1         Magazines 30.21689 21.33091 48.45219 3.254813 1.245086
5        Newspapers 37.29377 15.72688 46.97935 3.140282 1.442299
3           Fiction 41.77380 19.61739 38.60882 2.961111 1.342667
2       Comic books 62.43096 15.78368 21.78536 2.298768 1.292631
4 Non-fiction books 61.42466 19.55493 19.02042 2.322898 1.199176
> plot(l29)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> -> print.likert.bar.plot
Execution halted
Running examples in ‘LilRhino-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Monty_Hall
> ### Title: Monty Hall Simulator
> ### Aliases: Monty_Hall
> 
> ### ** Examples
> 
> Monty_Hall(100, 'Stay')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘lime-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_explanations
> ### Title: Plot a condensed overview of all explanations
> ### Aliases: plot_explanations
> 
> ### ** Examples
> 
> # Create some explanations
> library(MASS)
> iris_test <- iris[1, 1:4]
> iris_train <- iris[-1, 1:4]
> iris_lab <- iris[[5]][-1]
> model <- lda(iris_train, iris_lab)
> explanation <- lime(iris_train, model)
> explanations <- explain(iris_test, explanation, n_labels = 1, n_features = 2)
> 
> # Get an overview with the standard plot
> plot_explanations(explanations)
Error in Summary.unit(c(2, 2), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Understanding_lime.Rmd’ using rmarkdown
Quitting from lines 167-168 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Understanding_lime.Rmd’

SUMMARY: processing the following file failed:
  ‘Understanding_lime.Rmd’

Error: Vignette re-building failed.
Execution halted
plotBox: no visible global function definition for ‘sd’
plotBox: no visible global function definition for ‘rect’
plotBox: no visible global function definition for ‘qnorm’
plotBox: no visible global function definition for ‘segments’
plotInit: no visible global function definition for ‘plot’
plotInit: no visible global function definition for ‘runif’
plotInit: no visible global function definition for ‘mtext’
plotInit: no visible global function definition for ‘segments’
plotStack: no visible global function definition for ‘points’
Undefined global functions or variables:
  mtext plot points qnorm rect runif sd segments
Consider adding
  importFrom("graphics", "mtext", "plot", "points", "rect", "segments")
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
Plotranges.double: no visible global function definition for ‘strwidth’
Plotranges.double: no visible global function definition for
  ‘strheight’
Plotranges.double: no visible global function definition for ‘plot.new’
Plotranges.double: no visible global function definition for ‘par’
Plotranges.double: no visible global function definition for
  ‘plot.window’
Plotranges.double: no visible global function definition for ‘mtext’
Plotranges.double: no visible global function definition for ‘abline’
Plotranges.double: no visible global function definition for ‘points’
Plotranges.double: no visible global function definition for ‘segments’
Plotranges.double: no visible global function definition for ‘text’
Plotranges.double: no visible global function definition for ‘axis’
Plotranges.double: no visible global function definition for ‘box’
Plotranges.double: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axis box mtext par plot.new plot.window points segments
  strheight strwidth text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "mtext", "par",
             "plot.new", "plot.window", "points", "segments",
             "strheight", "strwidth", "text", "title")
to your NAMESPACE file.
class.calib: no visible global function definition for ‘lm’
class.calib: no visible global function definition for ‘coef’
class.calib: no visible global function definition for ‘qt’
hoad.calib: no visible global function definition for ‘lm’
hoad.calib: no visible global function definition for ‘anova’
hoad.calib: no visible global function definition for ‘qt’
hoad.calib: no visible global function definition for ‘rnorm’
huntlam.calib: no visible global function definition for ‘lm’
huntlam.calib: no visible global function definition for ‘anova’
huntlam.calib: no visible global function definition for ‘rnorm’
huntlam.calib: no visible global function definition for ‘qnorm’
inver.calib: no visible global function definition for ‘lm’
inver.calib: no visible global function definition for ‘coef’
inver.calib: no visible global function definition for ‘anova’
inver.calib: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  anova coef lm qnorm qt rnorm
Consider adding
  importFrom("stats", "anova", "coef", "lm", "qnorm", "qt", "rnorm")
to your NAMESPACE file.
Running examples in ‘lindia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_boxcox
> ### Title: Plot boxcox graph in ggplot with suggested lambda transformation
> ### Aliases: gg_boxcox
> 
> ### ** Examples
> 
> library(MASS)
> data(Cars93)
> cars_lm <- lm(Price ~ Passengers + Length + RPM, data = Cars93)
> gg_boxcox(cars_lm)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘linear.tools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: deleting_wrongeffect
> ### Title: check monotonicity of marginal impacts and re-estimate the
> ###   model.
> ### Aliases: deleting_wrongeffect
> 
> ### ** Examples
> 
> 
> ##
> set.seed(413)
> traing_data = ggplot2::diamonds[runif(nrow(ggplot2::diamonds))<0.05,]
> nrow(traing_data)
[1] 2642
> 
> diamond_lm3 = lm(formula = price ~ carat + I(carat^2) + I(carat^3) + cut +
+                    I(carat * depth) , data = traing_data)
> 
> 
> test = deleting_wrongeffect(model = diamond_lm3,
+                             focus_var_raw = 'carat',
+                             focus_var_model = c("I(carat^3)","I(carat*depth)",
+                                                 "I(carat^2)","I(carat)"),
+                             focus_value = list(carat=seq(0.5,6,0.1)),
+                             data = traing_data,
+                             PRINT = TRUE,STOP = FALSE,
+                             Reverse = FALSE)

coeff var:  I(carat)  cannot be found in the model, So not check them 

initial model: 
                    Estimate     Pr(>|t|)
(Intercept)        546.06400 2.960453e-03
carat             2592.30091 8.792262e-02
I(carat^2)       10430.65850 3.162007e-76
I(carat^3)       -2614.03182 5.320933e-68
cut.L              753.86085 1.967355e-10
cut.Q             -147.90059 1.474569e-01
cut.C              309.85410 4.583125e-04
cut^4              184.88962 1.151290e-02
I(carat * depth)   -97.58333 1.408239e-05


check raw var:  carat 
check model var:  I(carat^3), I(carat*depth), I(carat^2) 
Correct Monotonicity is supposed to be:  Increasing 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: deleting_wrongeffect ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘linear.tools.Rmd’ using rmarkdown
Quitting from lines 157-162 (linear.tools.Rmd) 
Error: processing vignette 'linear.tools.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘linear.tools.Rmd’

SUMMARY: processing the following file failed:
  ‘linear.tools.Rmd’

Error: Vignette re-building failed.
Execution halted
gcomb: no visible global function definition for ‘complete.cases’
linkim: no visible global function definition for ‘runif’
missing.dist: no visible global function definition for
  ‘complete.cases’
pgdata1: no visible global function definition for ‘barplot’
pgdata1: no visible global function definition for ‘layout’
pgdata1: no visible global function definition for ‘par’
pgdata1: no visible global function definition for ‘rainbow’
singim: no visible global function definition for ‘complete.cases’
singim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot complete.cases layout par rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "barplot", "layout", "par")
  importFrom("stats", "complete.cases", "runif")
to your NAMESPACE file.
gen.lms: no visible global function definition for ‘na.omit’
plot.idf: no visible global function definition for ‘plot’
plot.idf: no visible global function definition for ‘mtext’
plot.idf: no visible global function definition for ‘points’
plot.idf: no visible global function definition for ‘segments’
plot.idf: no visible global function definition for ‘ftable’
plot.idf: no visible global function definition for ‘image’
plot.idf: no visible global function definition for ‘gray’
plot.idf: no visible global function definition for ‘abline’
plot.s.linlir: no visible global function definition for ‘plot’
plot.s.linlir: no visible global function definition for ‘mtext’
plot.s.linlir: no visible global function definition for ‘polygon’
plot.s.linlir: no visible global function definition for ‘points’
plot.s.linlir: no visible global function definition for ‘curve’
s.linlir: no visible global function definition for ‘na.omit’
s.linlir: no visible global function definition for ‘dbinom’
s.linlir: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq plot
  points polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "plot",
             "points", "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘pkg.Rproj’
'library' or 'require' call to ‘lpSolve’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lpSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
solveLP: no visible global function definition for ‘lp’
Undefined global functions or variables:
  lp
Non-standard file/directory found at top level:
  ‘package.R’
last: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
getMatrix : <anonymous>: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in ‘listdtr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build.rule
> ### Title: Low-level Functions for Handling List-based Rules
> ### Aliases: build.rule build.rule.cv apply.rule show.rule verbalize.rule
> ###   draw.rule
> ### Keywords: tree
> 
> ### ** Examples
> 
>   x <- matrix(rnorm(200 * 10), 200, 10)
>   y <- cbind(
+     a1 = as.double(x[, 1] < 0) + rnorm(200, 0, 0.1),
+     a2 = as.double(x[, 2] > 0) + rnorm(200, 0, 0.1))
>   y[y < 0] <- 0
>   
>   obj <- build.rule(x, y)
>   show.rule(obj)
If x2 <= -0.064 then a2;
If x1 > 0.015 then a1;
If x10 <= -2.209 then a2;
If x1 > -0.009 then a1;
If x2 <= -0.002 then a2;
If x2 > 2.573 then a2;
If x9 > 2.388 then a1;
If x9 > 1.616 then a1;
If x7 > 2.499 then a1;
Else a2.
>   draw.rule(obj)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wine_quality.Rmd’ using rmarkdown
Loading required package: ParamHelpers
Welcome to live v1.5.10. Live is a part of DALEXverse. Find out more at https://github.com/pbiecek/DALEX.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'e1071'

The following object is masked from 'package:mlr':

    impute

Warning: Ignoring unknown aesthetics: x
Quitting from lines 98-99 (wine_quality.Rmd) 
Error: processing vignette 'wine_quality.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘wine_quality.Rmd’

SUMMARY: processing the following file failed:
  ‘wine_quality.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘scatterplot3d’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘LLSR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AQSys.plot
> ### Title: Dataset and Fitted Function plot
> ### Aliases: AQSys.plot
> 
> ### ** Examples
> 
> #Populating variable dataSET with binodal data
> dataSET <- peg4kslt[, 1:2]
> # Plot dataSET using Merchuk's function
> #
> AQSys.plot(dataSET)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: AQSys.plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
lm.beta: no visible global function definition for ‘coef’
lm.beta: no visible global function definition for ‘model.matrix’
lm.beta: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  coef model.frame model.matrix
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix")
to your NAMESPACE file.
Running examples in ‘lme4-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: profile-methods
> ### Title: Profile method for merMod objects
> ### Aliases: as.data.frame.thpr log.thpr logProf varianceProf
> ###   profile-methods profile.merMod
> ### Keywords: methods
> 
> ### ** Examples
> 
> fm01ML <- lmer(Yield ~ 1|Batch, Dyestuff, REML = FALSE)
> system.time(
+   tpr  <- profile(fm01ML, optimizer="Nelder_Mead", which="beta_")
+ )## fast; as only *one* beta parameter is profiled over
   user  system elapsed 
  0.195   0.004   0.207 
> ## full profiling (default which means 'all) needs
> ## ~2.6s (on a 2010 Macbook Pro)
> system.time( tpr  <- profile(fm01ML))
   user  system elapsed 
  0.527   0.000   0.682 
> ## ~1s, + possible warning about bobyqa convergence
> (confint(tpr) -> CIpr)
                 2.5 %     97.5 %
.sig01        12.19853   84.06305
.sigma        38.22998   67.65770
(Intercept) 1486.45150 1568.54849
> library("lattice")
> xyplot(tpr)
Error in unit(0.5 * showr, "strwidth", list(right)) : 
  no string supplied for 'strwidth/height' unit
Calls: <Anonymous> ... strip -> do.call -> strip.default -> paste.and.draw -> unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lmerperf.Rmd’ using rmarkdown
--- finished re-building ‘lmerperf.Rmd’

--- re-building ‘lmer.Rnw’ using knitr
Loading required package: Matrix
Computing profile confidence intervals ...
Computing bootstrap confidence intervals ...

