'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
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.
p3state: no visible global function definition for 'survfit'
p3state: no visible global function definition for 'terms'
p3state: no visible global function definition for 'as.formula'
p3state: no visible global function definition for 'coxph'
p3state: no visible binding for global variable 'na.exclude'
plot.p3state: no visible global function definition for 'matplot'
plot.p3state: no visible global function definition for 'devAskNewPage'
plot.p3state: no visible global function definition for 'persp'
plot.p3state: no visible global function definition for 'colours'
plot.p3state: no visible global function definition for
  'filled.contour'
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
pacbpred : thetaFunc: no visible global function definition for 'lsfit'
pacbpred : thetaFunc: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'var'
pacbpred: no visible global function definition for 'runif'
pacbpred: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Non-standard files/directories found at top level:
  'DESCRIPTION_EX' 'divers' 'main.R' 'testsDev'
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW: warning in return(x@u1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@u2): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@w1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW: warning in x@u1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@u2 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@w1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
Package suggested but not available for checking: 'tidyr'
Running examples in 'padr-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pad
> ### Title: Pad the datetime column of a data frame
> ### Aliases: pad
> 
> ### ** Examples
> 
> simple_df <- data.frame(day = as.Date(c('2016-04-01', '2016-04-03')),
+                         some_value = c(3,4))
> pad(simple_df)
pad applied on the interval: 2 day
         day some_value
1 2016-04-01          3
2 2016-04-03          4
> pad(simple_df, interval = "day")
         day some_value
1 2016-04-01          3
2 2016-04-02         NA
3 2016-04-03          4
> 
> library(dplyr) # for the pipe operator

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

> month <- seq(as.Date('2016-04-01'), as.Date('2017-04-01'),
+               by = 'month')[c(1, 4, 5, 7, 9, 10, 13)]
> month_df <- data.frame(month = month,
+                        y = runif(length(month), 10, 20) %>% round)
> # forward fill the padded values with tidyr's fill
> month_df %>% pad %>% tidyr::fill(y)
pad applied on the interval: month
Error in loadNamespace(name) : there is no package called 'tidyr'
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'padr.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

`summarise()` ungrouping output (override with `.groups` argument)
pad applied on the interval: day
Quitting from lines 101-102 (padr.Rmd) 
Error: processing vignette 'padr.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'padr.Rmd'

--- re-building 'padr_custom.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

pad applied on the interval: 3 hour
--- finished re-building 'padr_custom.Rmd'

--- re-building 'padr_implementation.Rmd' using rmarkdown
--- finished re-building 'padr_implementation.Rmd'

SUMMARY: processing the following file failed:
  'padr.Rmd'

Error: Vignette re-building failed.
Execution halted
paf: no visible global function definition for 'as.formula'
paf: no visible global function definition for 'model.response'
paf: no visible global function definition for 'model.frame'
paf: no visible global function definition for 'model.matrix'
plot.paf: no visible global function definition for 'lines'
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
CalGIF: no visible binding for global variable 'PAGIData'
CalGIF2: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible global function definition for 'p.adjust'
PAGI.Main: no visible global function definition for 'pt'
getclass.labels: no visible binding for global variable 'ExampleData'
getdataset: no visible binding for global variable 'ExampleData'
Undefined global functions or variables:
  ExampleData PAGIData p.adjust pt
Consider adding
  importFrom("stats", "p.adjust", "pt")
to your NAMESPACE file.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###

Rd file 'PAGI.Main.Rd':
  \examples lines wider than 100 characters:
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",

These lines will be truncated in the PDF manual.
paired.Loc: no visible global function definition for 'qt'
paired.Loc: no visible global function definition for 'median'
paired.Loc: no visible global function definition for 'qsignrank'
paired.Loc: no visible global function definition for 'qnorm'
paired.Scale: no visible global function definition for 'var'
paired.Scale: no visible global function definition for 'cor'
paired.Scale: no visible global function definition for 'qt'
paired.Scale: no visible global function definition for 'median'
paired.Scale: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  cor median qnorm qsignrank qt var
Consider adding
  importFrom("stats", "cor", "median", "qnorm", "qsignrank", "qt", "var")
to your NAMESPACE file.
Rd file 'paired.Loc.Rd':
  \usage lines wider than 90 characters:
     paired.Loc(x, y, method = "parametric", exact = FALSE, conf.level = 0.95, alternative = "two.sided")
  \examples lines wider than 100 characters:
     astra <- c(2.4, 4.8, 4, 4.9, 3.9, 4.1, 3.8, 3.5, 4.6, 2.9, 4.9, 3.7, 4.8, 3.7, 3.8, 4.1, 4.2, 4.3, 3.9, 3.8)
     flame <- c(2.4, 4.8, 4, 4.7, 3.9, 4.2, 3.8, 3.3, 4.6, 3, 5, 3.6, 4.9, 3.8, 3.9, 4.6, 4.2, 4.4, 4, 3.4)

Rd file 'paired.Scale.Rd':
  \examples lines wider than 100 characters:
     astra <- c(2.4, 4.8, 4, 4.9, 3.9, 4.1, 3.8, 3.5, 4.6, 2.9, 4.9, 3.7, 4.8, 3.7, 3.8, 4.1, 4.2, 4.3, 3.9, 3.8)
     flame <- c(2.4, 4.8, 4, 4.7, 3.9, 4.2, 3.8, 3.3, 4.6, 3, 5, 3.6, 4.9, 3.8, 3.9, 4.6, 4.2, 4.4, 4, 3.4)

Rd file 'pairedCI-package.Rd':
  \examples lines wider than 100 characters:
     astra <- c(2.4, 4.8, 4, 4.9, 3.9, 4.1, 3.8, 3.5, 4.6, 2.9, 4.9, 3.7, 4.8, 3.7, 3.8, 4.1, 4.2, 4.3, 3.9, 3.8)
     flame <- c(2.4, 4.8, 4, 4.7, 3.9, 4.2, 3.8, 3.3, 4.6, 3, 5, 3.6, 4.9, 3.8, 3.9, 4.6, 4.2, 4.4, 4, 3.4)

These lines will be truncated in the PDF manual.
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'pairheatmap.Rd':
  \examples lines wider than 100 characters:
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),

These lines will be truncated in the PDF manual.
pairsD3: no visible global function definition for 'gray.colors'
Undefined global functions or variables:
  gray.colors
Consider adding
  importFrom("grDevices", "gray.colors")
to your NAMESPACE file.
Packages required but not available:
  'broomExtra', 'ipmisc', 'tidyBF', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'GDPgrowthRESULTS.csv'
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'CorShrink'
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'lattice' 'vegan'
  Please remove these calls from your code.
Rd file 'syas.Rd':
  \examples lines wider than 100 characters:
     bcrossv.sa(modernq[,1],perq2,a.d,delta=25,method="canberra",quant=0.05,trials=c(5, 0.05),detrend=FALSE)

Rd file 'vcrossv.all.Rd':
  \examples lines wider than 100 characters:
     #build a dummy factor assuming that the first 10 species belong to group1 and the send ten belong to group 2

These lines will be truncated in the PDF manual.
Found the following files/directories:
  'Dispersion.pdf'
Packages suggested but not available for checking: 'tidyr', 'recipes'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GOpredict: no visible global function definition for 'fisher.test'
KEGGpredict: no visible global function definition for 'fisher.test'
ProteinCluster: no visible global function definition for 'ecdf'
ProteinCluster: no visible global function definition for 'as.hclust'
ProteinCluster: no visible global function definition for
  'as.dendrogram'
ProteinCluster : addE: no visible global function definition for
  'is.leaf'
SignificantSubcluster: no visible global function definition for
  'order.dendrogram'
SignificantSubcluster: no visible global function definition for
  'fisher.test'
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
Consider adding
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Paneldata.formula: no visible global function definition for
  'model.frame'
Paneldata.formula: no visible global function definition for
  'model.matrix'
Paneldata.formula: no visible global function definition for
  'model.response'
summary.Paneldata: no visible global function definition for 'coef'
summary.Paneldata: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'broom.mixed', 'clubSandwich', 'geepack', 'skimr', 'tidyr'
Running examples in 'panelr-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: asym_gee
> ### Title: Asymmetric effects models fit with GEE
> ### Aliases: asym_gee
> 
> ### ** Examples
> 
> data("WageData")
> wages <- panel_data(WageData, id = id, wave = t)
> model <- asym_gee(lwage ~ lag(union) + wks, data = wages)
Loading required namespace: geepack
Failed with error:  'there is no package called 'geepack''
Error: You must have 'geepack' installed to use this function.
Backtrace:
 1. panelr::asym_gee(lwage ~ lag(union) + wks, data = wages)
 2. panelr:::need_package("geepack")
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'reshape.Rmd' using rmarkdown
Loading required package: lme4
Loading required package: Matrix

Attaching package: 'panelr'

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

    filter

--- finished re-building 'reshape.Rmd'

--- re-building 'wbm.Rmd' using rmarkdown
Loading required package: lme4
Loading required package: Matrix

Attaching package: 'panelr'

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

    filter

Loading required namespace: geepack
Failed with error:  'there is no package called 'geepack''
Quitting from lines 379-381 (wbm.Rmd) 
Error: processing vignette 'wbm.Rmd' failed with diagnostics:
You must have 'geepack' installed to use this function.
--- failed re-building 'wbm.Rmd'

SUMMARY: processing the following file failed:
  'wbm.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
parallelSVM.default: no visible binding for global variable 'na.omit'
parallelSVM.formula: no visible binding for global variable 'na.omit'
predict.parallelSVM: no visible binding for global variable 'predict'
Undefined global functions or variables:
  na.omit predict
Consider adding
  importFrom("stats", "na.omit", "predict")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'clubSandwich', 'EGAnet', 'geepack', 'sjstats'
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'example.csv' 'example.tsv' 'example.xlsx'
Packages required but not available: 'plotly', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'easyalluvial', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.formula.make: no visible global function definition for 'formula'
regress: no visible global function definition for 'lm'
regress: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  formula lm model.matrix
Consider adding
  importFrom("stats", "formula", "lm", "model.matrix")
to your NAMESPACE file.
Package suggested but not available for checking: 'd3r'
Package vignette with placeholder title 'Vignette Title':
  'introduction-to-parcoords-.Rmd'
Error(s) in re-building vignettes:
  ...
--- re-building 'introduction-to-parcoords-.Rmd' using rmarkdown
Quitting from lines 80-93 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
there is no package called 'd3r'
--- failed re-building 'introduction-to-parcoords-.Rmd'

SUMMARY: processing the following file failed:
  'introduction-to-parcoords-.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  'NUL'
Package required but not available: 'hansard'

Package suggested but not available for checking: 'janitor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'flexsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Running examples in 'parSim-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parSim
> ### Title: Parallel Simulator
> ### Aliases: parSim parSim-package
> 
> ### ** Examples
> 
> # Some function we might use:
> bias <- function(x,y){abs(x-y)}
> 
> # Run the simulation:
> Results <- parSim(
+   # Any number of conditions:
+   sampleSize = c(50, 100, 250),
+   beta = c(0, 0.5, 1),
+   sigma = c(0.25, 0.5, 1),
+   
+   # Number of repititions?
+   reps = 25, # more is better!
+   
+   # Parallel?
+   nCores = 1,
+   
+   # Write to file?
+   write = FALSE,
+   
+   # Export objects (only needed when nCores > 1):
+   export = c("bias"),
+   
+   # R expression:
+   expression = {
+     # Load all R packages in the expression if needed
+     # library(...)
+     
+     # Want to debug? Enter browser() and run the function. Only works with nCores = 1!
+     # browser()
+     
+     # Enter whatever codes you want. I can use the conditions as objects.
+     X <- rnorm(sampleSize)
+     Y <- beta * X + rnorm(sampleSize, sigma)
+     fit <- lm(Y ~ X)
+     betaEst <- coef(fit)[2]
+     Rsquared <- summary(fit)$r.squared
+     
+     # Make a data frame with one row to return results (multple rows is 
+     # also possible but not reccomended):
+     data.frame(
+       betaEst = betaEst,
+       bias = bias(beta,betaEst),
+       Rsquared = Rsquared
+     )
+   }
+ )
> 
> # Analyze the results:
> library("ggplot2")
> library("tidyr")
Error in library("tidyr") : there is no package called 'tidyr'
Execution halted
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
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.
fitOR: no visible global function definition for 'multinom'
fitOR: no visible global function definition for 'formula'
fitOR: no visible global function definition for 'coef'
fitOR: no visible global function definition for 'optim'
reportOR: no visible global function definition for 'qnorm'
reportOR: no visible global function definition for 'pchisq'
reportOR: no visible global function definition for 'coef'
simData: no visible global function definition for 'rnorm'
simData: no visible global function definition for 'runif'
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
Package required but not available: 'tidygraph'

Package suggested but not available for checking: 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
partitionMap: no visible global function definition for 'predict'
partitionMap: no visible global function definition for 'rnorm'
partitionMap: no visible binding for global variable 'sd'
partitionMap: no visible global function definition for 'sd'
partitionMap: no visible global function definition for 'quantile'
Undefined global functions or variables:
  predict quantile rnorm sd
Consider adding
  importFrom("stats", "predict", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'co2' 'co2.1' 'co2.2' 'co2s.1' 'co2s.2' 'ctm.1' 'ctm.2' 'm' 'm.1'
  'm.2' 'test' 'test.1' 'test.2' 'testa.1' 'testa.2' 'xfile.1'
  'xfile.2'
Warning: no function found corresponding to methods exports from 'partsm' 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.
Malformed Description field: should contain one or more complete sentences.
parviol: no visible global function definition for 'plot.new'
parviol: no visible global function definition for 'plot.window'
parviol: no visible global function definition for 'title'
parviol: no visible global function definition for 'lines'
parviol: no visible global function definition for 'text'
parviol: no visible global function definition for 'rgb'
selecto: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot.new plot.window rgb text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot.new", "plot.window", "text",
             "title")
to your NAMESPACE file.
Packages required but not available: 'tidyverse', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building 'passport.Rmd' using rmarkdown
Quitting from lines 32-39 (passport.Rmd) 
Error: processing vignette 'passport.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'passport.Rmd'

SUMMARY: processing the following file failed:
  'passport.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'ape' 'caper'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
conch: no visible global function definition for 'read.tree'
conch: no visible global function definition for 'reorder'
conch: no visible global function definition for 'read.nexus'
conch: no visible global function definition for '.compressTipLabel'
conch: no visible global function definition for 'drop.tip'
conch: no visible global function definition for 'extract.clade'
conch: no visible global function definition for 'which.edge'
conch: no visible global function definition for 'write.tree'
pastis_main: no visible global function definition for 'combn'
read_input: no visible global function definition for 'read.tree'
read_input: no visible global function definition for 'reorder'
read_input: no visible global function definition for 'read.csv'
read_input: no visible global function definition for 'read.dna'
Undefined global functions or variables:
  .compressTipLabel combn drop.tip extract.clade read.csv read.dna
  read.nexus read.tree reorder which.edge write.tree
Consider adding
  importFrom("stats", "reorder")
  importFrom("utils", "combn", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  'pastis_data_1' 'pastis_data_2' 'pastis_data_3'
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'e1071'
  Please remove these calls from your code.
Package suggested but not available for checking: 'tidyr'
Package required but not available: 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package vignette with placeholder title 'Vignette Title':
  'pathlibr.Rmd'
Package required but not available: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Checking should be performed on sources prepared by 'R CMD build'.
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
add_noise: no visible global function definition for 'rnorm'
estimate_risk_dream6 : <anonymous>: no visible global function
  definition for 'var'
generate_sample: no visible global function definition for 'rnorm'
generate_sample: no visible global function definition for 'runif'
sample_function: no visible global function definition for 'runif'
sample_function : <anonymous>: no visible global function definition
  for 'var'
sample_function_multi_mod_weight: no visible global function definition
  for 'runif'
sample_function_multi_mod_weight : <anonymous>: no visible global
  function definition for 'var'
sample_function_single_mod: no visible global function definition for
  'runif'
Undefined global functions or variables:
  rnorm runif var
Consider adding
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'PAWL' 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.
'library' or 'require' calls to packages already attached by Depends:
  'foreach' 'ggplot2' 'reshape'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'foreach' 'ggplot2' 'methods' 'mvtnorm' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'createAdaptiveRandomWalkProposal.Rd':
  \usage lines wider than 90 characters:
         createAdaptiveRandomWalkProposal(nchains, targetdimension, adaptiveproposal, adaptationrate, sigma_init)

These lines will be truncated in the PDF manual.
Found the following sources/headers with CR or CRLF line endings:
  src/zmqsrc/src/condition_variable.hpp
Some Unix compilers require LF line endings.
Package required but not available: 'textclean'