7 message(s): boundary (singular) fit: see ?isSingular
186 warning(s): Model failed to converge with max|grad| = 0.00203996 (tol = 0.002, component 1) (and others)

Quitting from lines 2656-2657 (lmer.Rnw) 
Error: processing vignette 'lmer.Rnw' failed with diagnostics:
no string supplied for 'strwidth/height' unit
--- failed re-building ‘lmer.Rnw’

--- re-building ‘PLSvGLS.Rnw’ using Sweave
--- finished re-building ‘PLSvGLS.Rnw’

--- re-building ‘Theory.Rnw’ using Sweave
--- finished re-building ‘Theory.Rnw’

SUMMARY: processing the following file failed:
  ‘lmer.Rnw’

Error: Vignette re-building failed.
Execution halted
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  ‘compl’ to ‘complete’
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  ‘compl’ to ‘complete’
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
mq.diagnostics : mq_missinggenotype_plot: no visible global function
  definition for ‘plot.missing’
Undefined global functions or variables:
  plot.missing
Package in Depends field not imported from: ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
approx.Z : <anonymous>: no visible global function definition for
  ‘approx’
smspline: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  approx model.frame
Consider adding
  importFrom("stats", "approx", "model.frame")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘emulator’ ‘methods’ ‘miscTools’ ‘penalized’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error(s) in re-building vignettes:
  ...
--- re-building ‘LocalControl-jss-2018.Rnw’ using Sweave
Loading required package: data.table
Loading required package: colorspace
Loading required package: RColorBrewer
Loading required package: gridExtra
Loading required package: ggplot2
Loading required package: rpart
Loading required package: rpart.plot
Loading required package: LocalControl
Loading required package: xtable
Loading required package: TeachingDemos

Attaching package: 'TeachingDemos'

The following object is masked from 'package:xtable':

    digits


Error: processing vignette 'LocalControl-jss-2018.Rnw' failed with diagnostics:
 chunk 31 (label = figure_8) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building 'LocalControl-jss-2018.Rnw'

SUMMARY: processing the following file failed:
  'LocalControl-jss-2018.Rnw'

Error: Vignette re-building failed.
Execution halted
AnalyticalOptim: no visible global function definition for ‘optim’
LLConstructor : LL: no visible global function definition for ‘dpois’
MixtureDensity: no visible global function definition for ‘glm’
MixtureDensity : f_hat: no visible global function definition for
  ‘predict’
NullDensity : f0: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dpois glm optim predict
Consider adding
  importFrom("stats", "dpois", "glm", "optim", "predict")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘localfdr-intro-vignette.Rmd’ using rmarkdown
Quitting from lines 137-138 (localfdr-intro-vignette.Rmd) 
Error: processing vignette 'localfdr-intro-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘localfdr-intro-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘localfdr-intro-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘akima’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported objects:
  ‘lattice::render.3d.trellis’ ‘lattice::render.contour.trellis’
available.loglevels: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EstimateProbability: no visible global function definition for
  ‘predict’
LOGICOIL: no visible binding for global variable ‘pssm’
LOGICOIL: no visible binding for global variable ‘LOGICOILfit’
LOGICOIL: no visible binding for global variable ‘Model_Parameters’
plot_LOGICOIL: no visible global function definition for ‘png’
plot_LOGICOIL: no visible global function definition for ‘par’
plot_LOGICOIL: no visible global function definition for ‘plot’
plot_LOGICOIL: no visible global function definition for ‘lines’
plot_LOGICOIL: no visible global function definition for ‘axis’
plot_LOGICOIL: no visible global function definition for ‘mtext’
plot_LOGICOIL: no visible global function definition for ‘legend’
plot_LOGICOIL: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par plot
  png predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
Running examples in ‘logihist-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: logihist
> ### Title: Combined Graphs for Logistic Regression
> ### Aliases: logihist logibox logidot
> ### Keywords: ~aplot
> 
> ### ** Examples
> 
> 
> # Get some data from package popbio
> data(aq.trans, package="popbio")
> aq.trans$survived<-aq.trans$fate!="dead"
> a<-subset(aq.trans, leaf<50 & stage!="recruit", c(leaf,survived))
> 
> 
> # Transform the "survived" variable in numeric
> # This is necesary to correctly plot the combined graph.
>  
> a$survived <-a$survived*1
> 
> # Fit a logistic regression
> glm.a<- glm(survived~leaf, data=a, family=binomial)
> 
> 
> # Histograms
> # From individual variables
> # Modifying the appearence of histogram bins
> logihist(a$leaf,a$survived)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘logisticPCA.Rmd’ using rmarkdown
Quitting from lines 112-114 (logisticPCA.Rmd) 
Error: processing vignette 'logisticPCA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘logisticPCA.Rmd’

SUMMARY: processing the following file failed:
  ‘logisticPCA.Rmd’

Error: Vignette re-building failed.
Execution halted
test_compute_gradient: no visible global function definition for
  ‘rnorm’
test_compute_probabilities: no visible global function definition for
  ‘rnorm’
test_logitchoice: no visible global function definition for ‘rnorm’
test_solver: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
LogitNet.weight: no visible global function definition for ‘lowess’
LogitNet.weight: no visible global function definition for ‘median’
Undefined global functions or variables:
  lowess median
Consider adding
  importFrom("stats", "lowess", "median")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘logitnorm.Rmd’ using knitr
Quitting from lines 45-76 (logitnorm.Rmd) 
Error: processing vignette 'logitnorm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘logitnorm.Rmd’

SUMMARY: processing the following file failed:
  ‘logitnorm.Rmd’

Error: Vignette re-building failed.
Execution halted
rloglognorm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘aggregateCorrelated.Rmd’ using rmarkdown
Quitting from lines 70-77 (aggregateCorrelated.Rmd) 
Error: processing vignette 'aggregateCorrelated.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘aggregateCorrelated.Rmd’

--- re-building ‘lognorm.Rmd’ using rmarkdown
Quitting from lines 51-78 (lognorm.Rmd) 
Error: processing vignette 'lognorm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lognorm.Rmd’

--- re-building ‘lognormalSum.Rmd’ using rmarkdown
Quitting from lines 56-75 (lognormalSum.Rmd) 
Error: processing vignette 'lognormalSum.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lognormalSum.Rmd’

SUMMARY: processing the following files failed:
  ‘aggregateCorrelated.Rmd’ ‘lognorm.Rmd’ ‘lognormalSum.Rmd’

Error: Vignette re-building failed.
Execution halted
LogrankA: no visible global function definition for ‘is.Surv’
LogrankA: no visible global function definition for ‘na.omit’
LogrankA: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  is.Surv na.omit pchisq
Consider adding
  importFrom("stats", "na.omit", "pchisq")
to your NAMESPACE file.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:897:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lolR)
  > 
  > test_check("lolR")
  ── 1. Failure: Optimal Embedding Dimensions (@test-xval.R#45)  ─────────────────
  result.rs$optimal.lhat not equal to result.rs.noset$optimal.lhat.
  Lengths differ: 2 is not 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 446 SKIPPED: 0 FAILED: 1
  1. Failure: Optimal Embedding Dimensions (@test-xval.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘longitudinalcascade-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: longitudinalcascade
> ### Title: Longitudinal cascade statistics and charts
> ### Aliases: longitudinalcascade
> ### Keywords: cascade longitudinal survival
> 
> ### ** Examples
> 
> # Pull in data from example simulated dataset
> library(longitudinalcascade)
> data(events_long)
> 
> # Set up options
> stages.order <- c("First tested positive","Knows status","Linked to care","Eligible for ART",
+ "Initiated ART","Therapeutic response")
> groups.order <- c("Group 1","Group 2","Group 3")
> death.indicator <- "Death"
> retention.indicator <- "Clinic visit"
> censorship.indicator <- "LTFU"
> allow.sub.lines <- TRUE
> allow.skips <- TRUE
> 
> # Create cascade object
> longitudinalcascade.sim <- longitudinalcascade(events_long,stages.order=stages.order,
+ groups.order=groups.order,death.indicator=death.indicator,
+ censorship.indicator=censorship.indicator,
+ allow.sub.lines=allow.sub.lines,allow.skips=allow.skips)
> 
> # Print/output main chart
> longitudinalcascade.sim$chart
Error in Summary.unit(c(0, 0), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
fplot: no visible global function definition for ‘rnorm’
fplot: no visible global function definition for ‘plot’
fplot: no visible global function definition for ‘segments’
fplot: no visible global function definition for ‘points’
fplot: no visible global function definition for ‘text’
fplot.foodweb: no visible global function definition for ‘plot’
fplot.foodweb: no visible global function definition for ‘segments’
fplot.foodweb: no visible global function definition for ‘points’
fplot.foodweb: no visible global function definition for ‘text’
gplot: no visible global function definition for ‘runif’
groupplot: no visible global function definition for ‘rnorm’
groupplot: no visible global function definition for ‘plot’
groupplot: no visible global function definition for ‘segments’
groupplot: no visible global function definition for ‘points’
groupplot: no visible global function definition for ‘text’
groupplot.foodweb: no visible global function definition for ‘rnorm’
groupplot.foodweb: no visible global function definition for ‘plot’
groupplot.foodweb: no visible global function definition for ‘segments’
groupplot.foodweb: no visible global function definition for ‘points’
groupplot.foodweb: no visible global function definition for ‘text’
Undefined global functions or variables:
  plot points rnorm runif segments text
Consider adding
  importFrom("graphics", "plot", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
amendColumns: no visible global function definition for ‘setNames’
fillColumns: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Running examples in ‘loose.rock-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw.cov.matrix
> ### Title: Plot covariance heatmap from matrix
> ### Aliases: draw.cov.matrix
> 
> ### ** Examples
> 
> draw.cov.matrix(matrix(rnorm(100), ncol = 10))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [8s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(loose.rock)
  > 
  > test_check("loose.rock")
  ── 1. Error: single multiplot (@test-multiplot.R#4)  ───────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_silent(multiplot(ggplot2::qplot(1:10, 11:20))) at testthat/test-multiplot.R:4
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: multiplot(ggplot2::qplot(1:10, 11:20))
  10: print(plots[[1]])
  ...
  16: preDraw(x)
  17: preDraw.gTree(x)
  18: pushvpgp(x)
  19: pushgrobvp(x$vp)
  20: pushgrobvp.viewport(x$vp)
  21: pushViewport(vp, recording = FALSE)
  22: lapply(vps, push.vp, recording)
  23: FUN(X[[i]], ...)
  24: push.vp.viewport(X[[i]], ...)
  25: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 144 SKIPPED: 0 FAILED: 1
  1. Error: single multiplot (@test-multiplot.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning: Prefixing `UQ()` with the rlang namespace is deprecated as of rlang 0.3.0.
Please use the non-prefixed form or `!!` instead.

  # Bad:
  rlang::expr(mean(rlang::UQ(var) * 100))

  # Ok:
  rlang::expr(mean(UQ(var) * 100))

  # Good:
  rlang::expr(mean(!!var * 100))

This warning is displayed once per session.
Quitting from lines 112-126 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following file failed:
  ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘lpdensity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lpdensity.plot
> ### Title: Local Polynomial Density Plot with Robust Confidence Intervals
> ### Aliases: lpdensity.plot
> 
> ### ** Examples
> 
> set.seed(42); X <- rnorm(2000)
> 
> X <- X - 0.5; X[X>0] <- X[X>0] * 2
> est1 <- lpdensity(data = X[X<=0], grid = seq(-2.5, 0, 0.05), bwselect = "IMSE",
+   scale = sum(X<=0)/length(X))
> est2 <- lpdensity(data = X[X>0],  grid = seq(0, 2, 0.05), bwselect = "IMSE",
+   scale = sum(X>0)/length(X))
> lpdensity.plot(est1, est2, legendTitle="My Plot", legendGroups=c("Left", "Right"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
lpint : <anonymous>: no visible global function definition for
  ‘integrate’
lpint: no visible global function definition for ‘integrate’
lpint : lpint : <anonymous>: no visible global function definition for
  ‘integrate’
lplikint : lplikint.fun : <anonymous>: no visible global function
  definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
'library' or 'require' call to ‘Rsymphony’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
mipSolve.Rsymphony: no visible global function definition for
  ‘Rsymphony_solve_LP’
Undefined global functions or variables:
  Rsymphony_solve_LP
learnPattern.default: no visible global function definition for ‘runif’
plot.learnPattern: no visible global function definition for ‘matplot’
plotMDS: no visible global function definition for ‘par’
plotMDS: no visible global function definition for ‘rainbow’
plotMDS: no visible global function definition for ‘plot’
plotMDS: no visible global function definition for ‘pairs’
visualizePattern: no visible global function definition for ‘par’
visualizePattern: no visible global function definition for ‘plot’
visualizePattern: no visible global function definition for ‘points’
visualizePattern: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend matplot pairs par plot points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "plot",
             "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
LP.comoment: no visible global function definition for ‘cor’
LP.comoment: no visible global function definition for ‘cov’
LP.moment: no visible global function definition for ‘cor’
LPTrans: no visible global function definition for ‘ecdf’
VAR: no visible global function definition for ‘embed’
VAR: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cor cov ecdf embed lm
Consider adding
  importFrom("stats", "cor", "cov", "ecdf", "embed", "lm")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘LPWC.Rmd’ using rmarkdown
Quitting from lines 145-173 (LPWC.Rmd) 
Error: processing vignette 'LPWC.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘LPWC.Rmd’

SUMMARY: processing the following file failed:
  ‘LPWC.Rmd’

Error: Vignette re-building failed.
Execution halted
associate: no visible global function definition for ‘cor’
textmatrix: no visible global function definition for ‘xtabs’
textvector: no visible global function definition for ‘data’
Undefined global functions or variables:
  cor data xtabs
Consider adding
  importFrom("stats", "cor", "xtabs")
  importFrom("utils", "data")
to your NAMESPACE file.
Running examples in ‘lsbclust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meanbiplot
> ### Title: Biplots of
> ### Aliases: meanbiplot
> 
> ### ** Examples
> 
> set.seed(1)
> dat <- rlsbclust(ndata = 1, nobs = 100, size = c(10, 8), nclust = c(5, 4, 6, 5))
> meanbiplot(dat[[1]]$interactions$C, dat[[1]]$interactions$D)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lsbclust)
  Loading required package: ggplot2
  > 
  > test_check("lsbclust")
  K-means on overall means...	DONE
  ── 1. Failure: cluster vector (@test_orc.R#29)  ────────────────────────────────
  ovl$cluster not identical to ovltest$cluster.
  24/220 mismatches (average diff: 1.33)
  [1]    8 - 10 == -2
  [14]  10 -  9 ==  1
  [31]   9 -  8 ==  1
  [57]   9 -  8 ==  1
  [61]   8 - 10 == -2
  [64]   8 - 10 == -2
  [77]  10 -  9 ==  1
  [84]  10 -  9 ==  1
  [112]  9 -  8 ==  1
  ...
  
  ── 2. Failure: cluster means (@test_orc.R#33)  ─────────────────────────────────
  ovl$centers not equal to ovltest$centers.
  3/12 mismatches (average diff: 3.68)
  [8]  7.22 - 2.70 ==  4.52
  [9]  2.70 - 1.70 ==  1.00
  [10] 1.70 - 7.22 == -5.52
  
  K-means on row margins...	DONE
  K-means on column margins...	DONE
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 0 FAILED: 2
  1. Failure: cluster vector (@test_orc.R#29) 
  2. Failure: cluster means (@test_orc.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Lsdv.formula: no visible global function definition for ‘model.frame’
Lsdv.formula: no visible global function definition for ‘model.matrix’
Lsdv.formula: no visible global function definition for
  ‘model.response’
lsdv: no visible global function definition for ‘pf’
summary.Lsdv: no visible global function definition for ‘coef’
summary.Lsdv: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pf pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pf", "pt")
to your NAMESPACE file.
legend.lshorth: no visible global function definition for ‘legend’
legend.lshorth: no visible global function definition for ‘strwidth’
legend.lshorth: no visible global function definition for ‘text’
plot.lshorth: no visible global function definition for ‘plot.new’
plot.lshorth: no visible global function definition for ‘plot.window’
plot.lshorth: no visible global function definition for ‘axis’
plot.lshorth: no visible global function definition for ‘title’
plot.lshorth: no visible global function definition for ‘box’
plot.lshorth: no visible global function definition for ‘lines’
plot.lshorth: no visible global function definition for ‘legend’
plot.lshorth: no visible global function definition for ‘strwidth’
plot.lshorth: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box legend lines plot.new plot.window strwidth text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot.new",
             "plot.window", "strwidth", "text", "title")
to your NAMESPACE file.
Running examples in ‘lsl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lslSEM-class
> ### Title: A Reference Class for Learning a SEM model via penalized
> ###   likelihood.
> ### Aliases: lslSEM-class lslSEM
> 
> ### ** Examples
> 
> #Example: Holzinger and Swineford (1939) Data#
> lambda <- matrix(NA, 9, 3)
> lambda[c(1,2,3), 1] <- lambda[c(4,5,6), 2] <- lambda[c(7,8,9), 3] <- 1
> 
> rc_sem <- lslSEM()
> rc_sem$input(raw = lavaan::HolzingerSwineford1939)
> rc_sem$specify(pattern = list(lambda = lambda))
> rc_sem$learn(penalty = list(type = "l1", gamma = seq(.05, .10, .05)), variable = 7:15)
> rc_sem$draw(type = "individual", object = "lambda")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘factor-analysis.Rmd’ using rmarkdown
Quitting from lines 100-101 (factor-analysis.Rmd) 
Error: processing vignette 'factor-analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘factor-analysis.Rmd’

--- re-building ‘missing-data-analysis.Rmd’ using rmarkdown
--- finished re-building ‘missing-data-analysis.Rmd’

--- re-building ‘multi-group-analysis.Rmd’ using rmarkdown
--- finished re-building ‘multi-group-analysis.Rmd’

--- re-building ‘regression-analysis.Rmd’ using rmarkdown
Quitting from lines 89-90 (regression-analysis.Rmd) 
Error: processing vignette 'regression-analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘regression-analysis.Rmd’

--- re-building ‘structural-equation-modeling.Rmd’ using rmarkdown
--- finished re-building ‘structural-equation-modeling.Rmd’

SUMMARY: processing the following files failed:
  ‘factor-analysis.Rmd’ ‘regression-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘lspartition-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lsprobust.plot
> ### Title: Graphic Presentation of Results for 'lspartition' Package
> ### Aliases: lsprobust.plot
> 
> ### ** Examples
> 
> x   <- runif(500)
> y   <- sin(4*x)+rnorm(500)
> est <- lsprobust(y, x)
> lsprobust.plot(est)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lspline.Rmd’ using rmarkdown
Quitting from lines 69-75 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lspline.Rmd’

SUMMARY: processing the following file failed:
  ‘lspline.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘custom-models.Rmd’ using knitr
Loading required package: mcmc
Loading required package: MHadaptive
Loading required package: MASS
Loading required package: numDeriv
--- finished re-building ‘custom-models.Rmd’

--- re-building ‘example-plots.Rmd’ using knitr
Loading required package: mcmc
Loading required package: MHadaptive
Loading required package: MASS
Loading required package: numDeriv
Quitting from lines 24-59 (example-plots.Rmd) 
Error: processing vignette 'example-plots.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘example-plots.Rmd’

SUMMARY: processing the following file failed:
  ‘example-plots.Rmd’

Error: Vignette re-building failed.
Execution halted
OC : Lnapprox: no visible global function definition for ‘pnorm’
OC : Lnapprox: no visible global function definition for ‘qnorm’
OC : Lt: no visible global function definition for ‘pt’
OC : Lt: no visible global function definition for ‘qnorm’
OC : OC_emwa2: no visible global function definition for ‘pnorm’
OC : OC_emwa2: no visible global function definition for ‘qnorm’
OC: no visible global function definition for ‘pnorm’
OC: no visible global function definition for ‘qnorm’
cmBE : LAtHy: no visible global function definition for ‘phyper’
cmBE: no visible global function definition for ‘uniroot’
planAOQL : Gderivacex: no visible global function definition for
  ‘pnorm’
planAOQL : Mnk: no visible global function definition for ‘uniroot’
planAOQL : k0AOQL : delta: no visible global function definition for
  ‘pnorm’
planAOQL : alpha0: no visible global function definition for ‘pnorm’
planAOQL : alpha0: no visible global function definition for ‘qnorm’
planAOQL : fMSmodq2: no visible global function definition for
  ‘optimize’
planAOQL : kAOQL: no visible global function definition for ‘uniroot’
planLTPD : nAPPROXL : k0L : g: no visible global function definition
  for ‘qnorm’
planLTPD : nAPPROXL : k0L : h: no visible global function definition
  for ‘qnorm’
planLTPD : nAPPROXL : k0L: no visible global function definition for
  ‘qnorm’
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  ‘pnorm’
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  ‘qnorm’
planLTPD : nAPPROXL: no visible global function definition for
  ‘uniroot’
planLTPD : kEWMA: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  optimize phyper pnorm pt qnorm uniroot
Consider adding
  importFrom("stats", "optimize", "phyper", "pnorm", "pt", "qnorm",
             "uniroot")
to your NAMESPACE file.
Running examples in ‘LTRCtrees-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LTRCART
> ### Title: Fit a relative risk survival tree for LTRC data
> ### Aliases: LTRCART
> 
> ### ** Examples
> 
> ## The Assay of serum free light chain data in survival package
> ## Adjust data & clean data
> library(survival)
> library(LTRCtrees)
> Data <- flchain
> Data <- Data[!is.na(Data$creatinine),]
> Data$End <- Data$age + Data$futime/365
> DATA <- Data[Data$End > Data$age,]
> names(DATA)[6] <- "FLC"
> 
> ## Setup training set and test set
> Train = DATA[1:500,]
> Test = DATA[1000:1020,]
> 
> ## Fit LTRCART survival tree
> ## make sure to attach survival package (by library(survival) ) before using Surv function
> LTRCART.obj <- LTRCART(Surv(age, End, death) ~ sex + FLC + creatinine, Train)
> 
> ## Putting Surv(End, death) in formula would result an error message
> ## since LTRCART is expecting Surv(time1, time2, event)
> 
> ## Plot the fitted tree
> library(rpart.plot)
Loading required package: rpart

Attaching package: ‘rpart’

The following object is masked from ‘package:survival’:

    solder

> rpart.plot(LTRCART.obj)
Warning: Cannot retrieve the data used to build the model (model.frame: object 'Newtime' not found).
To silence this warning:
    Call rpart.plot with roundint=FALSE,
    or rebuild the rpart model with model=TRUE.
> 
> ## Plot as partykit::party object
> library(partykit)
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
> plot(as.party(LTRCART.obj))
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LTRCtrees.Rmd’ using rmarkdown
Quitting from lines 48-62 (LTRCtrees.Rmd) 
Error: processing vignette 'LTRCtrees.Rmd' failed with diagnostics:
no string supplied for 'strwidth/height' unit
--- failed re-building ‘LTRCtrees.Rmd’

SUMMARY: processing the following file failed:
  ‘LTRCtrees.Rmd’

Error: Vignette re-building failed.
Execution halted
fit.LTR: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘robustbase’
  Please remove these calls from your code.
ltsbase: no visible global function definition for ‘lm’
ltsbase: no visible global function definition for ‘lines’
ltsbase: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines lm
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "lm")
to your NAMESPACE file.
terrestrial.season: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘lvplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_lv
> ### Title: Side-by-side LV boxplots with ggplot2.
> ### Aliases: GeomLv StatLv geom_lv scale_fill_lv stat_lv
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> p <- ggplot(mpg, aes(class, hwy))
> p + geom_lv(aes(fill=..LV..)) + scale_fill_brewer()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
generate.clonal.data : pcr.rpareto.func: no visible global function
  definition for ‘runif’
generate.clonal.data : get.readcount.given.cellcount: no visible global
  function definition for ‘rlnorm’
generate.clonal.data: no visible global function definition for
  ‘rmultinom’
generate.clonal.data: no visible global function definition for ‘rpois’
infer.clonality: no visible global function definition for ‘cov’
infer.clonality: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output cov rlnorm rmultinom rpois runif
Consider adding
  importFrom("stats", "cov", "rlnorm", "rmultinom", "rpois", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown
Quitting from lines 266-272 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
project.M3.1.to.M3.2: no visible global function definition for
  ‘coordinates<-’
project.M3.1.to.M3.2: no visible global function definition for
  ‘proj4string<-’
project.M3.1.to.M3.2: no visible global function definition for ‘CRS’
project.M3.1.to.M3.2: no visible global function definition for
  ‘spTransform’
project.M3.1.to.M3.2: no visible global function definition for
  ‘coordinates’
Undefined global functions or variables:
  CRS coordinates coordinates<- proj4string<- spTransform
maboost.default: no visible global function definition for
  ‘flush.console’
maboost.default: no visible binding for global variable ‘na.pass’
maboost.default : predict.type: no visible global function definition
  for ‘predict’
maboost.formula: no visible global function definition for
  ‘model.extract’
maboost.machine.bin: no visible global function definition for ‘runif’
maboost.machine.bin: no visible binding for global variable ‘na.pass’
maboost.machine.multi: no visible global function definition for
  ‘runif’
maboost.machine.multi: no visible binding for global variable ‘na.pass’
projsplx_k: no visible global function definition for ‘tail’
varplot.maboost: no visible global function definition for ‘dotchart’
Undefined global functions or variables:
  dotchart flush.console model.extract na.pass predict runif tail
Consider adding
  importFrom("graphics", "dotchart")
  importFrom("stats", "model.extract", "na.pass", "predict", "runif")
  importFrom("utils", "flush.console", "tail")
to your NAMESPACE file.
Running examples in ‘MachineShop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calibration
> ### Title: Model Calibration
> ### Aliases: calibration Calibration
> 
> ### ** Examples
> 
> library(survival)
> library(MASS)
> 
> res <- resample(Surv(time, status != 2) ~ sex + age + year + thickness + ulcer,
+                 data = Melanoma, model = GBMModel,
+                 control = CVControl(times = 365 * c(2, 5, 10)))
> cal <- calibration(res)
> plot(cal)
$GBMModel
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning: Removed 70 rows containing missing values (geom_point).
Quitting from lines 126-136 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

--- re-building ‘MLModels.Rmd’ using rmarkdown
--- finished re-building ‘MLModels.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘macleish.Rmd’ using rmarkdown
Loading required package: etl
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

The following object is masked from 'package:base':

    date

Loading required package: mgcv
Loading required package: nlme

Attaching package: 'nlme'

The following object is masked from 'package:dplyr':

    collapse

This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Quitting from lines 94-104 (macleish.Rmd) 
Error: processing vignette 'macleish.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘macleish.Rmd’

SUMMARY: processing the following file failed:
  ‘macleish.Rmd’