Packages suggested but not available for checking: 'ggraph', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'foreach' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dotplot.pbo: no visible global function definition for 'reorder'
pbo: no visible global function definition for '%dopar%'
pbo: no visible global function definition for 'foreach'
pbo: no visible global function definition for 'lm'
xyplot.pbo: no visible global function definition for 'ecdf'
xyplot.pbo: no visible global function definition for 'doubleYScale'
xyplot.pbo: no visible global function definition for 'reorder'
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
a_get_native: no visible global function definition for 'par'
a_get_relative: no visible global function definition for 'par'
brackets: no visible global function definition for 'par'
brackets: no visible global function definition for 'dist'
brackets: no visible global function definition for 'lines'
Undefined global functions or variables:
  dist lines par
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "dist")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'mixOmics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
draw.pcaBootPlot: no visible global function definition for 'grid'
draw.pcaBootPlot: no visible global function definition for 'points'
draw.pcaBootPlot: no visible global function definition for 'symbols'
draw.pcaBootPlot: no visible global function definition for 'legend'
pcaBootPlot: no visible global function definition for 'prcomp'
pcaBootPlot: no visible global function definition for 'cor'
pcaBootPlot: no visible global function definition for 'quantile'
pcaBootPlot: no visible global function definition for 'pdf'
pcaBootPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  cor dev.off grid legend pdf points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
Packages suggested but not available for checking: 'plotly', 'vcfR'
PCDReg.wf: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Package suggested but not available for checking: 'qgraph'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'ggtree'
Error(s) in re-building vignettes:
  ...
--- re-building 'PCMBase.Rmd' using rmarkdown
Failed with error:  'there is no package called 'ggtree''
Quitting from lines 37-53 (PCMBase.Rmd) 
Error: processing vignette 'PCMBase.Rmd' failed with diagnostics:
argument is not interpretable as logical
--- failed re-building 'PCMBase.Rmd'

--- re-building 'PCMCreateModel.Rmd' using rmarkdown
Failed with error:  'there is no package called 'ggtree''
Quitting from lines 37-54 (PCMCreateModel.Rmd) 
Error: processing vignette 'PCMCreateModel.Rmd' failed with diagnostics:
argument is not interpretable as logical
--- failed re-building 'PCMCreateModel.Rmd'

--- re-building 'PCMParam.Rmd' using rmarkdown
--- finished re-building 'PCMParam.Rmd'

--- re-building 'PCMTracePruning.Rmd' using rmarkdown
Failed with error:  'there is no package called 'ggtree''
Quitting from lines 37-59 (PCMTracePruning.Rmd) 
Error: processing vignette 'PCMTracePruning.Rmd' failed with diagnostics:
argument is not interpretable as logical
--- failed re-building 'PCMTracePruning.Rmd'

SUMMARY: processing the following files failed:
  'PCMBase.Rmd' 'PCMCreateModel.Rmd' 'PCMTracePruning.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  'AbsolutePlot_Absolute Risk.pdf' 'ContrastPlot_OR.pdf'
Package required but not available: 'phylobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'FFTrees'
PdofCSGt.bootstrap5: no visible global function definition for 'rnorm'
PdofCSGt.bootstrap5: no visible global function definition for 'rt'
PdofCSt.T1or2: no visible global function definition for 'combn'
PofCSGt: no visible global function definition for 'combn'
PofCSLt.bootstrap5: no visible global function definition for 'rnorm'
PofCSLt.bootstrap5: no visible global function definition for 'rt'
PofCSt: no visible global function definition for 'pnorm'
tindep: no visible binding for global variable 'var'
tindep: no visible global function definition for 'pt'
Undefined global functions or variables:
  combn pnorm pt rnorm rt var
Consider adding
  importFrom("stats", "pnorm", "pt", "rnorm", "rt", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pdist: no visible global function definition for 'dist'
pdist: no visible global function definition for 'new'
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking: 'adabag', 'caret'
Malformed Description field: should contain one or more complete sentences.
band.chol.cv: no visible global function definition for 'cov'
pdsoft.cv: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Package vignette with placeholder title 'Vignette Title':
  'peakPick-vignette.Rmd'
peacf: no visible global function definition for 'is.ts'
peacf: no visible global function definition for 'cycle'
peacf: no visible global function definition for 'ts.intersect'
peacf: no visible global function definition for 'lag'
peacf: no visible global function definition for 'ts'
peacf: no visible global function definition for 'pchisq'
peacf.plot: no visible global function definition for 'segments'
peacf.plot: no visible global function definition for 'title'
pear: no visible global function definition for 'cycle'
pear: no visible global function definition for 'pchisq'
peboxplot: no visible global function definition for 'cycle'
peboxplot: no visible global function definition for 'boxplot'
peboxplot: no visible global function definition for 'title'
peplot: no visible global function definition for 'par'
peplot: no visible global function definition for 'cycle'
peplot: no visible global function definition for 'identify'
peplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq segments title ts
  ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
The following files should probably not be installed:
  'addendum.tex', 'slplot.tex', 'table1.tex', 'table3.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
PearsonICA: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'dev.new'
PearsonICAdemo: no visible global function definition for 'par'
PearsonICAdemo: no visible global function definition for 'axis'
PearsonICAdemo: no visible global function definition for 'title'
PearsonICAdemo: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis dev.new lines par rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Rd file 'PearsonICA.Rd':
  \usage lines wider than 90 characters:
     PearsonICA(X, n.comp = 0, row.norm = FALSE, maxit = 200, tol = 1e-04, border.base = c(2.6, 4), border.slope = c(0, 1), verbose = FALSE, ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo' 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AssoTestProc: no visible global function definition for 'rbinom'
AssoTestProc: no visible global function definition for 'princomp'
AssoTestProc: no visible global function definition for 'loadings'
AssoTestProc: no visible global function definition for 'lm'
CNVtypeAnay: no visible global function definition for 'cov'
ClusProc: no visible global function definition for 'princomp'
ClusProc: no visible global function definition for 'prcomp'
ClusProc0: no visible global function definition for 'kmeans'
ClusProc0: no visible global function definition for 'cov'
Inde: no visible global function definition for 'lm'
Inde: no visible global function definition for 'var'
STE: no visible global function definition for 'pchisq'
STIM: no visible global function definition for 'cor'
STIM: no visible global function definition for 'pchisq'
plot.clust: no visible global function definition for 'princomp'
plot.clust: no visible global function definition for 'loadings'
plot.clust: no visible global function definition for 'qplot'
plot.clust: no visible global function definition for 'geom_histogram'
plot.clust: no visible global function definition for 'aes_string'
plot.clust: no visible global function definition for 'barplot'
plot.clust: no visible global function definition for 'title'
plot.clust: no visible global function definition for 'mtext'
plot.clust: no visible global function definition for 'text'
Undefined global functions or variables:
  aes_string barplot cor cov geom_histogram kmeans lm loadings mtext
  pchisq prcomp princomp qplot rbinom text title var
Consider adding
  importFrom("graphics", "barplot", "mtext", "text", "title")
  importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq",
             "prcomp", "princomp", "rbinom", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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.
blup: no visible global function definition for 'model.matrix'
blup: no visible global function definition for 'model.frame'
blup: no visible global function definition for 'read.table'
calcG: no visible global function definition for 'as'
gblup: no visible global function definition for 'model.matrix'
gblup: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  as model.frame model.matrix read.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "model.frame", "model.matrix")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  'A.txt' 'Ainv.txt'
PEMM_fun : find.lambda: no visible global function definition for
  'optimize'
PEMM_fun: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'CoxBoost' 'codetools' 'locfit' 'penalized'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
complexity.LASSO: no visible global function definition for 'profL1'
complexity.ipec.CoxBoost: no visible global function definition for
  'CoxBoost'
complexity.ipec.CoxBoost: no visible global function definition for
  'locfit'
complexity.mincv.CoxBoost: no visible global function definition for
  'cv.CoxBoost'
complexity.ripec.CoxBoost: no visible global function definition for
  'CoxBoost'
complexity.ripec.CoxBoost: no visible global function definition for
  'locfit'
extract: no visible global function definition for 'findGlobals'
fit.CoxBoost: no visible global function definition for 'CoxBoost'
fit.LASSO: no visible global function definition for 'penalized'
Undefined global functions or variables:
  CoxBoost cv.CoxBoost findGlobals locfit penalized profL1
Rd file 'aggregation.brier.Rd':
  \usage lines wider than 90 characters:
     aggregation.brier(full.data=NULL, response, x, model, cplx=NULL,  type=c("apparent", "noinf"), 

Rd file 'aggregation.misclass.Rd':
  \usage lines wider than 90 characters:
     aggregation.misclass(full.data=NULL, response, x, model, cplx=NULL,  type=c("apparent", "noinf"), 

These lines will be truncated in the PDF manual.
Found the following files/directories:
  'PARMA21del1_ident'
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'perc_calculator_example.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


Please cite as: 

Cimentada, (2019). perccalc: An R package for estimating percentiles from categorical variables. Journal of Open Source Software, 4(44), 1796, https://doi.org/10.21105/joss.01796
--- finished re-building 'perc_calculator_example.Rmd'

--- re-building 'perc_warning_example.Rmd' using rmarkdown

Please cite as: 

Cimentada, (2019). perccalc: An R package for estimating percentiles from categorical variables. Journal of Open Source Software, 4(44), 1796, https://doi.org/10.21105/joss.01796

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 'perc_warning_example.Rmd'

--- re-building 'pisa_example.Rmd' using rmarkdown

Please cite as: 

Cimentada, (2019). perccalc: An R package for estimating percentiles from categorical variables. Journal of Open Source Software, 4(44), 1796, https://doi.org/10.21105/joss.01796
Quitting from lines 25-29 (pisa_example.Rmd) 
Error: processing vignette 'pisa_example.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'pisa_example.Rmd'

SUMMARY: processing the following file failed:
  'pisa_example.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'vcfR'
performance.curves.plot: no visible global function definition for
  'postscript'
performance.curves.plot: no visible global function definition for
  'axis'
performance.curves.plot: no visible global function definition for
  'lines'
performance.curves.plot: no visible global function definition for
  'legend'
performance.curves.plot: no visible global function definition for
  'grid'
performance.curves.plot: no visible global function definition for
  'dev.off'
precision.recall.curves.plot: no visible global function definition for
  'postscript'
precision.recall.curves.plot: no visible global function definition for
  'axis'
precision.recall.curves.plot: no visible global function definition for
  'lines'
precision.recall.curves.plot: no visible global function definition for
  'legend'
precision.recall.curves.plot: no visible global function definition for
  'grid'
precision.recall.curves.plot: no visible global function definition for
  'dev.off'
Undefined global functions or variables:
  axis dev.off grid legend lines postscript
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "grid", "legend", "lines")
to your NAMESPACE file.
Packages suggested but not available for checking: 'plotly', 'ggpubr'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'dendextendRcpp'
permalgorithm: 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').
Found the following files/directories:
  'permus_per_dist_4' 'permus_per_shape_bin_4_0'
  'permus_per_shape_bin_4_1' 'permus_per_shape_bin_4_2'
  'permus_per_shape_bin_4_3'
Malformed Description field: should contain one or more complete sentences.
ksample.pclt: no visible global function definition for 'pchisq'
pCI: no visible global function definition for 'qbeta'
permKS.formula: no visible global function definition for 'terms'
permTREND.default: no visible global function definition for 'cor'
permTREND.formula: no visible global function definition for 'terms'
permTS.formula: no visible global function definition for 'terms'
trend.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor pchisq pnorm qbeta terms
Consider adding
  importFrom("stats", "cor", "pchisq", "pnorm", "qbeta", "terms")
to your NAMESPACE file.
Rd file 'perm-internal.Rd':
  \usage lines wider than 90 characters:
     ksample.exact.mc(scores, group, nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TRUE)
     trend.exact.mc(scores, group, alternative = "two.sided", nmc = 10^3 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TR ... [TRUNCATED]
     twosample.exact.mc(scores, group, alternative = "two.sided", nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED  ... [TRUNCATED]

Rd file 'perm.Rd':
  \usage lines wider than 90 characters:
     permKS(x, g, exact = NULL, method = NULL, methodRule = methodRuleKS1, control=permControl(), ...)
     permTREND(x, y, alternative = c("two.sided", "less", "greater"), exact = NULL, method = NULL, methodRule = methodRuleTREND1, control=pe ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package required but not available: 'dabestr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'permutes.Rmd' using rmarkdown
Quitting from lines 169-183 (permutes.Rmd) 
Error: processing vignette 'permutes.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'permutes.Rmd'

SUMMARY: processing the following file failed:
  'permutes.Rmd'

Error: Vignette re-building failed.
Execution halted
hasMethod: no visible global function definition for 'getS3method'
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'neural_network-s0000r1000.html' 'neural_network-s1000r1000.html'
  'neural_network-s2000r1000.html' 'neural_network-s3000r1000.html'
Found the following files/directories:
  'Myfile.txt'
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
pGLS: no visible global function definition for 'model.response'
pGLS: no visible global function definition for 'model.matrix'
pGLS: no visible global function definition for 'pt'
Undefined global functions or variables:
  model.matrix model.response pt
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
prepare_Rd: data_fs.Rd:11: Dropping empty section \source
prepare_Rd: var_fs.Rd:12-14: Dropping empty section \references
Found the following files/directories:
  'animation.gif'
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building 'advanced_usage.Rmd' using rmarkdown
Quitting from lines 13-20 (advanced_usage.Rmd) 
Error: processing vignette 'advanced_usage.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'advanced_usage.Rmd'

--- re-building 'huxtable_tips.Rmd' using rmarkdown
Quitting from lines 13-20 (huxtable_tips.Rmd) 
Error: processing vignette 'huxtable_tips.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'huxtable_tips.Rmd'

--- re-building 'pharmaRTF.Rmd' using rmarkdown
Quitting from lines 13-20 (pharmaRTF.Rmd) 
Error: processing vignette 'pharmaRTF.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'pharmaRTF.Rmd'

--- re-building 'tf_from_file.Rmd' using rmarkdown
Quitting from lines 13-21 (tf_from_file.Rmd) 
Error: processing vignette 'tf_from_file.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'tf_from_file.Rmd'

SUMMARY: processing the following files failed:
  'advanced_usage.Rmd' 'huxtable_tips.Rmd' 'pharmaRTF.Rmd'
  'tf_from_file.Rmd'

Error: Vignette re-building failed.
Execution halted
PharmPow_crossover: no visible global function definition for
  'read.table'
PharmPow_crossover: no visible global function definition for
  'write.csv'
PharmPow_crossover: no visible global function definition for 'pdf'
PharmPow_crossover: no visible global function definition for 'dev.off'
PharmPow_parallel: no visible global function definition for
  'read.table'
PharmPow_parallel: no visible global function definition for
  'write.csv'
PharmPow_parallel: no visible global function definition for 'pdf'
PharmPow_parallel: no visible global function definition for 'dev.off'
fig_PharmPow_crossover: no visible global function definition for
  'read.csv'
fig_PharmPow_parallel: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  dev.off pdf read.csv read.table write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "read.csv", "read.table", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  'test.pdf'
Packages required but not available: 'broom', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
fox: no visible binding for global variable 'sd'
fox: no visible global function definition for 'cor'
fox: no visible global function definition for 'interaction.plot'
fox: no visible global function definition for 'reorder'
kang: no visible global function definition for 'var'
kang: no visible binding for global variable 'sd'
kang: no visible global function definition for 'cor'
kang: no visible global function definition for 'interaction.plot'
kang: no visible global function definition for 'reorder'
nahu: no visible global function definition for 'interaction.plot'
nahu: no visible global function definition for 'reorder'
thsu: no visible global function definition for 'median'
thsu: no visible binding for global variable 'sd'
thsu: no visible global function definition for 'cor'
thsu: no visible global function definition for 'interaction.plot'
thsu: no visible global function definition for 'reorder'
Undefined global functions or variables:
  cor interaction.plot median reorder sd var
Consider adding
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
Package required but not available: 'daymetr'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
pheno.ddm: no visible global function definition for 'new'
pheno.flm.fit: no visible binding for global variable 'na.exclude'
pheno.flm.fit: no visible global function definition for 'terms'
pheno.flm.fit: no visible global function definition for 'residuals'
pheno.flm.fit: no visible global function definition for 'qt'
pheno.lad.fit: no visible binding for global variable 'na.exclude'
pheno.mlm.fit: no visible binding for global variable 'na.exclude'
pheno.mlm.fit: no visible global function definition for 'residuals'
Undefined global functions or variables:
  na.exclude new qt residuals terms
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.exclude", "qt", "residuals", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'pheno.mlm.fit.Rd':
  \examples lines wider than 100 characters:
             R <- pheno.mlm.fit(DWD)                                                         # parameter estimation
             summary(tr)$coef[2]                                                                     # slope of trend
             summary(tr)$coef[4]                                                                     # standard error of trend

These lines will be truncated in the PDF manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  '1khz.wav' 'snd.wav'
Package suggested but not available for checking: 'ggspectra'
Running examples in 'photobiologyFilters-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: photobiologyFilters-package
> ### Title: photobiologyFilters: Spectral Transmittance Data for Filters
> ### Aliases: photobiologyFilters photobiologyFilters-package
> 
> ### ** Examples
> 
> library(ggspectra)
Error in library(ggspectra) : there is no package called 'ggspectra'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'user-guide.Rmd' using rmarkdown
Quitting from lines 29-34 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
there is no package called 'ggspectra'
--- failed re-building 'user-guide.Rmd'

SUMMARY: processing the following file failed:
  'user-guide.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'ggspectra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggspectra'
Error(s) in re-building vignettes:
  ...
--- re-building 'user-guide.Rmd' using rmarkdown
News at https://www.r4photobiology.info/
Quitting from lines 30-35 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
there is no package called 'ggspectra'
--- failed re-building 'user-guide.Rmd'

SUMMARY: processing the following file failed:
  'user-guide.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'ggspectra'
Running examples in 'photobiologyLEDs-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: leds.mspct
> ### Title: Spectral irradiance for diverse LEDs
> ### Aliases: leds.mspct
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(photobiology)
> library(ggspectra)
Error in library(ggspectra) : there is no package called 'ggspectra'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'user-guide.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 20-25 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
there is no package called 'ggspectra'
--- failed re-building 'user-guide.Rmd'

SUMMARY: processing the following file failed:
  'user-guide.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'ggspectra'
Error(s) in re-building vignettes:
  ...
--- re-building 'user-guide.Rmd' using rmarkdown
Quitting from lines 35-41 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
there is no package called 'ggspectra'
--- failed re-building 'user-guide.Rmd'

SUMMARY: processing the following file failed:
  'user-guide.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'ggspectra'
Running examples in 'photobiologySensors-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: photobiologySensors-package
> ### Title: photobiologySensors: Spectral Response Data for Light Sensors
> ### Aliases: photobiologySensors photobiologySensors-package
> 
> ### ** Examples
> 
> library(photobiology)
> library(photobiologyWavebands)
> library(ggspectra)
Error in library(ggspectra) : there is no package called 'ggspectra'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'user-guide.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
News at https://www.r4photobiology.info/
For news about 'photobiologySensors', please, see http://www.r4photobiology.info/
For on-line documentation see http://docs.r4photobiology.info/photobiologySensors/
Quitting from lines 30-35 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
there is no package called 'ggspectra'
--- failed re-building 'user-guide.Rmd'

SUMMARY: processing the following file failed:
  'user-guide.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'ggspectra'
Error(s) in re-building vignettes:
  ...
--- re-building 'user-guide.Rmd' using rmarkdown
News at https://www.r4photobiology.info/

Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 30-37 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
there is no package called 'ggspectra'
--- failed re-building 'user-guide.Rmd'

SUMMARY: processing the following file failed:
  'user-guide.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'tidyr'
Running 'testthat.R' [10s/12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(photosynthesis)
  Loading required package: units
  udunits system database from /usr/share/xml/udunits
  > 
  > test_check("photosynthesis")
  -- 1. Error: photosynthesis output has correct dimensions when tealeaves = TRUE 
  there is no package called 'tidyr'
  Backtrace:
    1. photosynthesis::photosynthesis(...)
    2. tealeaves::tleaves(...)
    3. pars %<>% purrr::map_if(~inherits(.x, "units"), drop_units)
   11. tealeaves:::make_parameter_sets(.)
    5. pars %<>% names()
    5. glue::glue("{x} = pars${x}", x = .)
    5. stringr::str_c(., collapse = ", ")
    5. glue::glue("tidyr::crossing({x})", x = .)
    5. base::parse(text = .)
    5. base::eval(.)
   12. purrr::transpose(.)
   22. base::getExportedValue(pkg, name)
   23. base::asNamespace(ns)
   24. base::getNamespace(ns)
   25. base::loadNamespace(name)
   26. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   27. base:::withOneRestart(expr, restarts[[1L]])
   28. base:::doWithOneRestart(return(expr), restart)
  
  == testthat results  ===========================================================
  [ OK: 91 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: photosynthesis output has correct dimensions when tealeaves = TRUE (@test-photosynthesis-crossing.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'photosynthesis-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

Loading required package: units
udunits system database from /usr/share/xml/udunits

Attaching package: 'purrr'

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

    set_names

Quitting from lines 173-219 (photosynthesis-introduction.Rmd) 
Error: processing vignette 'photosynthesis-introduction.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'photosynthesis-introduction.Rmd'

SUMMARY: processing the following file failed:
  'photosynthesis-introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'OutbreakTools'
Package required but not available: 'phylobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'output_values'
Package required but not available: 'RNeXML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'phylobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'adephylo', 'phylobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'phylobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tidyr', 'INLA', 'logistf'
Found the following files/directories:
  'subj_slp_sum.csv' 'wa_ps_V811043_sum.csv'
Packages suggested but not available for checking: 'childsds', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'Everest.Rmd' using rmarkdown
--- finished re-building 'Everest.Rmd'

--- re-building 'IdealWeightComparison.Rmd' using rmarkdown
Quitting from lines 16-43 (IdealWeightComparison.Rmd) 
Error: processing vignette 'IdealWeightComparison.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'IdealWeightComparison.Rmd'

--- re-building 'NeonatalVentilation.Rmd' using rmarkdown
Quitting from lines 21-31 (NeonatalVentilation.Rmd) 
Error: processing vignette 'NeonatalVentilation.Rmd' failed with diagnostics:
there is no package called 'childsds'
--- failed re-building 'NeonatalVentilation.Rmd'

SUMMARY: processing the following files failed:
  'IdealWeightComparison.Rmd' 'NeonatalVentilation.Rmd'

Error: Vignette re-building failed.
Execution halted
incident: no visible global function definition for 'splinefun'
incident: no visible global function definition for 'integrate'
phytoprod: no visible global function definition for 'approx'
phytoprod: no visible global function definition for 'splinefun'
phytoprod: no visible global function definition for 'integrate'
reflectance: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx integrate splinefun
Consider adding
  importFrom("stats", "approx", "integrate", "splinefun")
to your NAMESPACE file.
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File which contains pragma(s) suppressing diagnostics:
  'src/pijavski.cpp'
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
Running examples in 'pinnacle.data-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: USA_Election_2016
> ### Title: USA_Election_2016
> ### Aliases: USA_Election_2016
> ### Keywords: datasets
> 
> ### ** Examples
> 
> if (require("odds.converter")) {
+ library(tidyverse)
+ # What is Hilary Clinton's the highest implied winning probability at Pinnacle?
+ 
+ USA_Election_2016[which.min(USA_Election_2016$MoneyUS1),"EnteredDateTime"]
+ odds.converter::odds.us2prob(min(USA_Election_2016$MoneyUS1))
+ }
Loading required package: odds.converter
Error in library(tidyverse) : there is no package called 'tidyverse'
Execution halted
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building 'pinochet.Rmd' using rmarkdown
Quitting from lines 52-58 (pinochet.Rmd) 
Error: processing vignette 'pinochet.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'pinochet.Rmd'

SUMMARY: processing the following file failed:
  'pinochet.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'modelr', 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building 'Introduction.Rmd' using rmarkdown
Quitting from lines 119-141 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'Introduction.Rmd'

SUMMARY: processing the following file failed:
  'Introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
plot.pred.int: no visible global function definition for 'plot.default'
plot.pred.int: no visible global function definition for 'axis'
plot.pred.int: no visible global function definition for 'box'
plot.pred.int : cidist: no visible global function definition for
  'ecdf'
plot.pred.int : negcidist: no visible global function definition for
  'ecdf'
plot.pred.int : pi.col.fun: no visible global function definition for
  'gray'
plot.pred.int: no visible global function definition for 'segments'
plot.pred.int: no visible global function definition for 'points'
plot.pred.int: no visible global function definition for 'abline'
pred.int: no visible binding for global variable 'sd'
prop.test.mult: no visible global function definition for 'qnorm'
sim.basic: no visible global function definition for 'rbinom'
sim.basic: no visible global function definition for 'rnorm'
t.test.mult: no visible global function definition for 'qt'
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'ggsubplot'
Package required but not available: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
PKmod: no visible global function definition for 'deriv'
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
PKadjust: no visible binding for global variable 'jpeg'
PKadjust: no visible binding for global variable 'bmp'
PKadjust: no visible binding for global variable 'png'
PKadjust: no visible binding for global variable 'tiff'
PKadjust: no visible binding for global variable 'dev.new'
PKadjust: no visible global function definition for 'dev.off'
PKfigure: no visible global function definition for 'dev.cur'
PKfigure: no visible global function definition for 'dev.off'
PKoutput: no visible global function definition for 'heatmap'
PKoutput: no visible global function definition for
  'packageDescription'
PKshow: no visible global function definition for 'browseURL'
addList1: no visible global function definition for 'formula'
addList1.old: no visible global function definition for 'formula'
addList2: no visible global function definition for 'formula'
generate.plot: no visible global function definition for 'dev.off'
writeHTML: no visible global function definition for
  'packageDescription'
writeLst: no visible global function definition for
  'packageDescription'
writeLst.tab: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for 'quantile'
initialize,nonmem: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  'Indometh_Bolus_Linear_CoreOutput.txt'
  'Indometh_Bolus_Log_CoreOutput.txt'
  'Indometh_Infusion_Linear_CoreOutput.txt'
  'Indometh_Infusion_Log_CoreOutput.txt' 'Output'
  'Theoph_Linear_CoreOutput.txt' 'Theoph_Log_CoreOutput.txt'
Packages suggested but not available for checking:
  'BayesMallows', 'BradleyTerryScalable', 'PLMIX'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
bwfw.hmm: no visible global function definition for 'dnorm'
bwfw1.hmm: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Rd file 'em.hmm.Rd':
  \examples lines wider than 100 characters:
     #all.Rlts=cbind(rbind(chr1.data,chr6.data), LIS=c(chr1.L2rlts$LIS,chr6.L2rlts$LIS), gFDR=plis.rlts$aLIS, fdr001state=plis.rlts$States)

These lines will be truncated in the PDF manual.
Package required but not available: 'ggmcmc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'Formula' 'sm'
  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: 'clubSandwich'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'plotly'
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
plotAuto: no visible global function definition for 'window'
plotAuto: no visible global function definition for 'title'
plotAuto: no visible global function definition for 'axis'
plotAuto: no visible global function definition for 'box'
plotCumu: no visible global function definition for 'title'
plotCumu: no visible global function definition for 'axis'
plotCumu: no visible global function definition for 'box'
plotDens : panel.dens: no visible global function definition for 'var'
plotDens : panel.dens: no visible global function definition for
  'quantile'
plotDens : panel.dens: no visible global function definition for
  'median'
plotDens: no visible global function definition for 'tail'
plotQuant: no visible global function definition for 'par'
plotQuant: no visible binding for global variable 'quantile'
plotQuant: no visible global function definition for 'lines'
plotQuant: no visible global function definition for 'bxp'
plotQuant: no visible global function definition for 'matplot'
plotQuant: no visible global function definition for 'axis'
plotQuant: no visible global function definition for 'box'
plotQuant: no visible global function definition for 'title'
plotSplom: no visible global function definition for 'pairs'
plotTrace : panel.trace: no visible global function definition for
  'var'
plotTrace : panel.trace: no visible global function definition for
  'median'
plotTrace: no visible global function definition for 'tail'
Undefined global functions or variables:
  axis box bxp lines matplot median pairs par quantile tail title var
  window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
generateEnvelope: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Rd file 'envelopeArea_and_Perimeter.Rd':
  \examples lines wider than 100 characters:
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")

Rd file 'generateEnvelope.Rd':
  \examples lines wider than 100 characters:
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")
     grid.polygon(envelopeXY[,1], envelopeXY[,2], gp=gpar(fill="pink", col="transparent", lwd=5), default.units="npc")

Rd file 'tangentLine.Rd':
  \examples lines wider than 100 characters:
                     tangent <- tangentLine(centers[1,], centers[2,], r0, r[2], k=k)  # compute coefficients for the tangent line, if NA, th ... [TRUNCATED]
                             grid.abline(-tangent["c"] / tangent["b"], -tangent["a"] / tangent["b"], gp=gpar(col="blue", lwd=ii), units="npc ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
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.
llla.bi: no visible global function definition for 'as.formula'
llla.bi: no visible global function definition for 'glm'
llla.bi: no visible global function definition for 'binomial'
llla.bi: no visible binding for global variable 'logit'
llla.bi: no visible global function definition for 'vcov'
llla.bi: no visible global function definition for 'coef'
llla.mc: no visible global function definition for 'model.matrix'
llla.mc: no visible global function definition for 'as.formula'
llla.mc: no visible global function definition for 'coxph'
llla.mc: no visible global function definition for 'vcov'
llla.mc: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'as.formula'
llla.mle: no visible global function definition for 'glm'
llla.mle: no visible global function definition for 'poisson'
llla.mle: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'vcov'
mclgen: no visible global function definition for 'reshape'
simRasch.1D: no visible global function definition for 'rnorm'
simRasch.1D: no visible global function definition for 'runif'
vcov.sandwich.glm: no visible global function definition for
  'model.matrix'
vcov.sandwich.glm: no visible global function definition for 'weights'
vcov.sandwich.glm: no visible global function definition for
  'residuals'
vcov.sandwich.glm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
Package suggested but not available for checking: 'mixOmics'
Running examples in 'PLSbiplot1-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Mag.Bmat.plot
> ### Title: Magnitude of the Partial Least Squares Regression (PLSR)
> ###   coefficients matrix
> ### Aliases: Mag.Bmat.plot
> 
> ### ** Examples
> 
> if(require(pls))
+ data(oliveoil, package="pls")
Loading required package: pls

Attaching package: 'pls'

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

    loadings

> X = as.matrix(oliveoil$chemical, ncol=5)
> dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Acidity","Peroxide","K232","K270","DK")))
> Y = as.matrix(oliveoil$sensory, ncol=6)
> dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
> Mag.Bmat.plot(X, Y, algorithm=mod.SIMPLS, A=2)
> 
> #nutrimouse data
> if(require(mixOmics))
+ data(nutrimouse, package="mixOmics")
Loading required package: mixOmics
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'mixOmics'
> X1 = as.matrix(nutrimouse$lipid, ncol=21)
Error in as.matrix(nutrimouse$lipid, ncol = 21) : 
  object 'nutrimouse' not found
Execution halted
Package suggested but not available for checking: 'plspm'
Packages required but not available: 'parsnip', 'mixOmics', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mixOmics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package vignette with placeholder title 'Vignette Title':
  'introduction.Rmd'
print.densityEHpi: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Rd file 'predict.plus.Rd':
  \examples lines wider than 100 characters:
     extracted.values <- predict(object, lam = sort(object$lam.path[1:10],decreasing=TRUE), newx=object$x)

These lines will be truncated in the PDF manual.
Packages required but not available: 'bupaR', 'petrinetR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
.MCM: no visible global function definition for 'runif'
.MCM: no visible global function definition for 'rmultinom'
.MCM: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'optimize'
.MCM : f: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'alarm'
.igpark: no visible global function definition for 'kmeans'
.loglik: no visible global function definition for 'mahalanobis'
.plot.gpcm: no visible global function definition for 'lines'
.plot.gpcm: no visible global function definition for 'legend'
.rwgpar: no visible global function definition for 'rexp'
.weights: no visible global function definition for 'mahalanobis'
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize rexp rmultinom runif
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'MSnbase'
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'caret', 'rattle'
Running examples in 'pmml-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pmml.hclust
> ### Title: Generate the PMML representation for a hclust object from the
> ###   package 'amap'.
> ### Aliases: pmml.hclust
> 
> ### ** Examples
> 
> 
> # Cluster the 4 numeric variables of the iris dataset.
> library(amap)
> library(rattle)
Error in library(rattle) : there is no package called 'rattle'
Execution halted
Running 'testthat.R' [45s/47s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pmml, quietly = T)
  > 
  > test_check("pmml")
  -- 1. Error: (unknown) (@test_pmml.hclust.R#2)  --------------------------------
  there is no package called 'rattle'
  Backtrace:
   1. base::library(rattle)
  
  [01:04:40] WARNING: amalgamation/../src/objective/regression_obj.cu:170: reg:linear is now deprecated in favor of reg:squarederror.
  -- 2. Error: (unknown) (@test_schema_validation.R#7)  --------------------------
  there is no package called 'caret'
  Backtrace:
   1. base::library(caret)
  