Error: Vignette re-building failed.
Execution halted
logistic_z: no visible global function definition for ‘glm’
logistic_z: no visible binding for global variable ‘binomial’
logistic_z: no visible global function definition for ‘predict’
plsrf_x: no visible global function definition for ‘qnorm’
plsrf_x: no visible global function definition for ‘predict’
plsrf_x_pv: no visible global function definition for ‘qnorm’
plsrf_x_pv: no visible global function definition for ‘predict’
plsrf_xz: no visible global function definition for ‘qnorm’
plsrf_xz: no visible global function definition for ‘predict’
plsrf_xz_pv: no visible global function definition for ‘qnorm’
plsrf_xz_pv: no visible global function definition for ‘predict’
rf_z: no visible global function definition for ‘qnorm’
rf_z: no visible global function definition for ‘predict’
simuldata_list: no visible global function definition for ‘rnorm’
simuldatacluster_list: no visible global function definition for
  ‘rnorm’
svm_x: no visible global function definition for ‘predict’
Undefined global functions or variables:
  binomial glm predict qnorm rnorm
Consider adding
  importFrom("stats", "binomial", "glm", "predict", "qnorm", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘R2wd’
'library' or 'require' calls in package code:
  ‘R2wd’ ‘ggplot2’ ‘metafor’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘maddison_project_database.Rmd’ using rmarkdown
Warning: Removed 20 rows containing missing values (geom_path).
Quitting from lines 41-51 (maddison_project_database.Rmd) 
Error: processing vignette 'maddison_project_database.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘maddison_project_database.Rmd’

SUMMARY: processing the following file failed:
  ‘maddison_project_database.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘MAd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotcon
> ### Title: Meta Regression Scatterplot
> ### Aliases: plotcon
> ### Keywords: aplot
> 
> ### ** Examples
> 
> # SAMPLE DATA
> MA2 <-read.table(textConnection("
+ id       es1       var1 n.1 n.2 mod1 mod2
+ 1   1 0.5695938 0.04906967  26  30    a   20
+ 2   2 0.4123667 0.04362541  28  34    b   30
+ 3   3 0.4084333 0.04458363  34  28    a   25
+ 4   4 0.5014756 0.04186354  37  29    b   35
+ 5   5 0.5540745 0.04339382  31  32    b   40
+ 6   1 0.5695938 0.04906967  26  30    a   20
+ 7   2 0.4123667 0.04362541  28  34    b   30
+ 8   3 0.4084333 0.04458363  34  28    a   25
+ 9   4 0.5014756 0.04186354  37  29    b   35
+ 10  5 0.5540745 0.04339382  31  32    b   40"))
> 
> 
> # EXAMPLE
> plotcon(es1, var1, mod2, data=MA2, method= "fixed", modname="NULL",title="NULL")
Loading required package: ggplot2
Loading required package: metafor
Loading required package: Matrix
Loading 'metafor' package (version 2.0-0). For an overview 
and introduction to the package please type: help(metafor).
Warning in model.matrix.default(terms, mf, contrasts) :
  non-list contrasts argument ignored
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘mafs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_fit
> ### Title: Graphical results of forecast models
> ### Aliases: gg_fit
> 
> ### ** Examples
> 
> gg_fit(AirPassengers, 12, "snaive")
Warning: Removed 156 rows containing missing values (geom_path).
Warning: Removed 12 rows containing missing values (geom_point).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘magick-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: device
> ### Title: Magick Graphics Device
> ### Aliases: device image_graph image_device image_draw image_capture
> 
> ### ** Examples
> 
> # Regular image
> frink <- image_read("https://jeroen.github.io/images/frink.png")
> 
> # Produce image using graphics device
> fig <- image_graph(res = 96)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = cyl)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 414-418 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Package in Depends field not imported from: ‘rJava’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MalletLDA: no visible global function definition for ‘.jnew’
mallet.doc.topics: no visible global function definition for
  ‘.jevalArray’
mallet.import: no visible global function definition for ‘J’
mallet.import: no visible global function definition for ‘.jnew’
mallet.import: no visible global function definition for ‘.jcast’
mallet.subset.topic.words: no visible global function definition for
  ‘.jevalArray’
mallet.topic.hclust: no visible global function definition for ‘hclust’
mallet.topic.hclust: no visible global function definition for ‘dist’
mallet.topic.words: no visible global function definition for
  ‘.jevalArray’
mallet.word.freqs: no visible global function definition for
  ‘.jevalArray’
Undefined global functions or variables:
  .jcast .jevalArray .jnew J dist hclust
Consider adding
  importFrom("stats", "dist", "hclust")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘manhattanly.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Quitting from lines 105-106 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘manhattanly.Rmd’

SUMMARY: processing the following file failed:
  ‘manhattanly.Rmd’

Error: Vignette re-building failed.
Execution halted
mp_corpus: no visible binding for global variable ‘annotations’
print.ManifestoAvailability: no visible binding for global variable
  ‘annotations’
Undefined global functions or variables:
  annotations
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ManifoldOptim.Rcheck/00install.out’ for details.
cf1.sample: no visible global function definition for ‘rexp’
cf1.sample: no visible global function definition for ‘rmultinom’
dherlang : <anonymous> : <anonymous>: no visible global function
  definition for ‘dgamma’
erhmm.param.kmeans: no visible global function definition for ‘kmeans’
erhmm.param.kmeans: no visible global function definition for ‘var’
erhmm.param.kmeans: no visible global function definition for ‘runif’
gmmpp.param.kmeans: no visible global function definition for ‘kmeans’
gmmpp.param.kmeans: no visible global function definition for ‘runif’
herlang.param.kmeans: no visible global function definition for
  ‘kmeans’
herlang.param.kmeans: no visible global function definition for ‘var’
map.param.kmeans: no visible global function definition for ‘kmeans’
map.param.kmeans: no visible global function definition for ‘runif’
ph.param.random: no visible global function definition for ‘runif’
ph.sample: no visible global function definition for ‘rmultinom’
ph.sample: no visible global function definition for ‘rexp’
pherlang : <anonymous> : <anonymous>: no visible global function
  definition for ‘pgamma’
rherlang: no visible global function definition for ‘rmultinom’
rherlang : <anonymous>: no visible global function definition for
  ‘rgamma’
Undefined global functions or variables:
  dgamma kmeans pgamma rexp rgamma rmultinom runif var
Consider adding
  importFrom("stats", "dgamma", "kmeans", "pgamma", "rexp", "rgamma",
             "rmultinom", "runif", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘mgcv’ which was already attached by Depends.
  Please remove these calls from your code.
ageprofile: no visible global function definition for ‘model.frame’
ageprofile: no visible binding for global variable ‘poisson’
ageprofile: no visible global function definition for ‘predict.gam’
ageprofile: no visible global function definition for ‘as.formula’
ageprofile: no visible global function definition for ‘summary.gam’
ageprofile: no visible global function definition for ‘contrasts<-’
ageprofile: no visible global function definition for ‘anova.gam’
plotap: no visible global function definition for ‘dev.new’
plotap: no visible global function definition for ‘plot’
plotap: no visible global function definition for ‘lines’
plotap: no visible global function definition for ‘points’
plotap: no visible global function definition for ‘legend’
splitter: no visible global function definition for ‘reshape’
tabm: no visible global function definition for ‘coef’
tabm: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC anova.gam as.formula coef contrasts<- dev.new legend lines
  model.frame plot points poisson predict.gam reshape summary.gam
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "AIC", "as.formula", "coef", "contrasts<-",
             "model.frame", "poisson", "reshape")
to your NAMESPACE file.
Running examples in ‘mapr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hull
> ### Title: Add a convex hull to a map
> ### Aliases: hull
> 
> ### ** Examples
> 
> # map spocc output, here using a built in object
> data(occdat_eg1)
> map_plot(occdat_eg1, hull = TRUE)
> 
> # map rgbif output, here using a built in object
> hull(map_ggplot(occdat_eg1))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
calcStats: no visible global function definition for ‘as.formula’
calcStats: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  as.formula na.omit
Consider adding
  importFrom("stats", "as.formula", "na.omit")
to your NAMESPACE file.
plot.topics: no visible global function definition for ‘hist’
plot.topics: no visible global function definition for ‘grey’
plot.topics: no visible global function definition for ‘plot’
plot.topics: no visible global function definition for ‘par’
plot.topics: no visible global function definition for ‘image’
plot.topics: no visible global function definition for ‘axis’
plot.topics: no visible global function definition for ‘points’
plot.topics: no visible global function definition for ‘text’
rdir: no visible global function definition for ‘rgamma’
summary.topics: no visible global function definition for ‘pchisq’
tpxResids: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis grey hist image par pchisq plot points rgamma text
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "axis", "hist", "image", "par", "plot",
             "points", "text")
  importFrom("stats", "pchisq", "rgamma")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘markedVignette.Rnw’ using Sweave
Loading required package: lme4
Loading required package: Matrix
Loading required package: parallel
This is marked 1.2.1

Model: CJS

Processing data...

255 capture histories collapsed into 53
Creating design data...

Fitting model

Computing initial parameter estimates

Starting optimization for 2 parameters...
255 capture histories collapsed into 53
Fitting model

Computing initial parameter estimates

Starting optimization for 3 parameters...
255 capture histories collapsed into 53
Fitting model

Computing initial parameter estimates

Starting optimization for 3 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 4 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 7 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 8 parameters...
255 capture histories collapsed into 53
Fitting model

Computing initial parameter estimates

Starting optimization for 3 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 4 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 7 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 8 parameters...
255 capture histories collapsed into 171
Fitting model

Computing initial parameter estimates

Starting optimization for 7 parameters...
Computing hessian...
Error: processing vignette 'markedVignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘markedVignette.Rnw’

SUMMARY: processing the following file failed:
  ‘markedVignette.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MarketMatching-Vignette.Rmd’ using rmarkdown_notangle
Quitting from lines 109-110 (MarketMatching-Vignette.Rmd) 
Error: processing vignette 'MarketMatching-Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MarketMatching-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘MarketMatching-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
negbin.rel.clust: no visible global function definition for ‘kmeans’
negbin.rel.clust: no visible global function definition for ‘matplot’
negbin.rel.pca: no visible global function definition for ‘princomp’
negbin.rel.pca: no visible global function definition for ‘biplot’
pois.rel.clust: no visible global function definition for ‘kmeans’
pois.rel.clust: no visible global function definition for ‘matplot’
pois.rel.pca: no visible global function definition for ‘princomp’
pois.rel.pca: no visible global function definition for ‘biplot’
sim.negbin: no visible global function definition for ‘rnbinom’
sim.pois: no visible global function definition for ‘rpois’
wt.rel.negbin: no visible global function definition for ‘var’
wt.rel.negbin: no visible global function definition for ‘optimize’
wt.rel.negbin: no visible global function definition for ‘integrate’
wt.rel.pois: no visible global function definition for ‘optimize’
wt.rel.pois: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  biplot integrate kmeans matplot optimize princomp rnbinom rpois var
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "biplot", "integrate", "kmeans", "optimize",
             "princomp", "rnbinom", "rpois", "var")
to your NAMESPACE file.
Running examples in ‘marmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: etopo
> ### Title: Etopo colours
> ### Aliases: etopo etopo.colors etopo.colours scale_color_etopo
> ###   scale_colour_etopo scale_fill_etopo
> 
> ### ** Examples
> 
> # load NW Atlantic data and convert to class bathy
> data(nw.atlantic)
> atl <- as.bathy(nw.atlantic)
> 
> # plot with base graphics
> plot(atl, image=TRUE)
> 
> # using the etopo color scale
> etopo_cols <- rev(etopo.colors(8))
> plot(atl, image=TRUE, bpal=list(
+   c(min(atl), 0, etopo_cols[1:2]),
+   c(0, max(atl), etopo_cols[3:8])
+ ))
> 
> 
> # plot using ggplot2; in which case the limits of the scale are automatic
> library("ggplot2")
> ggplot(atl, aes(x=x, y=y)) + coord_quickmap() +
+   # background
+   geom_raster(aes(fill=z)) +
+   scale_fill_etopo() +
+   # countours
+   geom_contour(aes(z=z),
+     breaks=c(0, -100, -200, -500, -1000, -2000, -4000),
+     colour="black", size=0.2
+   ) +
+   scale_x_continuous(expand=c(0,0)) +
+   scale_y_continuous(expand=c(0,0))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
marqLevAlg: no visible global function definition for ‘flush.console’
print.marqLevAlg: no visible global function definition for ‘qnorm’
print.marqLevAlg: no visible global function definition for ‘pchisq’
summary.marqLevAlg: no visible global function definition for ‘qnorm’
summary.marqLevAlg: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  flush.console pchisq qnorm
Consider adding
  importFrom("stats", "pchisq", "qnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
mAr.pca: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Running examples in ‘MARSS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: augment.marssMLE
> ### Title: Return the model predicted values, residuals, and optionally
> ###   confidence intervals
> ### Aliases: augment.marssMLE augment_dfa augment_marss augmentmarxss
> 
> ### ** Examples
> 
>   dat <- t(harborSeal)
>   dat <- dat[c(2,11,12),]
>   MLEobj <- MARSS(dat, model=list(Z=factor(c("WA","OR","OR"))))
Success! abstol and log-log tests passed at 37 iterations.
Alert: conv.test.slope.tol is 0.5.
Test with smaller values (<0.1) to ensure convergence.