  == testthat results  ===========================================================
  [ OK: 257 | SKIPPED: 3 | WARNINGS: 13 | FAILED: 2 ]
  1. Error: (unknown) (@test_pmml.hclust.R#2) 
  2. Error: (unknown) (@test_schema_validation.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
dbm: no visible global function definition for 'optim'
dbm: no visible global function definition for 'new'
destat: no visible global function definition for 'weighted.mean'
local.knn: no visible global function definition for 'sd'
local.knn: no visible global function definition for 'optim'
mdpref: no visible global function definition for 'sd'
mdpref: no visible global function definition for 'text'
mdpref: no visible global function definition for 'lines'
phicom: no visible global function definition for 'optim'
phicom: no visible global function definition for 'new'
pl: no visible global function definition for 'optim'
pl: no visible global function definition for 'new'
rol: no visible global function definition for 'nlm'
rol: no visible global function definition for 'new'
wdbm: no visible global function definition for 'optim'
wdbm: no visible global function definition for 'new'
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: 'tidyverse'
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for 'pnorm'
pnmtrem1: no visible global function definition for 'dnorm'
pnmtrem1: no visible global function definition for 'ginv'
pnmtrem1 : fun: no visible global function definition for 'pnorm'
pnmtrem1 : derf: no visible global function definition for 'dnorm'
pnmtrem1 : derf: no visible global function definition for 'pnorm'
pnmtrem1 : fun: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  'TODO.md'
'library' or 'require' call to 'rgenoud' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
smooth: no visible global function definition for 'genoud'
Undefined global functions or variables:
  genoud
Package required but not available: 'logistf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bipoilogMLE: no visible global function definition for 'optim'
bipoilogMLE: no visible global function definition for 'write.table'
poilogMLE: no visible global function definition for 'optim'
rbipoilog : sim: no visible global function definition for 'rnorm'
rbipoilog : sim: no visible global function definition for 'rpois'
rpoilog : sim: no visible global function definition for 'rnorm'
rpoilog : sim: no visible global function definition for 'rpois'
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
approxMargMLE: no visible global function definition for 'optim'
approxMargMLECI : ciFunction: no visible global function definition for
  'qchisq'
approxMargMLECI: no visible global function definition for 'uniroot'
margMLE: no visible global function definition for 'optim'
margMLECI: no visible global function definition for 'optim'
margMLECI : unNormLikeMinusVal: no visible global function definition
  for 'qchisq'
margMLECI: no visible global function definition for 'uniroot'
profMLECI : ciFunction: no visible global function definition for
  'qchisq'
profMLECI: no visible global function definition for 'uniroot'
rtbinom: no visible global function definition for 'rbinom'
rtpois: no visible global function definition for 'rpois'
waldCI: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
Installation failed.
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/poismf.Rcheck/00install.out' for details.
Packages required but not available: 'parsnip', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Packages in Depends field not imported from:
  'combinat' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for 'quantile'
PS.FDR: no visible global function definition for 'quantile'
Permu.Ind: no visible global function definition for 'permn'
Permu.Ind: no visible global function definition for 'hcube'
Trans.Data: no visible global function definition for 'write.table'
Trans.Data: no visible global function definition for 'predict'
Trans.Data: no visible global function definition for 'lm'
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  'pow.txt'
rpoistweedie: no visible global function definition for 'runif'
testOmegaPT: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: poistweedie.Rd:51: Dropping empty section \references
prepare_Rd: ppoistweedie.Rd:37: Dropping empty section \references
prepare_Rd: qpoistweedie.Rd:40: Dropping empty section \references
prepare_Rd: rpoistweedie.Rd:36: Dropping empty section \references
prepare_Rd: varpt.Rd:31: Dropping empty section \references
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'MASS' 'scatterplot3d'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for 'layout'
plot.poLCA: no visible global function definition for 'par'
poLCA: no visible global function definition for 'model.frame'
poLCA: no visible global function definition for 'model.response'
poLCA: no visible global function definition for 'model.matrix'
poLCA: no visible global function definition for 'runif'
poLCA: no visible global function definition for 'ginv'
poLCA: no visible global function definition for 'flush.console'
poLCA.makeplot.dich: no visible global function definition for
  'scatterplot3d'
poLCA.makeplot.poly: no visible global function definition for
  'scatterplot3d'
poLCA.se: no visible global function definition for 'ginv'
poLCA.simdata: no visible global function definition for 'runif'
poLCA.simdata: no visible global function definition for 'rnorm'
poLCA.table: no visible global function definition for 'model.frame'
print.poLCA: no visible global function definition for 'pt'
print.poLCA: no visible global function definition for 'flush.console'
rmulti: no visible global function definition for 'runif'
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Package suggested but not available for checking: 'DiagrammeR'
Package required but not available: 'weights'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'textclean'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'gdd.Rmd' using rmarkdown
Quitting from lines 25-28 (gdd.Rmd) 
Error: processing vignette 'gdd.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'gdd.Rmd'

--- re-building 'intro.Rmd' using rmarkdown
--- finished re-building 'intro.Rmd'

SUMMARY: processing the following file failed:
  'gdd.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'pollimetrydata'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'examples.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 17-22 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'examples.Rmd'

SUMMARY: processing the following file failed:
  'examples.Rmd'

Error: Vignette re-building failed.
Execution halted
qPolyaAeppliSingle: no visible global function definition for 'qgamma'
rPolyaAeppli: no visible global function definition for 'rpois'
rPolyaAeppli: no visible global function definition for 'rgeom'
Undefined global functions or variables:
  qgamma rgeom rpois
Consider adding
  importFrom("stats", "qgamma", "rgeom", "rpois")
to your NAMESPACE file.
Found the following files/directories:
  'polyfreqs-mcmc.out'
Package required but not available: 'MDSMap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package vignette with placeholder title 'Vignette Title':
  'polynomials.Rmd'
Package required but not available: 'mixOmics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'SPAGfreqExample2.txt' 'SpagInputExample.txt' 'SpagOutExample.txt'
  'SpagTemp.txt' 'TetrasatExample.txt' 'atetraexample.txt'
  'atetratest.txt' 'exampleGMoutput.txt' 'forPOPDIST.txt'
  'genodiveExample.txt' 'readGMtest.txt' 'strtemp.txt' 'structtest.txt'
  'testGenoDive2.txt' 'testGenoDive3.txt' 'testPOPDIST.txt'
  'tetrasattest.txt'
Found the following files/directories:
  'test-data.R' 'test-inits.R' 'test.bug' 'test.cmd'
Package required but not available: 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Running examples in 'pomp-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bsflu
> ### Title: Influenza outbreak in a boarding school
> ### Aliases: bsflu
> 
> ### ** Examples
> 
> library(magrittr)
> library(tidyr)
Error in library(tidyr) : there is no package called 'tidyr'
Execution halted
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'matrixcalc' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'matrixcalc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for 'pnorm'
print.pom: no visible global function definition for 'pnorm'
siteocc : get.mod.matrix: no visible binding for global variable
  'na.pass'
siteocc : get.mod.matrix: no visible global function definition for
  'formula'
siteocc : get.mod.matrix: no visible global function definition for
  'model.matrix'
siteocc: no visible global function definition for 'nlminb'
siteocc: no visible global function definition for
  'is.positive.definite'
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  'extdata'
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'popgen.Rd':
  \usage lines wider than 90 characters:
     popgen(datafile, ndigit = 3, freq.overall = T, freq.by.pop = T, genetic.stats = T, pairwise.fst = T)

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: 'WhopGenome'
asymmetricIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'lm'
bonferroniIntervals: no visible global function definition for
  'predict'
bootstrapIntervals: no visible global function definition for 'stack'
component1a: no visible global function definition for 'pnorm'
component1b: no visible global function definition for 'pnorm'
component2: no visible global function definition for 'dgamma'
eqnForMin: no visible global function definition for 'pnorm'
eqnForMin: no visible global function definition for 'integrate'
integrand : <anonymous>: no visible global function definition for
  'pnorm'
integrand: no visible global function definition for 'dnorm'
integrate2: no visible global function definition for 'integrate'
integrate2a: no visible global function definition for 'integrate'
integrate2b: no visible global function definition for 'integrate'
integrate4a: no visible global function definition for 'integrate'
integrate4b: no visible global function definition for 'integrate'
optimalCScalar2: no visible global function definition for 'uniroot'
optimalLambda: no visible global function definition for 'optimise'
optimalLambdaC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dgamma dnorm integrate lm optimise pnorm predict stack uniroot
Consider adding
  importFrom("stats", "dgamma", "dnorm", "integrate", "lm", "optimise",
             "pnorm", "predict", "uniroot")
  importFrom("utils", "stack")
to your NAMESPACE file.
Package required but not available: 'timetk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'rMorningStar', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggfortify'
Packages required but not available: 'tidyr', 'naniar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'ggpubr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
fnfam: no visible global function definition for 'qnorm'
fx: no visible global function definition for 'qnorm'
normplot : <local> : replot: no visible global function definition for
  'qnorm'
normplot : <local> : replot: no visible global function definition for
  'pnorm'
normplot : <local> : replot: no visible global function definition for
  'dnorm'
normplot : <local> : replot: no visible global function definition for
  'points'
normplot : <local> : replot: no visible global function definition for
  'lines'
normplot : <local> : regen: no visible global function definition for
  'rnorm'
normplot : <local> : regen: no visible global function definition for
  'rexp'
nsibs: no visible global function definition for 'qnorm'
ntdt: no visible global function definition for 'uniroot'
plotNtdt: no visible global function definition for 'lines'
plotNtdt: no visible global function definition for 'legend'
ptdt: no visible global function definition for 'optimize'
ptdt: no visible global function definition for 'uniroot'
ptdt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm legend lines optimize pnorm points qnorm rexp rnorm uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Package suggested but not available for checking: 'factoextra'
Error(s) in re-building vignettes:
  ...
--- re-building 'fcm.Rmd' using rmarkdown
Quitting from lines 45-48 (fcm.Rmd) 
Error: processing vignette 'fcm.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building 'fcm.Rmd'

--- re-building 'upfc.Rmd' using rmarkdown
Quitting from lines 46-49 (upfc.Rmd) 
Error: processing vignette 'upfc.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building 'upfc.Rmd'

SUMMARY: processing the following files failed:
  'fcm.Rmd' 'upfc.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'Quad1.RData' 'Sp Env Data.RData' 'Sp PPM Data.RData'
  'SpEnvData.RData' 'Test.RData' 'TestPPM.RData' 'TestSP.RData'
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
pps1: no visible global function definition for 'runif'
ppss: no visible global function definition for 'runif'
ppswr: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: calif.Rd:5-6: Dropping empty section \arguments
prepare_Rd: calif.Rd:8-9: Dropping empty section \examples
prepare_Rd: califcty.Rd:5-6: Dropping empty section \arguments
prepare_Rd: califcty.Rd:8-9: Dropping empty section \examples
prepare_Rd: sizesok.Rd:12-13: Dropping empty section \examples
prepare_Rd: stratumsizes.Rd:11-12: Dropping empty section \examples
Malformed Description field: should contain one or more complete sentences.
LDA.Tree : Find.proj: no visible binding for global variable 'var'
LDA.Tree : Find.proj: no visible binding for global variable 'IQR'
LDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'var'
PDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.Tree : Find.proj: no visible binding for global variable 'var'
PP.Tree : Find.proj: no visible binding for global variable 'median'
PP.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.optimize.Huber: no visible binding for global variable 'sd'
PP.optimize.anneal: no visible binding for global variable 'sd'
PP.optimize.plot: no visible binding for global variable 'sd'
PP.optimize.plot: no visible global function definition for 'hist'
PP.optimize.plot: no visible global function definition for 'text'
PP.optimize.plot: no visible global function definition for 'par'
PP.optimize.plot: no visible global function definition for 'colors'
PP.optimize.plot: no visible global function definition for 'pairs'
PP.optimize.random: no visible binding for global variable 'sd'
Undefined global functions or variables:
  IQR colors hist median pairs par sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
Package suggested but not available for checking: 'doBy'
Malformed Title field: should not end in a period.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  'dev'
Malformed Description field: should contain one or more complete sentences.
TT.test : <anonymous>: no visible global function definition for
  't.test'
TT.test: no visible binding for global variable 'sd'
TT.test: no visible global function definition for 'setNames'
kirjelda : combo: no visible binding for global variable 'sd'
kor.tabel: no visible binding for global variable 'cor.test'
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
PKG_CXXFLAGS set in 'src/Makevars.win' without any corresponding files
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'escalation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggiraphExtra', 'modelr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking:
  'caret', 'ffbase'
Malformed Description field: should contain one or more complete sentences.
gausspred: no visible global function definition for 'qt'
mvapred: no visible global function definition for 'qt'
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
Packages required but not available: 'tidyverse', 'rattle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  'DESCRIPTION.bck'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'predmixcor/R/firstlib.r':
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

Predict.mix: no visible global function definition for 'dbinom'
abs_cor: no visible global function definition for 'cor'
gen.alpha.IGamma: no visible global function definition for 'qgamma'
gendata.mix: no visible global function definition for 'runif'
gendata.mix: no visible global function definition for 'rbeta'
mh1.unif: no visible global function definition for 'runif'
train_predict_mix: no visible global function definition for 'dbinom'
training: no visible global function definition for 'runif'
training: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'psycho'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Non-standard file/directory found at top level:
  'COPYRIGHTS'
Copyright information should be in file inst/COPYRIGHTS
Found the following files/directories:
  'hista.png' 'plotcd.png' 'test.R' 'test.html' 'testR2html.R'
  'testglm.csv' 'testglm.html' 'testglm.tab'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'tidyr'
basisplot: no visible global function definition for 'abline'
basisplot: no visible global function definition for 'text'
basisplot: no visible global function definition for 'par'
plot.prinsimp: no visible global function definition for 'screeplot'
plot.simpart: no visible global function definition for 'par'
position_text: no visible global function definition for 'par'
position_text: no visible global function definition for 'strwidth'
simpart.formula: no visible global function definition for 'terms'
simpart.formula: no visible global function definition for
  'model.matrix'
varperc: no visible global function definition for 'lines'
varperc: no visible global function definition for 'text'
varsimp: no visible global function definition for 'points'
varsimp: no visible global function definition for 'text'
varsimp: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline lines model.matrix par points screeplot strwidth terms text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "points", "strwidth",
             "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package vignette with placeholder title 'Vignette Title':
  'priorcd.Rmd'
Found the following files/directories:
  'network.html' 'network_files'
Package suggested but not available for checking: 'gurobi'
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
pr.conditional: no visible global function definition for 'qnorm'
pr.marginal: no visible global function definition for 'qnorm'
prLogisticDelta: no visible global function definition for 'glm'
prLogisticDelta: no visible binding for global variable 'binomial'
Undefined global functions or variables:
  binomial glm qnorm
Consider adding
  importFrom("stats", "binomial", "glm", "qnorm")
to your NAMESPACE file.
Packages suggested but not available for checking: 'parsnip', 'rsample'
Error(s) in re-building vignettes:
  ...
--- re-building 'equivocal-zones.Rmd' using rmarkdown

Attaching package: 'probably'

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

    as.factor, as.ordered


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 'equivocal-zones.Rmd'

--- re-building 'where-to-use.Rmd' using rmarkdown
Quitting from lines 29-46 (where-to-use.Rmd) 
Error: processing vignette 'where-to-use.Rmd' failed with diagnostics:
there is no package called 'parsnip'
--- failed re-building 'where-to-use.Rmd'

SUMMARY: processing the following file failed:
  'where-to-use.Rmd'

Error: Vignette re-building failed.
Execution halted
.pfda.fstep: no visible global function definition for 'dist'
.pfda.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov dist
Consider adding
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
prepare_Rd: ProbForecastGOP-package.Rd:42-43: Dropping empty section \seealso
Rd file 'Emp.variog.Rd':
  \usage lines wider than 90 characters:
     Emp.variog(day, obs, forecast, id, coord1, coord2, cut.points=NULL, max.dist=NULL, nbins=300)

Rd file 'EmpDir.variog.Rd':
  \usage lines wider than 90 characters:
     EmpDir.variog(day, obs, forecast, id, coord1, coord2, tol.angle1=45, tol.angle2=135, cut.points=NULL, max.dist=NULL, nbins=300, type) 
  \examples lines wider than 100 characters:
     plot(dir.variog$bin.midpoints,dir.variog$dir.variog,xlab="Distance",ylab="Semi-variance",main="Empirical Directional variogram")

Rd file 'Field.sim.Rd':
  \usage lines wider than 90 characters:
     Field.sim(obs, forecast, coord1.grid, coord2.grid, forecast.grid,variog.model="exponential", param.est, n.sim=99, n.displ=4, 

Rd file 'avg.variog.Rd':
  \examples lines wider than 100 characters:
     variogram <- avg.variog(day=day, coord1=coord1,coord2=coord2,id=id,variable=obs,cut.points=NULL,max.dist=NULL,nbins=NULL) 
     plot(variogram$bin.midpoints,variogram$empir.variog,xlab="Distance", ylab="Semi-variance",main="Empirical variogram")

Rd file 'avg.variog.dir.Rd':
  \examples lines wider than 100 characters:
     dir.variog <- avg.variog.dir(day,coord1,coord2,id,variable=obs, tol.angle1=NULL,tol.angle2=NULL,cut.points=NULL,max.dist=NULL, nbins=NU ... [TRUNCATED]
     plot(dir.variog$bin.midpoints,dir.variog$dir.variog,xlab="Distance", ylab="Semi-variance",main="Empirical Directional variogram")

Rd file 'linesmodel.Rd':
  \examples lines wider than 100 characters:
     lines(variogram$bin.midpoints,linesmodel(distance=variogram$bin.midpoints,variog.model="exponential",param=c(param.variog$nugget,

These lines will be truncated in the PDF manual.
Packages required but not available:
  'bupaR', 'processmapR', 'tidyr', 'DiagrammeR'