MARSS fit is
Estimation method: kem 
Convergence test: conv.test.slope.tol = 0.5, abstol = 0.001
Estimation converged in 37 iterations. 
Log-likelihood: 13.72233 
AIC: -11.44465   AICc: -8.918339   
 
                Estimate
A.OR.SouthCoast  0.49280
R.diag           0.02509
U.WA             0.06171
U.OR             0.03686
Q.(WA,WA)        0.01082
Q.(OR,OR)        0.00439
x0.WA            7.41712
x0.OR            6.56460
Initial states (x0) defined at t=0

Standard errors have not been calculated. 
Use MARSSparamCIs to compute CIs and bias estimates.

> 
> library(broom)
> library(ggplot2)
> theme_set(theme_bw())
> 
> # Make a plot of the observations and model fits
> d <- augment(MLEobj, interval="confidence")
> ggplot(data = d) + 
+   geom_line(aes(t, .fitted)) +
+   geom_point(aes(t, y)) +
+   geom_ribbon(aes(x=t, ymin=.conf.low, ymax=.conf.up), linetype=2, alpha=0.1) +
+   facet_grid(~.rownames) +
+   xlab("Time Step") + ylab("Count")
Warning: Removed 24 rows containing missing values (geom_point).
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘matching.Rnw’ using knitr_notangle
Quitting from lines 65-75 (././Sections/4_MonteCarloResults.Rnw) 
Quitting from lines 39-40 (././Sections/4_MonteCarloResults.Rnw) 
Error: processing vignette 'matching.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘matching.Rnw’

SUMMARY: processing the following file failed:
  ‘matching.Rnw’

Error: Vignette re-building failed.
Execution halted
Found the following possibly unsafe calls:
File ‘matlab/R/zzz.R’:
  unlockBinding("savedTime", .MatlabNamespaceEnv)

colorbar : colorbar.EO: no visible global function definition for ‘par’
colorbar : colorbar.EO: no visible global function definition for
  ‘axis’
colorbar : colorbar.EO: no visible global function definition for
  ‘axTicks’
colorbar : colorbar.EO: no visible global function definition for ‘box’
colorbar : colorbar.NO: no visible global function definition for
  ‘axis’
colorbar : colorbar.NO: no visible global function definition for
  ‘axTicks’
colorbar : colorbar.NO: no visible global function definition for ‘box’
imagesc : pretty.axp: no visible global function definition for ‘par’
imagesc: no visible global function definition for ‘axis’
imagesc: no visible global function definition for ‘box’
jet.colors: no visible global function definition for ‘rgb’
multiline.plot.colors : get.gca.colororder: no visible global function
  definition for ‘rgb’
std: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axTicks axis box par rgb sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axTicks", "axis", "box", "par")
  importFrom("stats", "sd")
to your NAMESPACE file.
'library' or 'require' call to ‘bigmemory’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
MAT: no visible global function definition for ‘dev.new’
MAT: no visible global function definition for ‘plot’
MAT: no visible global function definition for ‘points’
MAT: no visible global function definition for ‘abline’
MAT: no visible global function definition for ‘text’
MAT: no visible global function definition for ‘legend’
MAT: no visible global function definition for ‘lines’
MAT: no visible global function definition for ‘par’
MAT: no visible global function definition for ‘barplot’
MAT: no visible global function definition for ‘cor’
print.MAT: no visible global function definition for ‘sd’
print.MAT: no visible global function definition for ‘cor’
simM3PL: no visible global function definition for ‘rnorm’
simM3PL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par plot points rnorm runif
  sd text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "plot", "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘matsindf.Rmd’ using rmarkdown
Quitting from lines 385-397 (matsindf.Rmd) 
Error: processing vignette 'matsindf.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘matsindf.Rmd’

--- re-building ‘midf_apply_primer.Rmd’ using rmarkdown
--- finished re-building ‘midf_apply_primer.Rmd’

SUMMARY: processing the following file failed:
  ‘matsindf.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘mau-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Sim.Const.Weights
> ### Title: Simulation of constrained weights
> ### Aliases: Sim.Const.Weights
> 
> ### ** Examples
> 
> library( data.table )
> N<-10
> utilities<-data.table( id = 1:N, 
+                        u1 = runif( N, 0, 1 ), 
+                        u2 = runif( N, 0, 1 ), 
+                        u3 = runif( N, 0, 1 ),
+                        u4 = runif( N, 0, 1 ) )
> n<-100
> alpha<-c( 0.2, 0.5, 0.1, 0.2 )
> constraints<-list( list( c(1,2), 0.7 ), 
+                    list( c(3,4), 0.3 ) )
> S<-Sim.Const.Weights( n, utilities, alpha, constraints )
> plot.S<-Plot.Simulation.Weight( S$simulation, title = 'Simulations', 
+                                 xlab = 'ID', ylab = 'Utility' ) 
> plot( plot.S )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Running_MAUT.Rmd’ using rmarkdown

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 150-158 (Running_MAUT.Rmd) 
Error: processing vignette 'Running_MAUT.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Running_MAUT.Rmd’

SUMMARY: processing the following file failed:
  ‘Running_MAUT.Rmd’

Error: Vignette re-building failed.
Execution halted
GSTplot : <anonymous>: no visible global function definition for
  ‘t.test’
GSTplot: no visible global function definition for ‘rt’
GSTplot: no visible global function definition for ‘layout’
GSTplot: no visible global function definition for ‘par’
GSTplot: no visible global function definition for ‘plot’
GSTplot: no visible global function definition for ‘text’
GSTplot: no visible global function definition for ‘lines’
GSTplot: no visible global function definition for ‘polygon’
GSTplot: no visible global function definition for ‘abline’
GSTplot: no visible global function definition for ‘ecdf’
GSTplot: no visible global function definition for ‘knots’
GSTplot : <anonymous>: no visible global function definition for ‘aov’
GSTplot: no visible global function definition for ‘qf’
MAVTn : <anonymous>: no visible global function definition for ‘aov’
MAVTn: no visible global function definition for ‘p.adjust’
MAVTn: no visible global function definition for ‘plot’
MAVTn: no visible global function definition for ‘par’
MAVTn: no visible global function definition for ‘abline’
MAVTn: no visible global function definition for ‘legend’
MAVTn: no visible global function definition for ‘locator’
Tols : olsf: no visible global function definition for ‘t.test’
Tols: no visible global function definition for ‘cor’
Undefined global functions or variables:
  abline aov cor ecdf knots layout legend lines locator p.adjust par
  plot polygon qf rt t.test text
Consider adding
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "locator", "par", "plot", "polygon", "text")
  importFrom("stats", "aov", "cor", "ecdf", "knots", "p.adjust", "qf",
             "rt", "t.test")
to your NAMESPACE file.
Package in Depends field not imported from: ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catt.test: no visible global function definition for ‘pnorm’
fnorm2: no visible global function definition for ‘sadmvn’
fnorm3: no visible global function definition for ‘sadmvn’
Undefined global functions or variables:
  pnorm sadmvn
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
MI.2: no visible global function definition for ‘xtabs’
RNASeq.Data: no visible binding for global variable ‘quantile’
loc.node: no visible global function definition for ‘head’
loc.node: no visible global function definition for ‘tail’
plotHybrid.Tree: no visible global function definition for ‘par’
plotHybrid.Tree: no visible global function definition for ‘plot’
plotHybrid.Tree: no visible global function definition for ‘text’
plotHybrid.Tree: no visible global function definition for ‘image’
plotHybrid.Tree: no visible global function definition for ‘grey’
plotHybrid.Tree: no visible global function definition for
  ‘heat.colors’
plotHybrid.Tree: no visible global function definition for ‘head’
plotHybrid.Tree: no visible global function definition for ‘segments’
plotbr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  grey head heat.colors image par plot quantile segments tail text
  xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
cfull: no visible global function definition for ‘combn’
cl: no visible global function definition for ‘combn’
cn: no visible global function definition for ‘combn’
crep: no visible global function definition for ‘combn’
crich: no visible global function definition for ‘combn’
ct: no visible global function definition for ‘combn’
mjaccard: no visible global function definition for ‘combn’
ml: no visible global function definition for ‘combn’
mn: no visible global function definition for ‘combn’
mrep: no visible global function definition for ‘combn’
mrich: no visible global function definition for ‘combn’
msorensen: no visible global function definition for ‘combn’
mt: no visible global function definition for ‘combn’
wnodf: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Package in Depends field not imported from: ‘logistf’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mbmdr : NextModel: no visible global function definition for
  ‘read.table’
mbmdr : OffsetFit: no visible global function definition for ‘glm’
mbmdr : Regresion: no visible global function definition for ‘logistf’
mbmdr : Regresion: no visible global function definition for ‘glm’
mbmdr: no visible global function definition for ‘write.table’
mbmdr.PermTest: no visible global function definition for ‘read.table’
mbmdr.PermTest: no visible global function definition for ‘qnorm’
print.mbmdr: no visible global function definition for ‘read.table’
summary.mbmdr: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  glm logistf qnorm read.table write.table
Consider adding
  importFrom("stats", "glm", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Running examples in ‘MCAvariants-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.MCAvariants
> ### Title: Main plot function for classical and ordered multiple
> ###   correspondence analysis
> ### Aliases: plot.MCAvariants
> ### Keywords: graphical
> 
> ### ** Examples
> 
> data(satisfaction)
> ris1=MCAvariants(satisfaction, catype = "mca")
> plot.MCAvariants(ris1)
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot.MCAvariants ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘mccf1-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mccf1
> ### Title: Plot the MCC-F1 curve
> ### Aliases: plot.mccf1
> 
> ### ** Examples
> 
> response <- c(rep(1, 1000), rep(0, 10000))
> predictor <- c(rbeta(300, 12, 2), rbeta(700, 3, 4), rbeta(10000, 2, 3))
> plot(mccf1(response, predictor))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package in Depends field not imported from: ‘lpSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
laugreen: no visible global function definition for ‘combn’
laugreen: no visible global function definition for ‘lp’
maxpear: no visible global function definition for ‘hclust’
maxpear: no visible global function definition for ‘as.dist’
maxpear : <anonymous>: no visible global function definition for
  ‘cutree’
medv: no visible global function definition for ‘cutree’
medv: no visible global function definition for ‘hclust’
medv: no visible global function definition for ‘as.dist’
minbinder: no visible global function definition for ‘hclust’
minbinder: no visible global function definition for ‘as.dist’
minbinder : <anonymous>: no visible global function definition for
  ‘cutree’
relabel : min.perm.labels: no visible global function definition for
  ‘lp.transport’
Undefined global functions or variables:
  as.dist combn cutree hclust lp lp.transport
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
  importFrom("utils", "combn")
to your NAMESPACE file.
getbetap.A: no visible global function definition for ‘pbeta’
getbetap.A: no visible global function definition for ‘cor.test’
Undefined global functions or variables:
  cor.test pbeta
Consider adding
  importFrom("stats", "cor.test", "pbeta")
to your NAMESPACE file.
mcgibbsit: no visible global function definition for ‘is.mcmc.list’
mcgibbsit: no visible global function definition for ‘start’
mcgibbsit: no visible global function definition for ‘end’
mcgibbsit: no visible global function definition for ‘thin’
mcgibbsit: no visible global function definition for ‘nvar’
mcgibbsit: no visible global function definition for ‘mcmc’
mcgibbsit: no visible global function definition for ‘mcmc.list’
mcgibbsit: no visible global function definition for ‘varnames’
mcgibbsit: no visible global function definition for ‘qnorm’
mcgibbsit: no visible global function definition for ‘niter’
mcgibbsit: no visible global function definition for ‘quantile’
mcgibbsit : to.table: no visible global function definition for
  ‘window’
mcgibbsit: no visible global function definition for ‘var’
read.mcmc: no visible global function definition for ‘mcmc.list’
read.mcmc: no visible global function definition for ‘mcmc’
Undefined global functions or variables:
  end is.mcmc.list mcmc mcmc.list niter nvar qnorm quantile start thin
  var varnames window
Consider adding
  importFrom("stats", "end", "qnorm", "quantile", "start", "var",
             "window")
to your NAMESPACE file.
call_localoptim: no visible global function definition for ‘optim’
call_localoptim: no visible global function definition for ‘nlminb’
call_localoptim: no visible global function definition for
  ‘txtProgressBar’
call_localoptim: no visible global function definition for
  ‘setTxtProgressBar’
call_localoptim : <anonymous>: no visible global function definition
  for ‘optim’
call_localoptim : <anonymous>: no visible global function definition
  for ‘nlminb’
multiStartoptim: no visible global function definition for ‘median’
Undefined global functions or variables:
  median nlminb optim setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "median", "nlminb", "optim")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
mcheatmaps : coscolorFun: no visible global function definition for
  ‘rgb’
mcheatmaps : halfcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : fullcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘hclust’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘as.dist’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘sd’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘cophenetic’
mcheatmaps : printDiag: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘strwidth’
mcheatmaps: no visible global function definition for ‘pdf’
mcheatmaps: no visible global function definition for ‘plot.new’
mcheatmaps: no visible global function definition for ‘as.dendrogram’
mcheatmaps: no visible global function definition for ‘reorder’
mcheatmaps: no visible global function definition for ‘par’
mcheatmaps: no visible global function definition for ‘plot’
mcheatmaps: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘heat.colors’
mcheatmaps: no visible global function definition for ‘terrain.colors’
mcheatmaps: no visible global function definition for ‘as.dist’
mcheatmaps: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  as.dendrogram as.dist cophenetic dev.off hclust heat.colors
  order.dendrogram par pdf plot plot.new reorder rgb sd strwidth
  terrain.colors
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
             "terrain.colors")
  importFrom("graphics", "par", "plot", "plot.new", "strwidth")
  importFrom("stats", "as.dendrogram", "as.dist", "cophenetic", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
lik_locfit: no visible global function definition for ‘predict’
mcll_coeff: no visible global function definition for ‘optim’
mcll_est: no visible global function definition for ‘cov’
mcll_est: no visible global function definition for ‘optim’
mcll_se: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optim predict
Consider adding
  importFrom("stats", "cov", "optim", "predict")
to your NAMESPACE file.
Running examples in ‘mcmcabn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mcmcabn
> ### Title: Function to plot mcmcabn class objects
> ### Aliases: plot.mcmcabn
> 
> ### ** Examples
> 
> ## Example from the asia dataset from Lauritzen and Spiegelhalter (1988) provided by Scutari (2010)
> data("mcmc_run_asia")
> 
> #plot the mcmc run
> plot(mcmc.out.asia)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mcmcabn.Rmd’ using rmarkdown