Package suggested but not available for checking: 'edeaR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bupaR', 'edeaR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bupaR', 'edeaR', 'DiagrammeR', 'plotly', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bupaR', 'edeaR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rrtable', 'tidyr', 'predict3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
GPois: no visible global function definition for 'dnorm'
GPois: no visible binding for global variable 'poisson'
GPois: no visible global function definition for 'predict'
GPois: no visible global function definition for 'fitted'
GPois: no visible global function definition for 'residuals'
GPois: no visible global function definition for 'smooth.spline'
ProDenICA: no visible global function definition for 'rnorm'
d.gaussmix: no visible global function definition for 'dnorm'
djordan: no visible global function definition for 'dt'
djordan: no visible global function definition for 'dunif'
mixmat: no visible global function definition for 'rnorm'
mixmat: no visible global function definition for 'runif'
r.gaussmix: no visible global function definition for 'rmultinom'
r.gaussmix: no visible global function definition for 'rnorm'
rjordan: no visible global function definition for 'rt'
rjordan: no visible global function definition for 'runif'
rmix.dexp: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm dt dunif fitted poisson predict residuals rmultinom rnorm rt
  runif smooth.spline
Consider adding
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking: 'dm', 'DiagrammeR'
Packages in Depends field not imported from:
  'splines' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IndividualPROC: no visible global function definition for 'survfit'
IndividualPROC: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile survfit
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Packages required but not available: 'ggpubr', 'prophet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'plotly', 'SDMTools'
addpi: no visible global function definition for 'lines'
genPerms: no visible global function definition for 'combn'
getVar: no visible global function definition for 'glm'
getVar: no visible global function definition for 'binomial'
getVar: no visible global function definition for 'var'
pba: no visible global function definition for 'glm'
pba: no visible global function definition for 'binomial'
pba: no visible global function definition for 'predict'
pba: no visible global function definition for 'rbinom'
pcr: no visible global function definition for 'quantile'
plotpi: no visible global function definition for 'axis'
plotpi: no visible global function definition for 'abline'
plotpi: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline axis binomial combn glm lines predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: 'resemble'
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addIonSatistics: no visible binding for global variable 'median'
adjustOne: no visible binding for global variable 'median'
attachModifications: no visible global function definition for
  'na.omit'
avrgLoadingCalculation: no visible binding for global variable 'median'
channelResponses : estimate: no visible binding for global variable
  'var'
responseStatisics : func: no visible global function definition for
  'aggregate'
testing: no visible global function definition for 'aov'
testingOneshot: no visible global function definition for 'anova'
testingTukey: no visible global function definition for 'TukeyHSD'
Undefined global functions or variables:
  TukeyHSD aggregate anova aov median na.omit var
Consider adding
  importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "median",
             "na.omit", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'class' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'class'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addcircle: no visible global function definition for 'lines'
addclassifierboundary: no visible global function definition for 'par'
addclassifierboundary: no visible global function definition for
  'contour'
plot.protoclass: no visible global function definition for 'box'
plot.protoclass: no visible global function definition for 'rgb2hsv'
plot.protoclass: no visible global function definition for 'col2rgb'
plot.protoclass: no visible global function definition for 'points'
plot.protoclass: no visible global function definition for 'hsv'
predict.protoclass: no visible global function definition for 'knn1'
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "points")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  'doc'
Extract_plant_grapevine_function: 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.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
Package vignette with placeholder title 'Vignette Title':
  'TargetDecoyFDR_Example.Rmd'
Package in Depends field not imported from: 'rpart'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mahalanobisComposite: no visible global function definition for
  'princomp'
prepareComposite: no visible global function definition for 'cov'
winsorizor : f: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cov princomp quantile
Consider adding
  importFrom("stats", "cov", "princomp", "quantile")
to your NAMESPACE file.
Package required but not available: 'doBy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'miceadds', 'rsample', 'tidyr', 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package vignette with placeholder title 'Vignette Title':
  'PSF_vignette.Rmd'
Malformed Description field: should contain one or more complete sentences.
candidate.overlap: no visible global function definition for
  'write.table'
fisher: no visible global function definition for 'fisher.test'
fisher.iteration: no visible global function definition for
  'download.file'
fisher.iteration: no visible global function definition for
  'read.table'
pSI.list: no visible global function definition for 'write.table'
specificity.index: no visible global function definition for 'png'
specificity.index: no visible global function definition for 'par'
specificity.index: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off download.file fisher.test par png read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par")
  importFrom("stats", "fisher.test")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  'gene_count_1.csv'
'library' or 'require' call to 'numDeriv' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for 'grad'
test.problem: no visible global function definition for 'new'
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for 'new'
show,test.result: no visible global function definition for 'show'
show,test.result: no visible global function definition for 'sd'
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pspearman: no visible global function definition for 'pt'
spearman.test: no visible global function definition for
  'complete.cases'
spearman.test: no visible global function definition for 'cor'
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  'orig'
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'EffectsRelBaseline' 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable 'sumSqCat'
compExclusionFraction: no visible global function definition for
  'rpois'
compExclusionFraction: no visible global function definition for
  't.test'
compExclusionFraction: no visible global function definition for 'glm'
compExclusionFraction: no visible global function definition for
  'anova'
compPowerCatSelectivity: no visible binding for global variable
  'fRatioStat'
compPowerGeneralRespDetection: no visible binding for global variable
  'sumSqCat'
compPowerRespDetection: no visible binding for global variable
  'sumSqCat'
compRejectionFraction: no visible global function definition for
  'rpois'
compRejectionFraction: no visible global function definition for
  't.test'
compRejectionFraction: no visible global function definition for 'glm'
compRejectionFraction: no visible global function definition for
  'anova'
simCatResp: no visible global function definition for 'rpois'
simNormCatResp: no visible global function definition for 'rnorm'
testCatEffectBoot: no visible global function definition for 'boot'
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'multilevel' 'nlme'
A package should be listed in only one of these fields.
Non-standard file/directory found at top level:
  'README.txt'
'library' or 'require' calls to packages already attached by Depends:
  'multilevel' 'nlme'
  Please remove these calls from your code.
Packages required but not available: 'qgraph', 'tidyr'

Packages suggested but not available for checking:
  'semPlot', 'graphicalVAR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggmap'
Output for data("psyo_rounds_map", package = "psyosphere"):
  Warning: namespace 'ggmap' is not available and has been replaced
  by .GlobalEnv when processing object 'psyo_rounds_map'
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'DiagrammeR'
Running examples in 'psyverse-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_graph_theme
> ### Title: Apply multiple DiagrammeR global graph attributes
> ### Aliases: apply_graph_theme
> 
> ### ** Examples
> 
> exampleSpec <-
+   system.file("inst",
+               "extdata",
+               "example_dct_spec_1.dct",
+               package="psyverse");
> parsedSpecs <- load_dct_specs(exampleSpec);
> dctGraph <- parsedSpecs$output$basic_graph;
> dctGraph <- apply_graph_theme(dctGraph,
+                               c("color", "#0000AA", "node"),
+                               c("fillcolor", "#00FFFF", "node"));
Error: This function applies graph themes to a `DiagrammeR` object. Therefore, obviously, that object must first exist, and you need the `DiagrammeR` package to create it and work with it. Please install it using:

  install.packages('DiagrammeR');
Execution halted
Running 'testthat.R' [2s/2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > require(testthat);
  Loading required package: testthat
  > testthat::test_check("psyverse");
  Loading required package: psyverse
  -- 1. Error: a dct specification from a file with a single dct specification is 
  $ operator is invalid for atomic vectors
  Backtrace:
   1. testthat::expect_equal(...)
   2. testthat::quasi_label(enquo(object), label, arg = "object")
   3. rlang::eval_bare(expr, quo_get_env(quo))
  
  -- 2. Error: a directory with dct specifications is loaded correctly (@test-load
  $ operator is invalid for atomic vectors
  Backtrace:
   1. testthat::expect_equal(...)
   2. testthat::quasi_label(enquo(object), label, arg = "object")
   3. rlang::eval_bare(expr, quo_get_env(quo))
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: a dct specification from a file with a single dct specification is loaded correctly (@test-loading-dct-specs-from-files.R#16) 
  2. Error: a directory with dct specifications is loaded correctly (@test-loading-dct-specs-from-files.R#46) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plotly'
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'R.utils' 'rmeta'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChisqTest_expect: no visible global function definition for 'pchisq'
plot_chase_observed_expected: no visible global function definition for
  'meta.MH'
plot_chase_observed_expected: no visible global function definition for
  'txtProgressBar'
plot_chase_observed_expected: no visible global function definition for
  'setTxtProgressBar'
test.one.treated: no visible global function definition for
  'fisher.test'
test_one: no visible global function definition for 'rbinom'
test_one: no visible global function definition for 'fisher.test'
Undefined global functions or variables:
  fisher.test meta.MH pchisq rbinom setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "fisher.test", "pchisq", "rbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages required but not available: 'ggformula', 'sjPlot'

Packages suggested but not available for checking:
  'broom', 'ggfortify', 'ggpubr', 'mosaic', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'bibliometrix'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'VWPre', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
PurBayes: no visible global function definition for 'update'
PurBayes: no visible global function definition for 'sd'
plot.PurBayes: no visible global function definition for 'quantile'
plot.PurBayes: no visible global function definition for 'lines'
summary.PurBayes : <anonymous>: no visible global function definition
  for 'quantile'
Undefined global functions or variables:
  lines quantile sd update
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
CandidateBio.getBio : <anonymous>: no visible global function
  definition for 'na.omit'
Committee.getCommittee : <anonymous>: no visible global function
  definition for 'na.omit'
getAllBios: no visible global function definition for 'txtProgressBar'
getAllBios: no visible global function definition for
  'setTxtProgressBar'
getAllLocalOfficials: no visible global function definition for
  'txtProgressBar'
getAllLocalOfficials: no visible global function definition for
  'setTxtProgressBar'
getAllVotes: no visible global function definition for 'txtProgressBar'
getAllVotes: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  na.omit setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages required but not available: 'ggmap', 'openair', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.grid.matrix: no visible global function definition for 'slot'
.matrix2grid: no visible global function definition for 'as'
.poly2grid: no visible global function definition for 'is'
.poly2grid: no visible global function definition for 'slot'
.poly2grid: no visible global function definition for 'as'
.pycno.core : smooth2D : s1d: no visible global function definition for
  'filter'
.pycno.core: no visible global function definition for 'flush.console'
.pycno2matrix: no visible global function definition for 'slot'
Undefined global functions or variables:
  as filter flush.console is slot
Consider adding
  importFrom("methods", "as", "is", "slot")
  importFrom("stats", "filter")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  'exampleplot_1_blockdist_1.png' 'exampleplot_1_blockdist_2.png'
  'exampleplot_1_blockdist_3.png' 'exampleplot_1_bootdist.png'
  'exampleplot_1_dist.png' 'exampleplot_1_histogramtest_EMD.png'
  'exampleplot_1_roc_dynamic.png' 'exampleplot_1_slidedist_1.png'
  'exampleplot_1_slidedist_2.png' 'exampleplot_1_slidedist_3.png'
  'exampleplot_1_trimmeddist.png' 'exampleplot_blockdist_1.png'
  'exampleplot_blockdist_2.png' 'exampleplot_blockdist_3.png'
  'exampleplot_bootdist.png' 'exampleplot_dist.png'
  'exampleplot_lim_dyn.png' 'exampleplot_lim_sig.png'
  'exampleplot_lim_sta.png' 'exampleplot_noc.png'
  'exampleplot_roc_dyn.png' 'exampleplot_roc_sta.png'
  'exampleplot_slidedist_1.png' 'exampleplot_slidedist_2.png'
  'exampleplot_slidedist_3.png' 'exampleplot_trimmeddist.png'
  'myworkflow_result.xml' 'test_2_roc_dynamic.png' 'test_4_dist.png'
  'test_5_blockdist_1.png' 'test_5_blockdist_2.png'
  'test_5_blockdist_3.png' 'test_6_slidedist_1.png'
  'test_6_slidedist_2.png' 'test_6_slidedist_3.png'
  'test_7_trimmeddist.png' 'test_8_bootdist.png' 'test_emd_1d.png'
  'test_emd_2d.png' 'test_jsd_1d.png' 'test_jsd_2d.png'
  'test_kld_1d.png' 'test_kld_2d.png' 'test_ms_1d.png' 'test_ms_2d.png'
  'test_rms_1d.png' 'test_rms_2d.png'
csQCAbinTest: no visible global function definition for 'p.adjust'
fsQCApermTest: no visible global function definition for 'p.adjust'
mvQCAbinTest: no visible global function definition for 'p.adjust'
p.threshold.adjust: no visible global function definition for
  'p.adjust'
plot.fsQCApt: no visible global function definition for 'dev.cur'
plot.fsQCApt: no visible global function definition for 'dev.new'
plot.fsQCApt: no visible global function definition for 'par'
plot.fsQCApt: no visible global function definition for 'density'
plot.fsQCApt: no visible global function definition for 'axis'
plot.fsQCApt: no visible global function definition for 'polygon'
plot.fsQCApt: no visible global function definition for 'points'
plot.fsQCApt: no visible global function definition for 'hist'
summary.csQCAbt: no visible global function definition for
  'printCoefmat'
summary.fsQCApt: no visible global function definition for
  'printCoefmat'
summary.mvQCAbt: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "points", "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Found the following files/directories:
  'EWAS_QC_graph_effectsize.png' 'EWAS_QC_graph_precision.png'
  'EWAS_QC_legend.txt' 'sample1.txt.gz' 'sample2.txt.gz'
  'sample_map.txt.gz' 'sample_output.graph_M.png'
  'sample_output.graph_QQ.png' 'sample_output.graph_p.png'
  'sample_output.graph_volcano.png' 'sample_output.histo.png'
  'sample_output.txt' 'sample_output1.graph_M.png'
  'sample_output1.graph_QQ.png' 'sample_output1.graph_p.png'
  'sample_output1.graph_volcano.png' 'sample_output1.histo.png'
  'sample_output2.graph_M.png' 'sample_output2.graph_QQ.png'
  'sample_output2.graph_p.png' 'sample_output2.graph_volcano.png'
  'sample_output2.histo.png' 'translation_table.txt'
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  'sample_QQ.png' 'sample_QQ1.png' 'sample_QQ2.png' 'sample_QQ3.png'
  'sample_distribution.png' 'sample_graph_p-correlation.png'
  'sample_histogram.png' 'sample_histogram1.png'
  'sample_histogram2.png' 'sample_histogram3.png'
  'sample_plots_graph_M.png' 'sample_plots_graph_QQ.png'
  'sample_precision.png' 'sample_regional_association.png'
  'sample_skewness_kurtosis.png'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'broom', 'mice'
Packages required but not available: 'tidygraph', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'qicharts2.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 336-343 (qicharts2.Rmd) 
Error: processing vignette 'qicharts2.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'qicharts2.Rmd'

SUMMARY: processing the following file failed:
  'qicharts2.Rmd'

Error: Vignette re-building failed.
Execution halted
chooseMDoubleBootstrap: no visible global function definition for
  'model.matrix'
chooseMDoubleBootstrap: no visible global function definition for
  'as.formula'
chooseMDoubleBootstrap: no visible global function definition for
  'model.frame'
chooseMDoubleBootstrap: no visible global function definition for 'lm'
chooseMDoubleBootstrap: no visible global function definition for
  'coef'
chooseMDoubleBootstrap: no visible global function definition for
  'quantile'
chooseMDoubleBootstrap: no visible global function definition for
  'qnorm'
getModel: no visible global function definition for 'lm'
getModel: no visible global function definition for 'model.matrix'
getModel: no visible global function definition for 'as.formula'
getModel: no visible global function definition for 'model.frame'
getModel: no visible global function definition for 'model.response'
getModel: no visible global function definition for 'coef'
getModel: no visible global function definition for 'qnorm'
qLearn: no visible global function definition for 'model.matrix'
qLearn: no visible global function definition for 'as.formula'
qLearn: no visible global function definition for 'model.frame'
qLearn: no visible global function definition for 'coef'
qLearn: no visible global function definition for 'lm'
qLearn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
GNU make is a SystemRequirements.
pcAxisCubeMake: no visible global function definition for 'aggregate'
pcAxisCubeToCSV: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Rd file 'pcAxisCubeMake.Rd':
  \examples lines wider than 100 characters:
           # In the latter case, latin1 would also work, but accents, Ã±, ... would not be correctly read.

Rd file 'pcAxisParser.Rd':
  \examples lines wider than 100 characters:
           # In the latter case, latin1 would also work, but accents, Ã±, ... would not be correctly read.

These lines will be truncated in the PDF manual.
Found the following files/directories:
  'datInSFexample6_1pxCube.csv' 'datInSFexample6_1pxCubeA0.csv '
  'datInSFexample6_1pxCubeA1.csv ' 'datInSFexample6_1pxCubeData.csv '
  'datInSFexample6_1pxCubeVariable.csv'
  'datInSFexample6_1pxCubeVariableDomain.csv'
Found the following files/directories:
  'lambda.pdf' 'qqplot.pdf'
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
ci.length: no visible global function definition for 'qexp'
detectable.bc: no visible global function definition for 'uniroot'
detectable.f2: no visible global function definition for 'uniroot'
detectable.ri: no visible global function definition for 'uniroot'
nu: no visible global function definition for 'pnorm'
nullinfo: no visible global function definition for 'qnorm'
nullinfo: no visible global function definition for 'dnorm'
optselection.bc: no visible global function definition for 'optimize'
optselection.f2: no visible global function definition for 'optimize'
optspacing.bc: no visible global function definition for 'optim'
optspacing.bc: no visible global function definition for 'optimize'
optspacing.f2: no visible global function definition for 'optim'
optspacing.f2: no visible global function definition for 'optimize'
powercalc.bc: no visible global function definition for 'pchisq'
powercalc.f2: no visible global function definition for 'pchisq'
samplesize.bc: no visible global function definition for 'uniroot'
samplesize.f2: no visible global function definition for 'uniroot'
samplesize.ri: no visible global function definition for 'uniroot'
tailprob: no visible global function definition for 'pchisq'
thresh: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dnorm optim optimize pchisq pnorm qexp qnorm uniroot
Consider adding
  importFrom("stats", "dnorm", "optim", "optimize", "pchisq", "pnorm",
             "qexp", "qnorm", "uniroot")
to your NAMESPACE file.
Package suggested but not available for checking: 'survminer'
Package required but not available: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'Rmpfr' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
adjacencyMatrix: 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').
quadp: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
alphaf: no visible global function definition for 'pchisq'
alphaf: no visible global function definition for 'dbinom'
conout: no visible global function definition for 'sd'
ibgaout: no visible global function definition for 'qnorm'
ibgaout: no visible global function definition for 'pnorm'
plot.qualint: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'rnorm'
powerval: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'pnorm'
print.expplot: no visible global function definition for 'gray'
print.expplot: no visible binding for global variable 'coef'
print.outplot: no visible global function definition for 'gray'
print.outplot: no visible binding for global variable 'coef'
qualint: no visible global function definition for 'qnorm'
qualval: no visible global function definition for 'qnorm'
surout: no visible global function definition for 'tail'
surout: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef dbinom gray pchisq pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidycensus'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'wilcox1973.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 111-120 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'wilcox1973.Rmd'

SUMMARY: processing the following file failed:
  'wilcox1973.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'caret', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'quanteda.textmodels'
Error(s) in re-building vignettes:
  ...
--- re-building 'quickstart.Rmd' using rmarkdown
Package version: 2.1.1
Parallel computing: 2 of 32 threads used.
See https://quanteda.io for tutorials and examples.

Attaching package: 'quanteda'

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

    View

Quitting from lines 431-436 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
object 'data_corpus_irishbudget2010' not found
--- failed re-building 'quickstart.Rmd'

SUMMARY: processing the following file failed:
  'quickstart.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'RSSL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Found the following calls to attach():
File 'quantmod/R/attachSymbols.R':
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section 'Good practice' in '?attach'.
Non-standard file/directory found at top level:
  'README.txt'
Rd file 'graph.mod.Rd':
  \usage lines wider than 90 characters:
     graph.mod(ssmod, x, y, data, title = "", xlab = "Centered X", ylab = "Raw Y", ylimit = 1.5, ...)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  'Judge.pdf'
Found the following sources/headers with CR or CRLF line endings:
  inst/include/BackTest.h
Some Unix compilers require LF line endings.
Found the following files/directories:
  'Example'
Packages suggested but not available for checking: 'tidyr', 'janitor'
Running 'testthat.R' [3s/3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(questionr)
  
  Attaching package: 'questionr'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("questionr")
  -- 1. Error: (unknown) (@test_tables.R#4)  -------------------------------------
  there is no package called 'tidyr'
  Backtrace:
   1. base::library(tidyr)
  
  == testthat results  ===========================================================
  [ OK: 14 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test_tables.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'fastshp'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
mutualCoherence : .setOneMutualP: no visible global function definition
  for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
conf2d.default: no visible global function definition for 'polygon'
conf2d_int: no visible global function definition for 'contourLines'
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
Package vignette with placeholder title 'Vignette Title':
  'R2DGC.Rmd'
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'r2dii.match'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'rgdal' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'matrixStats' 'rgdal' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  'ndvi.rgf'
Found the following files/directories:
  'output.html'
Package required but not available: 'broom'

Package suggested but not available for checking: 'doBy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following calls to attach():
File 'R2OpenBUGS/R/attach.all.R':
  attach(x, name = name)
See section 'Good practice' in '?attach'.
Package suggested but not available for checking: 'caret'
Package suggested but not available for checking: 'tidyverse'
Found the following calls to attach():
File 'R2WinBUGS/R/attach.all.R':
  attach(x, name = name)
See section 'Good practice' in '?attach'.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'rgl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'leaps' 'rgl' 's20x'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package vignette with placeholder title 'Vignette Title':
  'r511-intro.Rmd'
Packages required but not available:
  'plotly', 'alakazam', 'tigger', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'destiny'
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'preparingData.Rmd' using rmarkdown
Quitting from lines 28-32 (preparingData.Rmd) 
Error: processing vignette 'preparingData.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'preparingData.Rmd'

SUMMARY: processing the following file failed:
  'preparingData.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'radiant.data', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'broom', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'radiant.data'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'radiant.data', 'radiant.basics', 'NeuralNetTools', 'tidyr',
  'DiagrammeR', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'radiant.data', 'radiant.model'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'radiant.data', 'radiant.design', 'radiant.basics', 'radiant.model',
  'radiant.multivariate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
getsonde: no visible global function definition for 'read.table'
plotsonde: no visible global function definition for 'par'
plotwind: no visible global function definition for 'mtext'
plotwind: no visible global function definition for 'abline'
skewt.axis: no visible global function definition for 'par'
skewt.axis: no visible global function definition for 'axis'
skewt.axis: no visible global function definition for 'mtext'
skewt.axis: no visible global function definition for 'segments'
skewt.axis: no visible global function definition for 'text'
skewt.axis: no visible global function definition for 'lines'
skewt.lines: no visible global function definition for 'lines'
skewt.points: no visible global function definition for 'points'
station.symbol: no visible global function definition for 'sd'
station.symbol: no visible global function definition for 'par'
station.symbol: no visible global function definition for 'lines'
station.symbol: no visible global function definition for 'polygon'
station.symbol: no visible global function definition for 'text'
station.symbol: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline axis lines mtext par points polygon read.table sd segments
  text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  'SondeFile.txt'
Package suggested but not available for checking: 'DiagrammeR'
Package required but not available: 'lexicon'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Rd file 'MDMnMod.Rd':
  \usage lines wider than 90 characters:
     MDMnMod(MDMn.form, data, ID, dist="MDMn", scale.covar=FALSE, est.var=TRUE, calc.resid=TRUE, trace=TRUE)
  \examples lines wider than 100 characters:
     model.nij <- MDMnMod(nij.form, data=n.data, ID=n.data$i, dist="MDMn", scale.covar=TRUE, est.var=FALSE, calc.resid=TRUE, trace=TRUE)

Rd file 'predict.MDMnMod.Rd':
  \examples lines wider than 100 characters:
     model.nij <- MDMnMod(nij.form, data=n.data, ID=n.data$i, dist="MDMn", scale.covar=TRUE, est.var=TRUE, calc.resid=TRUE, trace=TRUE)

Rd file 'truncMod.Rd':
  \usage lines wider than 90 characters:
     truncMod(trunc.form, trunc.pts, data, dist = 'NB', scale.covar=FALSE, est.var = TRUE, trace = TRUE)

These lines will be truncated in the PDF manual.
RnDif.het: no visible global function definition for 'runif'
RnDif.hom: no visible global function definition for 'runif'
RnDifAdv.hom: no visible global function definition for 'runif'
SoilAdv.hom: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'multivariate_analysis.Rmd' using rmarkdown
Quitting from lines 15-31 (multivariate_analysis.Rmd) 
Error: processing vignette 'multivariate_analysis.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'multivariate_analysis.Rmd'

--- re-building 'single_cell_projections.Rmd' using rmarkdown
Quitting from lines 58-61 (single_cell_projections.Rmd) 
Error: processing vignette 'single_cell_projections.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'single_cell_projections.Rmd'

SUMMARY: processing the following files failed:
  'multivariate_analysis.Rmd' 'single_cell_projections.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'quanteda.textmodels'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'xcms'
Installation failed.
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RAMClustR.Rcheck/00install.out' for details.
Found the following sources/headers not terminated with a newline:
  inst/include/ramcmc.h
Some compilers warn on such files.
Found the following files/directories:
  'blcs.dot' 'ex1.dot' 'ex1bridge1.dot' 'ex1bridge2.dot'
  'ex1bridge3.dot' 'ex1effect1.dot' 'ex1effect2.dot' 'gcmlinear.dot'
  'latent.dot' 'lcs.dot' 'mimic.dot'
Package required but not available: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  'COPYRIGHTS'
Copyright information should be in file inst/COPYRIGHTS
Package suggested but not available for checking: 'caret'
Malformed Description field: should contain one or more complete sentences.
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
.forwardSelection: no visible binding for global variable 'var'
.forwardSelection: no visible global function definition for 'glm'
.forwardSelection: no visible global function definition for 'formula'
.forwardSelection: no visible global function definition for 'binomial'
.forwardSelection: no visible global function definition for 'lm'
.forwardSelection: no visible global function definition for 'predict'
.predict.internal: no visible global function definition for 'predict'
randomGLM: no visible binding for global variable 'cor'
randomGLM: no visible binding for global variable 'sd'
randomGLM: no visible global function definition for 'var'
thinRandomGLM: no visible global function definition for 'glm'
thinRandomGLM: no visible global function definition for 'binomial'
thinRandomGLM: no visible global function definition for 'lm'
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File 'randomGLM/R/randomGLM.R':
  assign(".randomGLMparallelCluster", cluster, pos = ".GlobalEnv")
Rd file 'predict.randomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

Rd file 'randomGLM.Rd':
  \usage lines wider than 90 characters:
       # Multi-level classification options - only apply to classification with multi-level response

Rd file 'thinRandomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

These lines will be truncated in the PDF manual.
anovaF: no visible global function definition for 'anova'
anovaF: no visible global function definition for 'lm'
randInterval: no visible global function definition for 'quantile'
randInterval : <anonymous>: no visible global function definition for
  'quantile'
randPlot: no visible global function definition for 'par'
randPlot: no visible global function definition for 'hist'
randPlot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline anova hist lm par quantile
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "anova", "lm", "quantile")
to your NAMESPACE file.
Package required but not available: 'smoof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
bartels.rank.test: no visible global function definition for 'na.omit'
bartels.rank.test: no visible global function definition for 'pbeta'
bartels.rank.test: no visible global function definition for 'pnorm'
cox.stuart.test: no visible global function definition for 'pbinom'
difference.sign.test: no visible global function definition for
  'na.omit'
difference.sign.test: no visible global function definition for 'pnorm'
rank.test: no visible global function definition for 'na.omit'
rank.test: no visible global function definition for 'pnorm'
rruns: no visible global function definition for 'runif'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'na.omit'
runs.test: no visible global function definition for 'points'
runs.test: no visible global function definition for 'abline'
runs.test: no visible global function definition for 'gray'
runs.test: no visible global function definition for 'pnorm'
turning.point.test: no visible global function definition for 'embed'
turning.point.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'biomod2', 'ecospat', 'googlesheets'
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
rank.L2R: no visible global function definition for 'kmeans'
rank.L2R: no visible global function definition for 'pnorm'
rank.LN: no visible global function definition for 'kmeans'
rank.LN: no visible global function definition for 'pnorm'
rank.gs: no visible global function definition for 'qnorm'
rank.wald: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  kmeans pnorm qnorm
Consider adding
  importFrom("stats", "kmeans", "pnorm", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'BSgenome.Hsapiens.UCSC.hg19' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  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).
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.
freq: no visible global function definition for 'xtabs'
freq: no visible binding for global variable 'na.pass'
freq: no visible global function definition for 'melt'
freq: no visible global function definition for 'complete.cases'
freq: no visible global function definition for 'tail'
kurtosis: no visible global function definition for 'na.omit'
label: no visible global function definition for 'tail'
name: no visible global function definition for 'tail'
nvalid : <anonymous>: no visible global function definition for
  'na.omit'
rp.desc: no visible global function definition for 'melt.data.frame'
rp.desc: no visible global function definition for 'cast'
rp.desc: no visible global function definition for 'na.omit'
rp.desc : <anonymous>: no visible global function definition for 'tail'
rp.desc : <anonymous>: no visible global function definition for 'head'
rp.freq: no visible global function definition for 'xtabs'
rp.freq: no visible binding for global variable 'na.pass'
rp.freq: no visible global function definition for 'melt'
rp.freq: no visible global function definition for 'complete.cases'
rp.freq: no visible global function definition for 'tail'
rp.label: no visible global function definition for 'tail'
rp.name: no visible global function definition for 'tail'
rp.outlier : lundcrit: no visible global function definition for 'qf'
rp.outlier: no visible global function definition for 'lm'
rp.outlier: no visible global function definition for 'rstandard'
rp.valid : <anonymous>: no visible global function definition for
  'na.omit'
skewness: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  cast complete.cases head lm melt melt.data.frame na.omit na.pass qf
  rstandard tail xtabs
Consider adding
  importFrom("stats", "complete.cases", "lm", "na.omit", "na.pass", "qf",
             "rstandard", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
fnRAP: no visible global function definition for 'chisq.test'
fnRAP: no visible global function definition for 'combn'
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: 'gurobi'
Package required but not available: 'adiv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
INT_FIX: no visible global function definition for 'rbinom'
INT_FIX: no visible global function definition for 'glm'
INT_FIX: no visible global function definition for 'as.formula'
INT_FIX: no visible global function definition for 'residuals'
INT_FIX: no visible global function definition for 'var'
INT_RAN: no visible global function definition for 'rbinom'
INT_RAN: no visible global function definition for 'as.formula'
INT_RAN: no visible global function definition for 'predict'
JOINT: no visible global function definition for 'rbinom'
JOINT: no visible global function definition for 'glm'
JOINT: no visible global function definition for 'as.formula'
JOINT: no visible global function definition for 'var'
JOINT: no visible global function definition for 'residuals'
pKuonen: no visible global function definition for 'pchisq'
pKuonen: no visible global function definition for 'uniroot'
pKuonen: no visible global function definition for 'pnorm'
rareGE: no visible global function definition for 'rbinom'
rareGE: no visible global function definition for 'as.formula'
rareGE: no visible global function definition for 'predict'
rareGE: no visible global function definition for 'glm'
rareGE: no visible global function definition for 'residuals'
rareGE: no visible global function definition for 'var'
rareGE_joint_mc: no visible global function definition for 'pchisq'
rareGE_joint_mc: no visible global function definition for 'qchisq'
wuweights: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  as.formula dbeta glm pchisq pnorm predict qchisq rbinom residuals
  uniroot var
Consider adding
  importFrom("stats", "as.formula", "dbeta", "glm", "pchisq", "pnorm",
             "predict", "qchisq", "rbinom", "residuals", "uniroot",
             "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
BiogTest.individual: no visible global function definition for 'combn'
BiogTest.individual: no visible global function definition for 'runif'
BiogTest.individual: no visible global function definition for 'rlnorm'
BiogTest.individual: no visible global function definition for
  'rnbinom'
BiogTest.sample: no visible global function definition for 'combn'
BiogTest.sample: no visible global function definition for 'runif'
BiogTest.sample: no visible global function definition for 'rlnorm'
BiogTest.sample: no visible global function definition for 'rnbinom'
BiogTest.sample: no visible global function definition for 'aggregate'
EcoTest.individual: no visible global function definition for 'xtabs'
plot.BiogTest: no visible global function definition for 'quantile'
plot.BiogTest: no visible global function definition for 'combn'
plot.EcoTest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate combn quantile rlnorm rnbinom runif xtabs
Consider adding
  importFrom("stats", "aggregate", "quantile", "rlnorm", "rnbinom",
             "runif", "xtabs")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
rateratio.test: no visible global function definition for
  'complete.cases'
rateratio.test: no visible global function definition for 'pbinom'
rateratio.test : p.L: no visible global function definition for 'qbeta'
rateratio.test : p.U: no visible global function definition for 'qbeta'
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
concordance: no visible global function definition for 'quantile'
concordance : Normal: no visible global function definition for 'qnorm'
concordance : Normal: no visible global function definition for 'pnorm'
concordance : MC: no visible global function definition for 'rmultinom'
concordance : MC: no visible global function definition for 'quantile'
concordance: no visible global function definition for 'qnorm'
concordance: no visible global function definition for 'pnorm'
concordance : Chisq: no visible global function definition for 'qchisq'
concordance : Chisq: no visible global function definition for 'pchisq'
concordance : Normal2: no visible global function definition for
  'qnorm'
concordance : Normal2: no visible global function definition for
  'pnorm'
concordance : MC2: no visible global function definition for
  'rmultinom'
concordance : MC2: no visible global function definition for 'quantile'
wlin.conc: no visible global function definition for 'quantile'
wlin.conc : MC: no visible global function definition for 'rmultinom'
wlin.conc : MC: no visible global function definition for 'quantile'
wquad.conc: no visible global function definition for 'quantile'
wquad.conc : MC: no visible global function definition for 'rmultinom'
wquad.conc : MC: no visible global function definition for 'quantile'
Undefined global functions or variables:
  pchisq pnorm qchisq qnorm quantile rmultinom
Consider adding
  importFrom("stats", "pchisq", "pnorm", "qchisq", "qnorm", "quantile",
             "rmultinom")
to your NAMESPACE file.
.GCD: no visible global function definition for 'as.polynomial'
.LCM: no visible global function definition for 'as.polynomial'
.is_zero_polynomial: no visible global function definition for 'coef'
.poly2expr: no visible global function definition for 'coef'
integral.rationalfun: no visible global function definition for 'coef'
integraterf.transcendent: no visible global function definition for
  'coef'
rationalfun: no visible global function definition for 'polynomial'
rationalfun.poly: no visible global function definition for
  'polynomial'
rationalfun.poly: no visible global function definition for
  'is.polynomial'
rfun: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'is.polynomial'
simplify: no visible global function definition for 'coef'
simplify: no visible global function definition for 'polynomial'
Undefined global functions or variables:
  as.polynomial coef is.polynomial polynomial
Consider adding
  importFrom("stats", "coef")
to your NAMESPACE file.
Packages required but not available: 'ggpubr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rattle'
Package required but not available: 'tidyr'