Attaching package: 'bnlearn'

The following object is masked from 'package:stats':

    sigma

Loading required package: nnet
Loading required package: Cairo
Loading required package: MASS
Loading required package: lme4
Loading required package: Matrix

Attaching package: 'abn'

The following object is masked from 'package:bnlearn':

    mb

Loading required package: magrittr

Attaching package: 'magrittr'

The following object is masked from 'package:abn':

    or


Attaching package: 'cowplot'

The following object is masked from 'package:ggpubr':

    get_legend

The following object is masked from 'package:ggplot2':

    ggsave


Attaching package: 'ggdag'

The following object is masked from 'package:ggplot2':

    expand_scale

The following object is masked from 'package:stats':

    filter

Quitting from lines 79-111 (mcmcabn.Rmd) 
Error: processing vignette 'mcmcabn.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mcmcabn.Rmd’

SUMMARY: processing the following file failed:
  ‘mcmcabn.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Generation.Rmd’ using rmarkdown
Loading required package: BBmisc

Attaching package: 'BBmisc'

The following object is masked from 'package:base':

    isFALSE

Loading required package: ecr
Loading required package: smoof
Loading required package: ParamHelpers
Loading required package: checkmate
Quitting from lines 30-36 (Generation.Rmd) 
Error: processing vignette 'Generation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Generation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Loading required package: BBmisc

Attaching package: 'BBmisc'

The following object is masked from 'package:base':

    isFALSE

Loading required package: ecr
Loading required package: smoof
Loading required package: ParamHelpers
Loading required package: checkmate
Quitting from lines 28-39 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘Generation.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘Mcomp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.Mdata
> ### Title: Plotting M Competition data
> ### Aliases: plot.Mdata autoplot.Mdata autoplot.Mdata
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 
> library(ggplot2)
> plot(M1[[1]])
> autoplot(M1$YAF3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
do.linear.conjoint: no visible global function definition for
  ‘as.formula’
do.linear.conjoint: no visible global function definition for ‘lm’
do.linear.conjoint: no visible global function definition for
  ‘coefficients’
is.close.to.orthogonal: no visible global function definition for ‘cor’
mc.add.to.design: no visible global function definition for ‘combn’
mc.good.designs: no visible global function definition for ‘combn’
Undefined global functions or variables:
  as.formula coefficients combn cor lm
Consider adding
  importFrom("stats", "as.formula", "coefficients", "cor", "lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to ‘scatterplot3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.nsga2: no visible global function definition for ‘plot’
plot.nsga2: no visible global function definition for ‘lines’
plot.nsga2: no visible global function definition for ‘pairs’
plot.nsga2.collection: no visible global function definition for
  ‘devAskNewPage’
plot.nsga2.collection: no visible binding for global variable ‘plot’
Undefined global functions or variables:
  devAskNewPage lines pairs plot
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "lines", "pairs", "plot")
to your NAMESPACE file.
Running examples in ‘mcprofile-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hoa
> ### Title: Higher order asymptotics using the modified likelihood root
> ### Aliases: hoa
> ### Keywords: misc
> 
> ### ** Examples
> 
> #######################################
> ## cell transformation assay example ##
> #######################################
> 
> str(cta)
'data.frame':	80 obs. of  2 variables:
 $ conc: num  0 0 0 0 0 0 0 0 0 0 ...
 $ foci: int  0 1 0 0 0 0 0 0 0 2 ...
> ## change class of cta$conc into factor
> cta$concf <- factor(cta$conc, levels=unique(cta$conc))
> 
> ggplot(cta, aes(y=foci, x=concf)) + 
+    geom_boxplot() +
+    geom_dotplot(binaxis = "y", stackdir = "center", binwidth = 0.2) +    
+    xlab("concentration")
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mcprofile.Rmd’ using knitr
Loading required package: ggplot2
Quitting from lines 111-119 (mcprofile.Rmd) 
Error: processing vignette 'mcprofile.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mcprofile.Rmd’

SUMMARY: processing the following file failed:
  ‘mcprofile.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘coda’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘car’ ‘spatstat’ ‘spdep’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RANN’ ‘maptools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘mdpeer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Adj2Lap
> ### Title: Compute graph Laplacian matrix from graph adjacency matrix
> ### Aliases: Adj2Lap
> 
> ### ** Examples
> 
> # Define exemplary adjacency matrix
> p1 <- 10
> p2 <- 40
> p <- p1 + p2
> A <- matrix(rep(0, p * p), p, p)
> A[1:p1, 1:p1] <- 1
> A[(p1 + 1):p, (p1 + 1):p] <- 1
> vizu.mat(A, "adjacency matrix")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_and_usage_examples.Rmd’ using rmarkdown
Quitting from lines 62-79 (Intro_and_usage_examples.Rmd) 
Error: processing vignette 'Intro_and_usage_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Intro_and_usage_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro_and_usage_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘data_input.Rmd’ using rmarkdown
--- finished re-building ‘data_input.Rmd’

--- re-building ‘meaRtoolsGeneralUsage.Rmd’ using rmarkdown
Quitting from lines 374-380 (meaRtoolsGeneralUsage.Rmd) 
Error: processing vignette 'meaRtoolsGeneralUsage.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘meaRtoolsGeneralUsage.Rmd’

--- re-building ‘sttc.Rmd’ using rmarkdown
--- finished re-building ‘sttc.Rmd’

SUMMARY: processing the following file failed:
  ‘meaRtoolsGeneralUsage.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced.Rmd’ using rmarkdown
Quitting from lines 50-60 (advanced.Rmd) 
Error: processing vignette 'advanced.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘advanced.Rmd’

--- re-building ‘medicalrisk.Rmd’ using rmarkdown
--- finished re-building ‘medicalrisk.Rmd’

SUMMARY: processing the following file failed:
  ‘advanced.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cost-report-analysis.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Quitting from lines 164-189 (cost-report-analysis.Rmd) 
Error: processing vignette 'cost-report-analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cost-report-analysis.Rmd’

--- re-building ‘provider_of_service_naming.Rmd’ using rmarkdown
--- finished re-building ‘provider_of_service_naming.Rmd’

SUMMARY: processing the following file failed:
  ‘cost-report-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘AUTHORS’
Authors information should be in file inst/AUTHORS
conf.interval: no visible global function definition for ‘pbinom’
conf.statement: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  pbinom
Consider adding
  importFrom("stats", "pbinom")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘KernSmooth’ ‘Matrix’ ‘ROCR’ ‘methods’ ‘pcaMethods’ ‘seqLogo’
  ‘seqinr’
  Please remove these calls from your code.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MEGENA_pipeline_10062016.Rmd’ using rmarkdown
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 120-128 (MEGENA_pipeline_10062016.Rmd) 
Error: processing vignette 'MEGENA_pipeline_10062016.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MEGENA_pipeline_10062016.Rmd’

SUMMARY: processing the following file failed:
  ‘MEGENA_pipeline_10062016.Rmd’

Error: Vignette re-building failed.
Execution halted
.df: no visible global function definition for ‘logLik’
coef_simple: no visible global function definition for ‘coef’
fitall: no visible binding for global variable ‘as.formula’
fitbest: no visible binding for global variable ‘as.formula’
lmboot: no visible global function definition for ‘lm’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘resid’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘rstudent’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘fitted’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘influence.measures’
stdcoef: no visible global function definition for ‘coef’
stdcoef: no visible global function definition for ‘update’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘logLik’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘AIC’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘fitted’
summary.resid_ensemble: no visible binding for global variable
  ‘rstudent’
summary.resid_ensemble: no visible global function definition for ‘sd’
summary.variable_ensemble: no visible global function definition for
  ‘sd’
Undefined global functions or variables:
  AIC as.formula coef fitted influence.measures lm logLik resid
  rstudent sd update
Consider adding
  importFrom("stats", "AIC", "as.formula", "coef", "fitted",
             "influence.measures", "lm", "logLik", "resid", "rstudent",
             "sd", "update")
to your NAMESPACE file.
Running examples in ‘mekko-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: barmekko
> ### Title: Create a bar mekko plot.
> ### Aliases: barmekko
> 
> ### ** Examples
> 
> library(ggplot2)
> df <- data.frame(
+   region = c('Northeast', 'Southeast', 'Central', 'West'),
+   sales = c(1200, 800, 450, 900),
+   avg_margin = c(3.2, -1.4, 0.1, 2.1)
+   )
> barmekko(df, region, avg_margin, sales)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mekko-vignette.Rmd’ using rmarkdown
Quitting from lines 58-60 (mekko-vignette.Rmd) 
Error: processing vignette 'mekko-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mekko-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘mekko-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘meme.Rmd’ using rmarkdown
Quitting from lines 167-177 (meme.Rmd) 
Error: processing vignette 'meme.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘meme.Rmd’

SUMMARY: processing the following file failed:
  ‘meme.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘memery-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meme
> ### Title: Generate a meme
> ### Aliases: meme meme meme_gif
> 
> ### ** Examples
> 
> # Prepare data and make a graph
> library(ggplot2)
> x <- seq(0, 2*pi, length.out = 50)
> panels <- rep(c("Plot A", "Plot B"), each = 50)
> d <- data.frame(x = x, y = sin(x), grp = panels)
> txt <- c("Philosoraptor's plots", "I like to make plots",
+   "Figure 1. (A) shows a plot and (B) shows another plot.")
> 
> p <- ggplot(d, aes(x, y)) + geom_line(colour = "cornflowerblue", size = 2) +
+   geom_point(colour = "orange", size = 4) + facet_wrap(~grp) +
+   labs(title = txt[1], subtitle = txt[2], caption = txt[3])
> 
> # meme image background and text labels
> img <- system.file("philosoraptor.jpg", package = "memery")
> lab <- c("Title meme text", "Subtitle text")
> 
> ## Not run: 
> ##D 
> ##D # Not run due to file size
> ##D # basic meme
> ##D meme(img, lab[1:2], "meme_basic.jpg")
> ##D # data analyst's meme
> ##D meme(img, lab[1:2], "meme_data.jpg", size = 2, inset = p, mult = 2)
> ## End(Not run)
> 
> # data meme with additional content control
> vp_bg <- list(fill = "#FF00FF50", col = "#FFFFFF80") # graph background
> # arbitrary number of labels, placement, and other vectorized attributes
> lab <- c(lab, "Middle plot text")
> pos <- list(w = rep(0.9, 3), h = rep(0.3, 3), x = c(0.35, 0.65, 0.5),
+   y = c(0.95, 0.85, 0.3))
> fam <- c("Impact", "serif", "Impact")
> clrs1 <- c("black", "orange", "white")
> clrs2 <- clrs1[c(2, 1, 1)]
> meme(img, lab, "meme_data2.jpg", size = c(2, 1.5, 1), family = fam, col = clrs1,
+   shadow = clrs2, label_pos = pos, inset = p, inset_bg = vp_bg, mult = 2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: meme ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(memery)
  Loading required package: showtext
  Loading required package: sysfonts
  Loading required package: showtextdb
  > 
  > test_check("memery")
  ── 1. Error: meme runs as expected (@test-meme.R#24)  ──────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_is(meme(loc, lab[1], out[1]), x) at testthat/test-meme.R:24
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: meme(loc, lab[1], out[1])
  5: print(p0, vp = vp_back)
  6: print.ggplot(p0, vp = vp_back)
  7: grid.draw(gtable)
  8: grid.draw.gTree(gtable)
  9: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  10: drawGTree(x)
  11: preDraw(x)
  12: preDraw.gTree(x)
  13: pushvpgp(x)
  14: pushgrobvp(x$vp)
  15: pushgrobvp.viewport(x$vp)
  16: pushViewport(vp, recording = FALSE)
  17: lapply(vps, push.vp, recording)
  18: FUN(X[[i]], ...)
  19: push.vp.viewport(X[[i]], ...)
  20: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 23 SKIPPED: 3 FAILED: 1
  1. Error: meme runs as expected (@test-meme.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘memery.Rmd’ using rmarkdown
Loading required package: showtext
Loading required package: sysfonts
Loading required package: showtextdb
Quitting from lines 19-23 (memery.Rmd) 
Error: processing vignette 'memery.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘memery.Rmd’

SUMMARY: processing the following file failed:
  ‘memery.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' calls in package code:
  ‘adegenet’ ‘geosphere’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
codomToPropShared: no visible global function definition for
  ‘df2genind’
codomToPropShared: no visible global function definition for
  ‘propShared’
mgLandscape: no visible global function definition for ‘SpatialPoints’
mgQuick: no visible global function definition for ‘distm’
mgQuick: no visible binding for global variable ‘distMeeus’
Undefined global functions or variables:
  SpatialPoints df2genind distMeeus distm propShared
Running examples in ‘MendelianRandomization-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mr_plot
> ### Title: Draw a scatter plot of the genetic associations and/or causal
> ###   estimates
> ### Aliases: mr_plot mr_plot,MRInput-method mr_plot,MRAll-method
> 
> ### ** Examples
> 
> mr_plot(mr_input(bx = ldlc, bxse = ldlcse, by = chdlodds, byse = chdloddsse),
+   line="egger", orientate = TRUE)
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: mr_plot ... unitConvert -> <Anonymous> -> convertUnit -> grid.Call
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette_MR.Rmd’ using rmarkdown
Quitting from lines 338-340 (Vignette_MR.Rmd) 
Error: processing vignette 'Vignette_MR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Vignette_MR.Rmd’

SUMMARY: processing the following file failed:
  ‘Vignette_MR.Rmd’

Error: Vignette re-building failed.
Execution halted
workspace_management : tellme: no visible global function definition
  for ‘file.edit’
workspace_management: no visible global function definition for
  ‘object.size’
Undefined global functions or variables:
  file.edit object.size
Consider adding
  importFrom("utils", "file.edit", "object.size")
to your NAMESPACE file.
Running examples in ‘merTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotFEsim
> ### Title: Plot the results of a simulation of the fixed effects
> ### Aliases: plotFEsim
> 
> ### ** Examples
> 
>  fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
>  (p1 <- plotFEsim(FEsim(fm1)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package suggested but not available for checking: ‘GenABEL’
dometa: no visible global function definition for ‘qchisq’
dometa: no visible global function definition for ‘median’
dometa: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘qnorm’
forestplot: no visible global function definition for ‘plot’
forestplot: no visible global function definition for ‘points’
forestplot: no visible global function definition for ‘text’
metagwa.files: no visible global function definition for ‘read.csv’
metagwa.files: no visible global function definition for ‘write.csv’
metagwa.tables: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  median pchisq plot points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "plot", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Running examples in ‘metacart-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FEmrt
> ### Title: Fixed effect meta-tree
> ### Aliases: FEmrt
> 
> ### ** Examples
> 
> data(dat.BCT2009)
> FEtree <- FEmrt(g ~ T1 + T2+ T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5)
Warning in FEmrt(g ~ T1 + T2 + T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5) :
  no moderator effect was detected
> print(FEtree)

Fixed Effects Meta-Tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected
use summary() to see the meta-analysis results> summary(FEtree)

Fixed Effects meta-tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected

Test for Heterogeneity under FE assumption:
Q = 253.0357 (df = 105), p-value < 1e-04;

Fixed Effect Meta-analysis Results:
   no.      g     se   zval   pval  ci.lb  ci.ub        
   106  0.229  0.012 18.803  0.000  0.206  0.253    *** 
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 

> plot(FEtree)
Error in `rownames<-`(`*tmp*`, value = rank(as.numeric(rownames(frame)))) : 
  attempt to set 'rownames' on an object with no dimensions
Calls: plot -> plot.FEmrt -> rownames<-
Execution halted
Running examples in ‘MetaComp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_edge_assignment
> ### Title: Generates a single column ggplot for a taxonomic assignment
> ###   table and also outputs a PDF.
> ### Aliases: plot_edge_assignment
> 
> ### ** Examples
> 
> pa_fpath <- system.file("extdata", "HMP_even//allReads-pangia.list.txt", package="MetaComp")
> pangia_assignment = load_edge_assignment(pa_fpath, type = "pangia")
> 
> plot_edge_assignment(pangia_assignment, "phylum", "Pangia", "HMP Even",
+                                                      file.path(tempdir(), "assignment.pdf"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_edge_assignment ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘gsl’ ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
metacor.DSL: no visible global function definition for ‘qnorm’
metacor.DSL: no visible global function definition for ‘pnorm’
metacor.DSL: no visible global function definition for ‘metaplot’
metacor.OP: no visible global function definition for ‘hyperg_2F1’
metacor.OP: no visible global function definition for ‘qnorm’
metacor.OP: no visible global function definition for ‘pnorm’
metacor.OP: no visible global function definition for ‘metaplot’
Undefined global functions or variables:
  hyperg_2F1 metaplot pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
Running examples in ‘metaforest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ClusterMF
> ### Title: Clustered MetaForest analysis for dependent data.
> ### Aliases: ClusterMF
> 
> ### ** Examples
> 
> #Load and clean data from metafor
> data <- get(data(dat.bourassa1996))
> data <- escalc(measure = "OR", ai = lh.le, bi = lh.re, ci = rh.le, di= rh.re,
+                data = data, add = 1/2, to = "all")
> data$mage[is.na(data$mage)] <- median(data$mage, na.rm = TRUE)
> data[c(5:8)] <- lapply(data[c(5:8)], factor)
> data$yi <- as.numeric(data$yi)
> mf.cluster.b1996 <- ClusterMF(formula = yi~ selection + investigator +
+                               hand_assess + eye_assess + mage +sex,
+                               data, study = "sample",
+                               whichweights = "unif", num.trees = 300)
> #Print MetaForest object
> mf.cluster.b1996
Call:
ClusterMF(formula = yi ~ selection + investigator + hand_assess + 
    eye_assess + mage + sex, data = data, study = "sample", whichweights = "unif", 
    num.trees = 300)

R squared (OOB):                  0.0231 
Residual heterogeneity (tau2):    0.3075 
> #Check convergence plot
> plot(mf.cluster.b1996)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
bcgVaccineData: no visible global function definition for ‘data’
bcgVaccineData: no visible global function definition for ‘qnorm’
hConfidence: no visible global function definition for ‘qchisq’
intervalEstimates_OneSgnf : crt: no visible global function definition
  for ‘qt’
intervalEstimates_OneSgnf: no visible binding for global variable
  ‘qnorm’
metagenGeneralised: no visible binding for global variable ‘quantile’
performancePointH : property: no visible global function definition for
  ‘var’
performancePointR : property: no visible global function definition for
  ‘var’
pfunc : pfun: no visible global function definition for ‘uniroot’
pivotalStream: no visible global function definition for ‘rchisq’
pivotalStream : <anonymous>: no visible global function definition for
  ‘rchisq’
pivotalStream: no visible global function definition for ‘rnorm’
rBinomGauss: no visible global function definition for ‘rnorm’
rBinomGauss: no visible global function definition for ‘rbinom’
rD: no visible global function definition for ‘rchisq’
rY: no visible global function definition for ‘rnorm’
render: no visible global function definition for ‘pdf’
render: no visible global function definition for ‘dev.off’
renderSVG: no visible global function definition for ‘svg’
renderSVG: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  data dev.off pdf qchisq qnorm qt quantile rbinom rchisq rnorm svg
  uniroot var
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "svg")
  importFrom("stats", "qchisq", "qnorm", "qt", "quantile", "rbinom",
             "rchisq", "rnorm", "uniroot", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
Running examples in ‘metagen-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDensityH
> ### Title: Pivotal distributions: Plot pivotal distribution of
> ###   heterogeneity
> ### Aliases: plotDensityH
> 
> ### ** Examples
> 
> bcg   <- bcgVaccineData()
> bcg_y <- bcg$logrisk
> bcg_d <- bcg$sdiv
> bcg_s <- bcg$size
> bcg_x <- cbind(1,bcg$x)
> 
> set.seed(865287113)
> pivUn <- pivotalStream(50, y=bcg_y, d=bcg_d, x=bcg_x,
+   adjusted=FALSE)
> set.seed(865287113)
> pivAd <- pivotalStream(50, y=bcg_y, d=bcg_d, x=bcg_x, s=bcg_s,
+   adjusted=TRUE)
> 
> pivh <- joinPivotalHeterogeneity(pivUn, pivAd)
> plotDensityH(pivh)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘metaheur-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotsearchpath
> ### Title: plot search path
> ### Aliases: plotsearchpath
> 
> ### ** Examples
> 
> plotsearchpath(examplesearch)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Metaheur.Rmd’ using rmarkdown
Quitting from lines 79-80 (Metaheur.Rmd) 
Error: processing vignette 'Metaheur.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Metaheur.Rmd’

SUMMARY: processing the following file failed:
  ‘Metaheur.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘MetaIntegrator-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggForestPlot
> ### Title: Compare effect sizes of a gene across all datasets in
> ###   meta-analysis
> ### Aliases: ggForestPlot
> ### Keywords: graphs hplot
> 
> ### ** Examples
> 
> # compare effect sizes of the Gene1 for all discovery datasets in tinyMetaObject 
> ggForestPlot(tinyMetaObject, genes="Gene1")
Warning: Removed 2 rows containing missing values (geom_errorbarh).
Warning: Removed 2 rows containing missing values (geom_point).
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaIntegrator.Rmd’ using rmarkdown
Quitting from lines 187-188 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MetaIntegrator.Rmd’

--- re-building ‘MetaIntegratorRealExample.Rmd’ using rmarkdown_notangle
--- finished re-building ‘MetaIntegratorRealExample.Rmd’

SUMMARY: processing the following file failed:
  ‘MetaIntegrator.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘MetaLonDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: visualizeFeature
> ### Title: Visualize Longitudinal Feature
> ### Aliases: visualizeFeature
> 
> ### ** Examples
> 
> data(metalonda_test_data)
> n.sample = 5
> n.timepoints = 10
> n.group = 2
> Group = factor(c(rep(0, n.sample*n.timepoints), rep(1, n.sample*n.timepoints)))
> Time = rep(rep(1:n.timepoints, times = n.sample), 2)
> ID = factor(rep(1:(2*n.sample), each = n.timepoints))
> points = seq(1, 10, length.out = 10)
> aggregate.df = data.frame(Count = metalonda_test_data[1,], Time = Time, Group = Group, ID = ID)
> visualizeFeature(aggregate.df, text = rownames(metalonda_test_data)[1], Group)
Visualizing Feature =  OTU_1 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: visualizeFeature ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaLonDA.Rmd’ using knitr
Quitting from lines 68-73 (MetaLonDA.Rmd) 
Error: processing vignette 'MetaLonDA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MetaLonDA.Rmd’

SUMMARY: processing the following file failed:
  ‘MetaLonDA.Rmd’

Error: Vignette re-building failed.
Execution halted
EScombination: no visible global function definition for ‘model.matrix’
EScombination: no visible global function definition for ‘p.adjust’
EScombination: no visible global function definition for ‘pt’
EScombination.paired: no visible global function definition for
  ‘p.adjust’
EScombination.paired: no visible global function definition for ‘pt’
calcfit2Diffrep: no visible global function definition for
  ‘model.matrix’
directEScombi: no visible global function definition for ‘pnorm’
directEScombi: no visible global function definition for ‘p.adjust’
directpvalcombi : fstatmeta: no visible global function definition for
  ‘qnorm’
directpvalcombi: no visible global function definition for ‘pnorm’
directpvalcombi: no visible global function definition for ‘p.adjust’
pvalcombination: no visible global function definition for
  ‘model.matrix’
pvalcombination: no visible global function definition for ‘p.adjust’
pvalcombination: no visible global function definition for ‘pt’
pvalcombination.paired: no visible global function definition for
  ‘p.adjust’
pvalcombination.paired: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.matrix p.adjust pnorm pt qnorm
Consider adding
  importFrom("stats", "model.matrix", "p.adjust", "pnorm", "pt", "qnorm")
to your NAMESPACE file.
Running examples in ‘metamisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Zhang
> ### Title: Meta-analysis of the prognostic role of hormone receptors in
> ###   endometrial cancer
> ### Aliases: Zhang
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Zhang)
> 
> # Display the hazard ratios for overall survival in a forest plot
> ds <- subset(Zhang, outcome=="OS")
> with(ds, forest(theta = HR, theta.ci.lb = HR.025, theta.ci.ub = HR.975, 
+                 theta.slab = Study, xlab = "Hazard ratio of HER2 versus OS", refline = 1))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘guide.Rnw’ using knitr
Quitting from lines 288-294 (guide.Rnw) 
Error: processing vignette 'guide.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘guide.Rnw’

SUMMARY: processing the following file failed:
  ‘guide.Rnw’