Packages suggested but not available for checking:
  'arulesViz', 'biclust', 'doBy', 'mice', 'rggobi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.avisApiBusAvanzada: no visible global function definition for
  'read.csv'
.avisRenderMapAdmin: no visible global function definition for 'points'
.avisRenderMapAdmin: no visible global function definition for 'rect'
.avisRenderMapPhysical: no visible global function definition for
  'points'
avisMap: no visible global function definition for 'par'
avisMap: no visible global function definition for 'layout'
Undefined global functions or variables:
  layout par points read.csv rect
Consider adding
  importFrom("graphics", "layout", "par", "points", "rect")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
Packages suggested but not available for checking: 'broom', 'tidyr'
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building 'PoS_codata.Rmd' using rmarkdown
--- finished re-building 'PoS_codata.Rmd'

--- re-building 'PoS_interim.Rmd' using rmarkdown
--- finished re-building 'PoS_interim.Rmd'

--- re-building 'customizing_plots.Rmd' using rmarkdown
Loading required package: Rcpp
This is RBesT version 1.6.1

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 38-59 (customizing_plots.Rmd) 
Error: processing vignette 'customizing_plots.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'customizing_plots.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

--- re-building 'introduction_normal.Rmd' using rmarkdown
--- finished re-building 'introduction_normal.Rmd'

--- re-building 'robustMAP.Rmd' using rmarkdown
Quitting from lines 32-52 (robustMAP.Rmd) 
Error: processing vignette 'robustMAP.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'robustMAP.Rmd'

--- re-building 'variances_MAP.Rmd' using rmarkdown
--- finished re-building 'variances_MAP.Rmd'

SUMMARY: processing the following files failed:
  'customizing_plots.Rmd' 'robustMAP.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GetHistoricTradeData: 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.
Package vignette with placeholder title 'Vignette Title':
  'RBitmoji.Rmd'
Found the following notes/warnings:
  Non-staged installation was used
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rblpapi.Rcheck/00install.out' for details.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
SumTestSens: no visible global function definition for 'pnorm'
binarysens: no visible global function definition for 'dbinom'
hlsens: no visible global function definition for 'wilcox.test'
iv_sens: no visible global function definition for 'pnorm'
mcontrol: no visible global function definition for 'pnorm'
psens: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dbinom pnorm wilcox.test
Consider adding
  importFrom("stats", "dbinom", "pnorm", "wilcox.test")
to your NAMESPACE file.
Package required but not available: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
find_available_versions: no visible global function definition for
  'contrib.url'
find_available_versions: no visible global function definition for
  'available.packages'
install_version: no visible global function definition for
  'contrib.url'
install_version: no visible global function definition for
  'available.packages'
install_version: no visible global function definition for
  'install_url'
load_available_packages: no visible global function definition for
  'contrib.url'
validate_installed_package: no visible global function definition for
  'installed.packages'
Undefined global functions or variables:
  available.packages contrib.url install_url installed.packages
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "installed.packages")
to your NAMESPACE file.
Package vignette with placeholder title 'Vignette Title':
  'rcane.Rmd'
Found the following files/directories:
  'rcanvec.cache'
RC.read.table: 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.
Found the following files/directories:
  'temp.RData'
Found the following sources/headers not terminated with a newline:
  inst/include/cereal/types/memory.hpp
Some compilers warn on such files.
Malformed Description field: should contain one or more complete sentences.
.onAttach: no visible global function definition for
  'packageDescription'
rselect.list: no visible global function definition for 'select.list'
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
Found the following files/directories:
  'data.csv'
Malformed Description field: should contain one or more complete sentences.
get_ClinicalCodes: no visible global function definition for 'read.csv'
get_ClinicalCodes : <anonymous>: 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.
Found the following files/directories:
  'file1.arp' 'file2.arp' 'test.txt' 'test2.txt'
Package required but not available: 'factoextra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cmaOptimDP: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console
Consider adding
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following files/directories:
  'outcmaesdisp.dat'
Packages required but not available:
  'biclust', 'iBBiG', 'superbiclust', 's4vd', 'BiBitR'

Package suggested but not available for checking: 'rqubic'

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
enterTableMHTest : onOK: no visible global function definition for
  'na.omit'
startStop: 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.
Namespace with empty importFrom: 'tcltk'
'library' or 'require' calls to packages already attached by Depends:
  'depthTools' 'tcltk'
  Please remove these calls from your code.
computeMBD : OnOutput: no visible global function definition for
  'tkbutton'
computeMBD: no visible global function definition for 'tkbutton'
computeMBD : OnPlot: no visible global function definition for
  'tkcanvas'
computeMBD : OnPlot: no visible global function definition for
  'tkbutton'
computeTmean: no visible global function definition for 'tkcanvas'
computeTmean: no visible global function definition for 'tkbutton'
computeTmean : onOK: no visible global function definition for 'par'
plotCentralCurves: no visible global function definition for 'tkcanvas'
plotCentralCurves: no visible global function definition for 'tkbutton'
plotCentralCurves : onOK: no visible global function definition for
  'par'
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
'library' or 'require' call to 'FrF2.catlg128' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
managedata: no visible binding for global variable 'data'
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'abind' 'e1071' 'qcc'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
BOXWP: no visible binding for global variable 'top'
BOXWP: no visible binding for global variable 'buttonsFrame'
HIST: no visible binding for global variable 'top'
HIST: no visible binding for global variable 'buttonsFrame'
QQN: no visible binding for global variable 'top'
QQN: no visible binding for global variable 'buttonsFrame'
Undefined global functions or variables:
  buttonsFrame top
Package suggested but not available for checking: 'qgraph'
Namespaces with empty importFrom:
  'stats' 'tcltk'
Malformed Description field: should contain one or more complete sentences.
fncLRpROC: no visible global function definition for 'palette'
fncLRpROC : onOK : convert: no visible global function definition for
  'col2rgb'
fncLRpROC : onOK : convert: no visible global function definition for
  'rgb'
fncPairedpROC: no visible global function definition for 'palette'
fncPairedpROC : onOK : convert: no visible global function definition
  for 'col2rgb'
fncPairedpROC : onOK : convert: no visible global function definition
  for 'rgb'
fncUnpairedpROC: no visible global function definition for 'palette'
fncUnpairedpROC : onOK : convert: no visible global function definition
  for 'col2rgb'
fncUnpairedpROC : onOK : convert: no visible global function definition
  for 'rgb'
fncvpROC: no visible global function definition for 'palette'
fncvpROC : onOK : convert: no visible global function definition for
  'col2rgb'
fncvpROC : onOK : convert: no visible global function definition for
  'rgb'
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
SampleSizes: no visible global function definition for 'xtabs'
SampleSizes: no visible global function definition for 'weighted.mean'
SampleSizes: no visible global function definition for 'reshape'
stage1Sample.fn: no visible global function definition for 'runif'
stage2Sample.fn: no visible global function definition for 'runif'
strata.options : onOK: no visible global function definition for
  'packageDescription'
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Package required but not available: 'SCVA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'SLC' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'SLC'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.steeptestDij : onOK: no visible binding for global variable
  'replications'
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  'replications'
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Package suggested but not available for checking: 'ROpenOffice'
Malformed Description field: should contain one or more complete sentences.
brewer.pal: no visible global function definition for 'rgb'
display.brewer.all: no visible global function definition for 'par'
display.brewer.all: no visible global function definition for 'rect'
display.brewer.all: no visible global function definition for 'text'
display.brewer.pal: no visible global function definition for 'image'
Undefined global functions or variables:
  image par rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
addLine: no visible global function definition for 'abline'
ellipse: no visible global function definition for 'approx'
ellipse: no visible global function definition for 'tail'
Undefined global functions or variables:
  abline approx tail
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following sources/headers not terminated with a newline:
  inst/include/Rcpp/traits/static_max_int.h
Some compilers warn on such files.
Gauss: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Found the following sources/headers not terminated with a newline:
  inst/include/pflineart.h
Some compilers warn on such files.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package vignette with placeholder title 'Vignette Title':
  'rcreds.Rmd'
Package required but not available: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/rCRM.h
  inst/include/rCRM_RcppExports.h
Some Unix compilers require LF line endings.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'ggpubr'
Error(s) in re-building vignettes:
  ...
--- re-building 'Rdca.Rmd' using rmarkdown
Quitting from lines 141-171 (Rdca.Rmd) 
Error: processing vignette 'Rdca.Rmd' failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building 'Rdca.Rmd'

SUMMARY: processing the following file failed:
  'Rdca.Rmd'

Error: Vignette re-building failed.
Execution halted
distimage: no visible binding for global variable 'terrain.colors'
distimage: no visible global function definition for 'filled.contour'
distimage: no visible global function definition for 'title'
distimage: no visible global function definition for 'axis'
distimage: no visible global function definition for 'lines'
drawkpc: no visible global function definition for 'segments'
drawkpc: no visible global function definition for 'lines'
modelimage: no visible binding for global variable 'topo.colors'
modelimage: no visible global function definition for 'filled.contour'
modelimage: no visible global function definition for 'title'
modelimage: no visible global function definition for 'axis'
modelimage: no visible global function definition for 'lines'
sincdata: no visible global function definition for 'runif'
sincdata: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  axis filled.contour lines rnorm runif segments terrain.colors title
  topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "segments",
             "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
sumry_categorical: no visible global function definition for 'freq'
sumry_continous: no visible global function definition for 'quantile'
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: 'vcfR'
Package suggested but not available for checking: 'shinyMolBio'
'library' or 'require' call to 'synchronicity' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  'a.desc' 'b.desc' 'barrnumleft.desc' 'barrsense.desc' 'c.desc'
  'm.desc' 'u.desc' 'x' 'x.desc'
ip2coordinates: no visible global function definition for 'URLencode'
street2coordinates: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Found the following files/directories:
  'example.pdf'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'temp.txt' 'temp2.csv' 'temp3.rda'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'Introduction_to_readsdr.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 167-179 (Introduction_to_readsdr.Rmd) 
Error: processing vignette 'Introduction_to_readsdr.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'Introduction_to_readsdr.Rmd'

SUMMARY: processing the following file failed:
  'Introduction_to_readsdr.Rmd'

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  'devel'
'library' or 'require' calls to packages already attached by Depends:
  'leaps' 'mgcv'
  Please remove these calls from your code.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for 'abline'
bestmods: no visible global function definition for 'axis'
bestmods: no visible global function definition for 'lines'
cic: no visible global function definition for 'lsfit'
cic: no visible global function definition for 'var'
cvic: no visible global function definition for 'lsfit'
cvic: no visible global function definition for 'lm'
eic: no visible global function definition for 'lsfit'
eic: no visible global function definition for 'lm'
ic.min: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'var'
xy: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File 'reams/R/xy.R':
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
prepare_Rd: bestmods.Rd:47-49: Dropping empty section \note
prepare_Rd: bestmods.Rd:43-44: Dropping empty section \references
prepare_Rd: cic.Rd:24-26: Dropping empty section \details
prepare_Rd: cic.Rd:40-42: Dropping empty section \note
prepare_Rd: cvic.Rd:49-51: Dropping empty section \note
prepare_Rd: eic.Rd:31-33: Dropping empty section \details
prepare_Rd: eic.Rd:50-52: Dropping empty section \note
prepare_Rd: eic.Rd:56-58: Dropping empty section \seealso
prepare_Rd: ic.min.Rd:22-24: Dropping empty section \details
prepare_Rd: ic.min.Rd:47-49: Dropping empty section \note
prepare_Rd: ic.min.Rd:53-55: Dropping empty section \seealso
prepare_Rd: reams-package.Rd:16-17: Dropping empty section \references
prepare_Rd: reams-package.Rd:19-20: Dropping empty section \seealso
prepare_Rd: reams-package.Rd:21-22: Dropping empty section \examples
prepare_Rd: scoremods.Rd:26-28: Dropping empty section \details
prepare_Rd: scoremods.Rd:43-45: Dropping empty section \note
prepare_Rd: xy.Rd:46-48: Dropping empty section \note
prepare_Rd: xy.Rd:52: Dropping empty section \seealso
ReCiPa: no visible global function definition for 'count.fields'
ReCiPa: no visible global function definition for 'read.table'
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'rsample'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ffbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'flexsurvcure'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'qwraps2'
Error(s) in re-building vignettes:
  ...
--- re-building 'api.Rmd' using rmarkdown
Quitting from lines 53-62 (api.Rmd) 
Error: processing vignette 'api.Rmd' failed with diagnostics:
there is no package called 'qwraps2'
--- failed re-building 'api.Rmd'

--- re-building 'export.Rmd' using rmarkdown
Quitting from lines 29-33 (export.Rmd) 
Error: processing vignette 'export.Rmd' failed with diagnostics:
there is no package called 'qwraps2'
--- failed re-building 'export.Rmd'

SUMMARY: processing the following files failed:
  'api.Rmd' 'export.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'Filled.RData' 'cleaned.RData' 'days' 'gridded'
Package suggested but not available for checking: 'tidyr'
AutoCorrelationLRtest: no visible global function definition for
  'logLik'
AutoCorrelationLRtest: no visible global function definition for
  'pchisq'
REEMtree: no visible global function definition for 'terms'
REEMtree: no visible binding for global variable 'SubsetVector'
REEMtree: no visible global function definition for 'predict'
REEMtree: no visible global function definition for 'logLik'
fitted.REEMtree: no visible global function definition for 'fitted'
predict.REEMtree: no visible global function definition for 'predict'
residuals.REEMtree: no visible global function definition for
  'residuals'
Undefined global functions or variables:
  SubsetVector fitted logLik pchisq predict residuals terms
Consider adding
  importFrom("stats", "fitted", "logLik", "pchisq", "predict",
             "residuals", "terms")
to your NAMESPACE file.
Rd file 'REEMtree.Rd':
  \usage lines wider than 90 characters:
                     ErrorTolerance=0.001, MaxIterations=1000, verbose=FALSE, tree.control=rpart.control(), 
                     lme.control=lmeControl(returnObject=TRUE), method="REML", correlation=NULL)

These lines will be truncated in the PDF manual.
S3 methods shown with full name in documentation object 'fitted.REEMtree':
  'fitted.REEMtree'

S3 methods shown with full name in documentation object 'logLik':
  'logLik.REEMtree'

S3 methods shown with full name in documentation object 'plot':
  'plot.REEMtree'

S3 methods shown with full name in documentation object 'predict':
  'predict.REEMtree'

S3 methods shown with full name in documentation object 'print':
  'print.REEMtree'

S3 methods shown with full name in documentation object 'ranef.REEMtree':
  'ranef.REEMtree'

S3 methods shown with full name in documentation object 'residuals.REEMtree':
  'residuals.REEMtree'

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.
Packages required but not available: 'tidyr', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
cluster.reg: no visible global function definition for 'rnorm'
cluster.reg: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  'EnvironmentalA.txt' 'EnvironmentalB.txt' 'Example.txt'
  'Example_Predictions.txt' 'Example_RRDist.txt'
  'Example_RRDistCol.TIF' 'Example_RRDistGrey.TIF' 'GeneticA.txt'
  'GeneticB.txt' 'Inds.txt'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'geepack', 'mice', 'modelr', 'tidyverse'
Package required but not available: 'rattle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'caret', 'semPlot'
Error(s) in re-building vignettes:
  ...
--- re-building 'short_intro.Rmd' using knitr
Quitting from lines 13-18 (short_intro.Rmd) 
Error: processing vignette 'short_intro.Rmd' failed with diagnostics:
there is no package called 'semPlot'
--- failed re-building 'short_intro.Rmd'

SUMMARY: processing the following file failed:
  'short_intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Non-standard files/directories found at top level:
  'prebuild.sh' 'regtest-Ex.R'
Warning in fun(libname, pkgname) :
  package regtest is under development and still may change considerably

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.
binregtest: no visible global function definition for 'str'
binregtest: no visible binding for global variable 'str'
binregtest: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif str
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
Rd file 'binregtest.rd':
  \usage lines wider than 90 characters:
     binregtest(FUN1, FUN2, ..., PARS = NULL, PAR1 = NULL, PAR2 = NULL, WHICH = sample(1:n), TRYALL = TRUE, COMP = is.all.equal, NAME = "UNN ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package required but not available: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'vcfR'
'library' or 'require' call to 'lars' which was already attached by Depends.
  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.
relaxo: no visible global function definition for 'lars'
Undefined global functions or variables:
  lars
Rd file 'cvrelaxo.Rd':
  \usage lines wider than 90 characters:
     cvrelaxo(X, Y, K = 5, phi = seq(0, 1, length = 10), max.steps = min( 2* length(Y), 2 * ncol(X)), fast = TRUE, keep.data = TRUE, warn=TR ... [TRUNCATED]

Rd file 'plot.relaxo.Rd':
  \usage lines wider than 90 characters:
     plot(x, type = "l", lty = 1, main = NULL, xlab = "|beta|/max|beta| (phi=1)", ylab = expression("coefficients  " * beta[j]), plotphi = u ... [TRUNCATED]

Rd file 'relaxo.Rd':
  \usage lines wider than 90 characters:
     relaxo(X, Y, phi = seq(0, 1, length = 4), max.steps = min(2*length(Y), 2 * ncol(X)), fast = TRUE,  keep.data = TRUE, warn=TRUE)