Error: Vignette re-building failed.
Execution halted
MAPE: no visible global function definition for ‘is’
MAPE: no visible global function definition for ‘new’
Undefined global functions or variables:
  is new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘doSMP’
Package in Depends field not imported from: ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘pcaPP:::l1median_HoCr’ ‘pcaPP:::l1median_VaZh’
  See the note in ?`:::` about the use of this operator.
Running examples in ‘metaplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: boxplot.data.frame
> ### Title: Boxplot Method for Data Frame
> ### Aliases: boxplot.data.frame
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(magrittr)
> Theoph %<>% mutate(site = ifelse(as.numeric(Subject) > 6, 'Site A','Site B'))
> boxplot(Theoph,'Subject','conc')
> boxplot(Theoph,Subject,conc)
> boxplot(Theoph,Subject,conc, gg = T)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘metaplotr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crosshairs
> ### Title: Creates a Cross-hairs Plot.
> ### Aliases: cross-hairs crosshairs
> 
> ### ** Examples
> 
> ## Not run: 
> ##D # Load and attach metaplotr package to the Global Environment
> ##D library(metaplotr)
> ##D 
> ##D # Remove all variables in the .GlobalEnv, effectively clearing .GlobalEvn
> ##D rm(list = ls())
> ##D 
> ##D # Find out more about the data set from Ferguson and Brannick (2012)
> ##D # help("FergusonBrannick2012")
> ##D 
> ##D # You can check out help file of the \code{crosshairs} function.
> ##D # help(crosshairs)
> ## End(Not run)
> 
> # Basic usage of the \code{crosshairs} function.
> crosshairs(FergusonBrannick2012$pub_z, FergusonBrannick2012$dis_z,
+ FergusonBrannick2012$pub_z_se, FergusonBrannick2012$dis_z_se)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: crosshairs ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘how_to_use_crosshairs.Rmd’ using rmarkdown
Quitting from lines 50-51 (how_to_use_crosshairs.Rmd) 
Error: processing vignette 'how_to_use_crosshairs.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘how_to_use_crosshairs.Rmd’

SUMMARY: processing the following file failed:
  ‘how_to_use_crosshairs.Rmd’

Error: Vignette re-building failed.
Execution halted
fishercomb: no visible global function definition for ‘pchisq’
fishercomb: no visible global function definition for ‘p.adjust’
invnorm : <anonymous>: no visible global function definition for
  ‘qnorm’
invnorm: no visible global function definition for ‘pnorm’
invnorm: no visible global function definition for ‘p.adjust’
sim.function : <anonymous>: no visible global function definition for
  ‘rnorm’
sim.function : <anonymous>: no visible global function definition for
  ‘rnbinom’
Undefined global functions or variables:
  p.adjust pchisq pnorm qnorm rnbinom rnorm
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
             "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  MatFile.cpp:40:16: warning: converting to non-pointer type ‘char’ from NULL [-Wconversion-null]
  MatFile.cpp:65:16: warning: converting to non-pointer type ‘char’ from NULL [-Wconversion-null]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MetaSKAT.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaStan_BNHM.Rmd’ using rmarkdown
Quitting from lines 44-70 (MetaStan_BNHM.Rmd) 
Error: processing vignette 'MetaStan_BNHM.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MetaStan_BNHM.Rmd’

SUMMARY: processing the following file failed:
  ‘MetaStan_BNHM.Rmd’

Error: Vignette re-building failed.
Execution halted
fit.bivar: no visible binding for global variable ‘binomial’
summary.fit.bivar: no visible global function definition for ‘qt’
summary.fit.bivar: no visible global function definition for ‘pt’
Undefined global functions or variables:
  binomial pt qt
Consider adding
  importFrom("stats", "binomial", "pt", "qt")
to your NAMESPACE file.
Running examples in ‘metaviz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: viz_forest
> ### Title: Forest plot variants for meta-analyses
> ### Aliases: viz_forest
> 
> ### ** Examples
> 
> library(metaviz)
> # Plotting the mozart data using a classic forest plot
> viz_forest(x = mozart[, c("d", "se")],
+ study_labels = mozart[, "study_name"], xlab = "Cohen d")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘funnelinf.Rmd’ using rmarkdown
Quitting from lines 48-49 (funnelinf.Rmd) 
Error: processing vignette 'funnelinf.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘funnelinf.Rmd’

--- re-building ‘metaviz.Rmd’ using rmarkdown
Quitting from lines 38-40 (metaviz.Rmd) 
Error: processing vignette 'metaviz.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘metaviz.Rmd’

SUMMARY: processing the following files failed:
  ‘funnelinf.Rmd’ ‘metaviz.Rmd’

Error: Vignette re-building failed.
Execution halted
crosssection: no visible global function definition for
  ‘colorRampPalette’
crosssection: no visible global function definition for
  ‘filled.contour’
crosssection: no visible global function definition for ‘axis’
crosssection: no visible global function definition for ‘par’
crosssection: no visible global function definition for ‘contour’
temperatures: no visible binding for global variable ‘time’
Undefined global functions or variables:
  axis colorRampPalette contour filled.contour par time
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "contour", "filled.contour", "par")
  importFrom("stats", "time")
to your NAMESPACE file.
Running examples in ‘meteogRam-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: temperatures
> ### Title: Temperature meteogram
> ### Aliases: temperatures
> ### Keywords: temperatures
> 
> ### ** Examples
> 
> data(example_temperature.data)
> temperatures(temperature.data,plot.dewt=TRUE,plot.surf=TRUE,
+ 	plot.min_max=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
getdata: no visible global function definition for ‘read.csv’
plotdata: no visible global function definition for ‘head’
Undefined global functions or variables:
  head read.csv
Consider adding
  importFrom("utils", "head", "read.csv")
to your NAMESPACE file.
Running examples in ‘Methplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotdata
> ### Title: This function visualizes the dataframe yielded by function
> ###   "getdata".
> ### Aliases: plotdata
> 
> ### ** Examples
> 
> data(mydata)
> plotdata(mydata, x.title="Methylation Plot", condition="P1_A1", n=10, legendpos="right")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
RUVRand: no visible global function definition for ‘barplot’
RUVRand: no visible global function definition for ‘prcomp’
RuvRandIter: no visible global function definition for ‘kmeans’
RuvRandIter: no visible global function definition for ‘barplot’
RuvRandIter: no visible global function definition for ‘prcomp’
opt: no visible global function definition for ‘optim’
printdata: no visible global function definition for ‘head’
Undefined global functions or variables:
  barplot head kmeans optim prcomp
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "kmeans", "optim", "prcomp")
  importFrom("utils", "head")
to your NAMESPACE file.
Running examples in ‘metR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ConvertLongitude
> ### Title: Converts between longitude conventions
> ### Aliases: ConvertLongitude
> 
> ### ** Examples
> 
> library(ggplot2)
> library(data.table)
> data(geopotential)
> ggplot(geopotential[date == date[1]], aes(lon, lat, z = gh)) +
+     geom_contour(color = "black") +
+     geom_contour(aes(x = ConvertLongitude(lon)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Visualization-tools.Rmd’ using rmarkdown
Quitting from lines 32-41 (Visualization-tools.Rmd) 
Error: processing vignette 'Visualization-tools.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Visualization-tools.Rmd’

--- re-building ‘Working-with-data.Rmd’ using rmarkdown
Quitting from lines 45-50 (Working-with-data.Rmd) 
Error: processing vignette 'Working-with-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Working-with-data.Rmd’

SUMMARY: processing the following files failed:
  ‘Visualization-tools.Rmd’ ‘Working-with-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘MASS’ ‘abind’ ‘pls’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
show,mewTyp: no visible global function definition for ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
Running examples in ‘mfbvar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mfbvar_minn
> ### Title: Plotting method for class 'mfbvar_minn'
> ### Aliases: plot.mfbvar_minn
> 
> ### ** Examples
> 
> prior_obj <- set_prior(Y = mf_sweden[, 4:5], freq = c("m", "q"),
+                        n_lags = 4, n_burnin = 20, n_reps = 20, n_fcst = 4)
Warning: prior_Pi_AR1: 0 used as prior mean for AR(1) coefficients.

Warning: lambda1: 0.2 used as the value for the overall tightness hyperparameter.

Warning: lambda2: 1 used as the value for the lag decay hyperparameter.

Warning: lambda3: 10000 used for the constant's prior variance.

> mod_minn <- estimate_mfbvar(prior_obj, prior_type = "minn")
> plot(mod_minn)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Discriminability.Rmd’ using rmarkdown
Quitting from lines 53-55 (Discriminability.Rmd) 
Error: processing vignette 'Discriminability.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Discriminability.Rmd’

--- re-building ‘MGC.Rmd’ using rmarkdown
Quitting from lines 72-73 (MGC.Rmd) 
Error: processing vignette 'MGC.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MGC.Rmd’

--- re-building ‘simulations.Rmd’ using rmarkdown
Loading required package: mgc
Loading required package: ggplot2
Quitting from lines 64-69 (simulations.Rmd) 
Error: processing vignette 'simulations.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simulations.Rmd’

SUMMARY: processing the following files failed:
  ‘Discriminability.Rmd’ ‘MGC.Rmd’ ‘simulations.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘mgcViz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check.gamViz
> ### Title: Some diagnostics for a fitted gam model
> ### Aliases: check.gamViz
> 
> ### ** Examples
> 
> library(mgcViz)
> set.seed(0)
> dat <- gamSim(1, n = 200)
Gu & Wahba 4 term additive model
> b <- gam(y ~ s(x0) + s(x1) + s(x2) + s(x3), data = dat)
> b <- getViz(b)
> 
> # Checks using default options
> check(b)

Method: GCV   Optimizer: magic
Smoothing parameter selection converged after 8 iterations.
The RMS GCV score gradient at convergence was 1.072609e-05 .
The Hessian was positive definite.
Model rank =  37 / 37 

Basis dimension (k) checking results. Low p-value (k-index<1) may
indicate that k is too low, especially if edf is close to k'.

        k'  edf k-index p-value
s(x0) 9.00 2.32    1.00    0.51
s(x1) 9.00 2.31    0.97    0.30
s(x2) 9.00 7.65    0.96    0.27
s(x3) 9.00 1.23    1.04    0.67
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgcviz.rmd’ using rmarkdown
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
Loading required package: qgam
Loading required package: ggplot2
Registered S3 method overwritten by 'mgcViz':
  method from  
  +.gg   GGally

Attaching package: 'mgcViz'

The following objects are masked from 'package:stats':

    qqline, qqnorm, qqplot

Quitting from lines 66-70 (mgcviz.rmd) 
Error: processing vignette 'mgcviz.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mgcviz.rmd’

SUMMARY: processing the following file failed:
  ‘mgcviz.rmd’

Error: Vignette re-building failed.
Execution halted
maglm: no visible global function definition for ‘combn’
maglm: no visible global function definition for ‘glm’
maglm: no visible global function definition for ‘logLik’
mamglm: no visible global function definition for ‘combn’
mamglm: no visible global function definition for ‘logLik’
ses.maglm: no visible global function definition for ‘rnorm’
ses.maglm: no visible binding for global variable ‘sd’
ses.mamglm: no visible global function definition for ‘rnorm’
ses.mamglm: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  combn glm logLik rnorm sd
Consider adding
  importFrom("stats", "glm", "logLik", "rnorm", "sd")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘corpcor’ ‘evd’ ‘fields’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to ‘RJSONIO’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for ‘packageVersion’
.onAttach: no visible binding for global variable ‘.MGRAST’
build.MGRAST: no visible binding for global variable ‘.MGRAST’
build.MGRAST: no visible global function definition for ‘fromJSON’
call.MGRAST: no visible binding for global variable ‘.MGRAST’
call.MGRAST: no visible global function definition for ‘download.file’
call.MGRAST: no visible global function definition for ‘isValidJSON’
call.MGRAST: no visible global function definition for ‘fromJSON’
doc.MGRAST: no visible binding for global variable ‘.MGRAST’
doc.MGRAST: no visible global function definition for ‘str’
load.MGRAST: no visible binding for global variable ‘.MGRAST’
parse.MGRAST: no visible binding for global variable ‘.MGRAST’
this.package: no visible binding for global variable ‘.MGRAST’
Undefined global functions or variables:
  .MGRAST download.file fromJSON isValidJSON packageVersion str
Consider adding
  importFrom("utils", "download.file", "packageVersion", "str")
to your NAMESPACE file.
calc_z_var: no visible binding for global variable ‘median’
diffScore: no visible global function definition for ‘new’
diffScore: no visible global function definition for ‘model.matrix’
logNORMcdf: no visible global function definition for ‘pnorm’
mGSZ.adj.mean.std: no visible binding for global variable ‘sd’
pick.data.cols: no visible binding for global variable ‘var’
plotProfile: no visible binding for global variable ‘quantile’
plotProfile: no visible global function definition for ‘plot’
plotProfile: no visible global function definition for ‘lines’
plotProfile: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines median model.matrix new plot pnorm quantile sd var
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("methods", "new")
  importFrom("stats", "median", "model.matrix", "pnorm", "quantile",
             "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').