These lines will be truncated in the PDF manual.
print.summary.rem: no visible global function definition for
  'printCoefmat'
print.summary.rem: no visible global function definition for 'pnorm'
print.summary.rem: no visible binding for global variable 'quantile'
print.summary.rem: no visible global function definition for 'pchisq'
print.summary.rem.dyad: no visible global function definition for
  'printCoefmat'
print.summary.rem.dyad: no visible global function definition for
  'pnorm'
print.summary.rem.dyad: no visible global function definition for
  'pchisq'
rem: no visible global function definition for 'rnorm'
rem: no visible global function definition for 'dnorm'
rem: no visible global function definition for 'runif'
rem: no visible global function definition for 'rchisq'
rem: no visible global function definition for 'cov'
rem.dyad: no visible global function definition for 'rnorm'
rem.dyad: no visible global function definition for 'optim'
rem.dyad: no visible global function definition for 'rchisq'
rem.dyad: no visible global function definition for 'quantile'
rem.dyad: no visible global function definition for 'sd'
rem.dyad: no visible global function definition for 'var'
rem.dyad.lprior: no visible global function definition for 'dnorm'
rem.dyad.lprior: no visible global function definition for 'dt'
Undefined global functions or variables:
  cov dnorm dt optim pchisq pnorm printCoefmat quantile rchisq rnorm
  runif sd var
Consider adding
  importFrom("stats", "cov", "dnorm", "dt", "optim", "pchisq", "pnorm",
             "printCoefmat", "quantile", "rchisq", "rnorm", "runif",
             "sd", "var")
to your NAMESPACE file.
duane: no visible global function definition for 'optim'
duane.plot: no visible global function definition for 'lines'
duane.plot: no visible global function definition for 'legend'
duane.plot: no visible global function definition for 'title'
littlewood.verall: no visible global function definition for 'optim'
littlewood.verall.plot: no visible global function definition for
  'lines'
littlewood.verall.plot: no visible global function definition for
  'legend'
littlewood.verall.plot: no visible global function definition for
  'title'
moranda.geometric: no visible global function definition for 'optimize'
moranda.geometric.plot: no visible global function definition for
  'lines'
moranda.geometric.plot: no visible global function definition for
  'legend'
moranda.geometric.plot: no visible global function definition for
  'title'
musa.okumoto: no visible global function definition for 'optimize'
musa.okumoto.plot: no visible global function definition for 'lines'
musa.okumoto.plot: no visible global function definition for 'legend'
musa.okumoto.plot: no visible global function definition for 'title'
rel.plot: no visible global function definition for 'lines'
rel.plot: no visible global function definition for 'segments'
rel.plot: no visible global function definition for 'legend'
rel.plot: no visible global function definition for 'title'
total.plot: no visible global function definition for 'lines'
total.plot: no visible global function definition for 'legend'
total.plot: no visible global function definition for 'title'
Undefined global functions or variables:
  legend lines optim optimize segments title
Consider adding
  importFrom("graphics", "legend", "lines", "segments", "title")
  importFrom("stats", "optim", "optimize")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
CapDistSlope: no visible global function definition for 'coef'
CapDistSlope: no visible global function definition for 'lm'
EnergyEntropyDecomp: no visible global function definition for 'legend'
FernholzDecomp: no visible global function definition for 'legend'
Invest: no visible global function definition for 'par'
Invest: no visible global function definition for 'legend'
SimMarketModel: no visible global function definition for 'rnorm'
plot.capdist: no visible global function definition for 'abline'
plot.capdist: no visible global function definition for 'lm'
plot.toymkt: no visible global function definition for 'par'
plot.toymkt: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline coef legend lm par rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
  ...
--- re-building 'rentrez_tutorial.Rmd' using rmarkdown
Quitting from lines 257-259 (rentrez_tutorial.Rmd) 
Error: processing vignette 'rentrez_tutorial.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'rentrez_tutorial.Rmd'

SUMMARY: processing the following file failed:
  'rentrez_tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
RearrangeData: no visible global function definition for 'rainbow'
RearrangeData: no visible global function definition for 'hclust'
RearrangeData: no visible global function definition for
  'as.dendrogram'
RearrangeData: no visible global function definition for 'heatmap'
RearrangeData: no visible global function definition for 'pdf'
RearrangeData: no visible global function definition for
  'colorRampPalette'
RearrangeData: no visible global function definition for 'legend'
RearrangeData: no visible global function definition for 'dev.off'
RearrangeJoseph: no visible global function definition for
  'write.table'
RearrangeJoseph: no visible global function definition for
  'as.dendrogram'
RearrangeJoseph: no visible global function definition for
  'order.dendrogram'
colorDendClass : colLab: no visible global function definition for
  'is.leaf'
colorDendClass: no visible global function definition for 'dendrapply'
testData1: no visible global function definition for 'runif'
testData1: no visible global function definition for 'image'
testData2: no visible global function definition for 'runif'
testData2: no visible global function definition for 'image'
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf rainbow runif write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  'A.txt' 'minI.txt' 'minJ.txt'
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'MASS' 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GlobTestMissing: no visible global function definition for 'lme'
GlobTestMissing: no visible global function definition for 'anova'
TestStatSP: no visible global function definition for 'pf'
TestStatSimple: no visible global function definition for 'ginv'
TestStatSimple: no visible global function definition for 'pf'
Undefined global functions or variables:
  anova ginv lme pf
Consider adding
  importFrom("stats", "anova", "pf")
to your NAMESPACE file.
Package required but not available: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'PackageCites.bib'
MBoxtest: no visible global function definition for 'var'
jrparams: no visible global function definition for 'prcomp'
jrparams: no visible global function definition for 'predict'
jrparams: no visible global function definition for 'qchisq'
jrparams: no visible global function definition for 'qf'
Undefined global functions or variables:
  prcomp predict qchisq qf var
Consider adding
  importFrom("stats", "prcomp", "predict", "qchisq", "qf", "var")
to your NAMESPACE file.
Rd file 'jrparams.Rd':
  \usage lines wider than 90 characters:
     jrparams(BLOCK.1, BLOCK.2, ncomp = min(c(dim(BLOCK.1), dim(BLOCK.2))), Cscrit=0.6, Rscrit=0.6)

These lines will be truncated in the PDF manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'plotly'
call.eqs: no visible global function definition for 'write.table'
read.eqs: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  read.fwf write.table
Consider adding
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Rd file 'call.eqs.rd':
  \examples lines wider than 100 characters:
     ##res <- call.eqs(EQSpgm = "C:/Program Files/EQS61/WINEQS.EXE", EQSmodel = "c:/eqs61/examples/manul7.eqs", serial = "1234")

Rd file 'run.eqs.rd':
  \examples lines wider than 100 characters:
     ##res <- run.eqs(EQSpgm = "C:/Program Files/EQS61/WINEQS.EXE", EQSmodel = "c:/eqs61/examples/manul7.eqs", serial = "1234")
     ##  res <- run.eqs(EQSpgm = "C:/Program Files/EQS61/WINEQS.EXE", EQSmodel = "c:/eqs61/examples/manul7.eqs", data = X, datname = "manul7 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package required but not available: 'plotdap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'P.csv' 'correct_alpha.csv' 'correct_beta.csv' 'correct_gamma.csv'
  'correct_lambda.csv' 'correct_perm_list.csv' 'correct_psi.csv'
PKG_CFLAGS set in 'src/Makevars' without any corresponding files
Found the following files/directories:
  'forest.out'
.resampleMakeFunction: no visible global function definition for 'is'
.resampleSetSeed: no visible global function definition for 'runif'
CI.bca: no visible global function definition for 'is'
CI.bca: no visible global function definition for 'qnorm'
CI.bca: no visible global function definition for 'pnorm'
CI.t: no visible global function definition for 'qt'
ExpandProbs: no visible global function definition for 'pnorm'
ExpandProbs: no visible global function definition for 'qt'
colVars : f: no visible global function definition for 'var'
colVars: no visible global function definition for 'var'
hist.resample: no visible global function definition for 'density'
hist.resample: no visible global function definition for 'lines'
hist.resample: no visible global function definition for 'points'
hist.resample: no visible global function definition for 'approx'
hist.resample: no visible global function definition for 'segments'
resample: no visible global function definition for 'is'
samp.bootknife: no visible global function definition for 'runif'
samp.bootstrap: no visible global function definition for 'runif'
Undefined global functions or variables:
  approx density is lines pnorm points qnorm qt runif segments var
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "approx", "density", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: 'sparklyr'
Package required but not available: 'PKNCA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GUI_template : onHelp: no visible global function definition for 'help'
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Warning: no function found corresponding to methods exports from 'retimes' 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.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dexgauss: no visible global function definition for 'pnorm'
loglik: no visible global function definition for 'pnorm'
mexgauss: no visible global function definition for 'sd'
rexgauss: no visible global function definition for 'rnorm'
rexgauss: no visible global function definition for 'rexp'
timefit: no visible global function definition for 'optim'
timefit: no visible global function definition for 'sd'
timefit: no visible global function definition for 'par'
timefit: no visible global function definition for 'hist'
timefit: no visible global function definition for 'density'
timefit: no visible global function definition for 'curve'
timefit: no visible global function definition for 'new'
plot,timefit: no visible global function definition for 'density'
plot,timefit: no visible global function definition for 'par'
plot,timefit: no visible global function definition for 'curve'
Undefined global functions or variables:
  curve density hist new optim par pnorm rexp rnorm sd
Consider adding
  importFrom("graphics", "curve", "hist", "par")
  importFrom("methods", "new")
  importFrom("stats", "density", "optim", "pnorm", "rexp", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
plot.reweight: no visible global function definition for 'par'
plot.reweight: no visible global function definition for 'density'
plot.reweight: no visible global function definition for 'rug'
reweight: no visible global function definition for 'aggregate'
search.best.h: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate density par quantile rug
Consider adding
  importFrom("graphics", "par", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
FDSNGetTimeSeries: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
Package required but not available: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
fs_author_ids : <anonymous>: no visible global function definition for
  'select.list'
fs_download : <anonymous>: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  BSD 3-clause License
Packages in Depends field not imported from:
  'XML' 'xts'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
quoteFXTsData : function.fx: no visible global function definition for
  'xmlValue'
quoteFundTsData : function.fund: no visible global function definition
  for 'xmlValue'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlSize'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlValue'
quoteTsData: no visible global function definition for 'xmlRoot'
quoteTsData: no visible global function definition for 'htmlTreeParse'
quoteTsData: no visible global function definition for
  'xmlErrorCumulator'
quoteTsData: no visible global function definition for 'xmlSize'
toXts: no visible global function definition for 'as.xts'
Undefined global functions or variables:
  as.xts htmlTreeParse xmlErrorCumulator xmlRoot xmlSize xmlValue
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'Test.txt'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'swfscMisc', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.testLTS: no visible binding for global variable 'stackloss'
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
Found the following files/directories:
  'interactions.dot'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
gabriel.plot: no visible global function definition for 'barplot'
gabriel.plot: no visible global function definition for 'arrows'
rgabriel: no visible binding for global variable 'sd'
rgabriel : psmm_x: no visible global function definition for 'pnorm'
rgabriel : psmm: no visible global function definition for 'integrate'
rgabriel : qsmm: no visible global function definition for 'qnorm'
rgabriel : qsmm: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  arrows barplot integrate pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "arrows", "barplot")
  importFrom("stats", "integrate", "pnorm", "qnorm", "sd", "uniroot")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: 'gsl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gammaIntegral: no visible global function definition for 'integrate'
gammaIntegral : <anonymous>: no visible global function definition for
  'hyperg_1F1'
gammaMLE: no visible global function definition for 'weighted.mean'
gammaMME: no visible binding for global variable 'sd'
gammaMME: no visible binding for global variable 'var'
Undefined global functions or variables:
  hyperg_1F1 integrate sd var weighted.mean
Consider adding
  importFrom("stats", "integrate", "sd", "var", "weighted.mean")
to your NAMESPACE file.
Package required but not available: 'mixOmics'

Package suggested but not available for checking: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
genoud: multiple local function definitions for 'fn1.bfgs' with
  different formal arguments
genoud: multiple local function definitions for 'gr1' with different
  formal arguments
genoud: multiple local function definitions for 'hess.fn' with
  different formal arguments
genoud_transform: multiple local function definitions for 'fn1.bfgs'
  with different formal arguments
genoud_transform: multiple local function definitions for 'gr1' with
  different formal arguments
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'MD_display.csv' 'kola.c_COUNTRY_Cu.csv'
  'kola.c_COUNTRY_Cu_fences.txt' 'ogrady.mvalloc_mvalloc.csv'
  'sind.mat2open_NGR_summary.csv' 'sind.save_PC-loadings.csv'
  'sind.save_PC-scores.csv' 'test.save.mvalloc_mvalloc.csv'
Found a 'configure.in' file: 'configure.ac' has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
File 'RGtk2/libs/RGtk2.so':
  Found non-API calls to R: 'R_CStackLimit', 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
.quick_fetch: no visible global function definition for 'POST'
.quick_fetch: no visible global function definition for 'add_headers'
.quick_fetch: no visible global function definition for
  'stop_for_status'
.quick_fetch: no visible global function definition for 'content'
fetch_healthdata: no visible binding for global variable 'resources'
fetch_healthdata : <anonymous>: no visible binding for global variable
  'filters'
Undefined global functions or variables:
  POST add_headers content filters resources stop_for_status
Package suggested but not available for checking: 'ggtree'
Error(s) in re-building vignettes:
  ...
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 40-46 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'ggtree'
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'mydata.rda' 'thedata.rda'
Packages in Depends field not imported from:
  'RCurl' 'XML' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ECL: no visible global function definition for 'new'
ECLDataset: no visible global function definition for 'new'
ECLDedUp: no visible global function definition for 'new'
ECLDistribute: no visible global function definition for 'new'
ECLIterate: no visible global function definition for 'new'
ECLJoin: no visible global function definition for 'new'
ECLOutput: no visible global function definition for 'new'
ECLProject: no visible global function definition for 'new'
ECLRecord: no visible global function definition for 'new'
ECLRollUp: no visible global function definition for 'new'
ECLSort: no visible global function definition for 'new'
ECLTOPN: no visible global function definition for 'new'
ECLTable: no visible global function definition for 'new'
ECLTransform: no visible global function definition for 'new'
eclDirectCall: no visible global function definition for 'postForm'
parseResults: no visible global function definition for 'xmlRoot'
parseResults: no visible global function definition for 'xmlTreeParse'
parseResults: no visible global function definition for 'getNodeSet'
parseResults: no visible global function definition for 'xmlGetAttr'
parseResults: no visible global function definition for 'xmlValue'
parseResults: no visible global function definition for 'write.table'
Undefined global functions or variables:
  getNodeSet new postForm write.table xmlGetAttr xmlRoot xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Unknown package 'TSA' in Rd xrefs
RHT.2samp : my.HotellingT2 : my.InvCov2: no visible global function
  definition for 'cov'
RHT.2samp : get.lambda : get.para: no visible global function
  definition for 'optimize'
RHT.2samp : get.lambda : gg: no visible global function definition for
  'qchisq'
RHT.2samp : get.lambda : ggl: no visible global function definition for
  'qnorm'
RHT.2samp : <anonymous>: no visible global function definition for
  'cov'
RHT.fun : my.HotellingT : my.InvCov: no visible global function
  definition for 'cov'
RHT.fun : get.lambda : get.para: no visible global function definition
  for 'optimize'
RHT.fun : get.lambda : gg: no visible global function definition for
  'qchisq'
RHT.fun : get.lambda : ggl: no visible global function definition for
  'qnorm'
RHT.fun : <anonymous>: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optimize qchisq qnorm
Consider adding
  importFrom("stats", "cov", "optimize", "qchisq", "qnorm")
to your NAMESPACE file.
Running 'testthat.R' [2s/5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rhymer)
  > 
  > test_check("rhymer")
  -- 1. Failure: datamuse_api errors if it doesn't return JSON (@test_rhymer.R#77)
  `datamuse_api("bad_path")` threw an error with unexpected message.
  Expected match: "API did not return json"
  Actual message: ""
  Backtrace:
   1. testthat::expect_error(datamuse_api("bad_path"), "API did not return json")
   6. rhymer::datamuse_api("bad_path")
  
  == testthat results  ===========================================================
  [ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: datamuse_api errors if it doesn't return JSON (@test_rhymer.R#77) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
FusedQDA : <anonymous>: no visible global function definition for 'cov'
RidgeFused: no visible binding for global variable 'cov2cor'
RidgeFusedCV : <anonymous>: no visible global function definition for
  'cov'
SSRidgeFused : <anonymous>: no visible global function definition for
  'cov'
Undefined global functions or variables:
  cov cov2cor
Consider adding
  importFrom("stats", "cov", "cov2cor")
to your NAMESPACE file.
ridit.raw: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Packages required but not available: 'tidyr', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
R2ngon: no visible global function definition for 'approx'
plotR2pre: no visible global function definition for 'points'
plotR2pre: no visible global function definition for 'gray'
plotR2pre: no visible global function definition for 'legend'
plotR2pre: no visible global function definition for 'rainbow'
Undefined global functions or variables:
  approx gray legend points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
Packages suggested but not available for checking: 'plotly', 'tidyr'
plot.ijzip: no visible global function definition for 'axis'
read.ijzip: no visible global function definition for 'unzip'
Undefined global functions or variables:
  axis unzip
Consider adding
  importFrom("graphics", "axis")
  importFrom("utils", "unzip")
to your NAMESPACE file.
File 'RInside/libs/RInside.so':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/RInside.so':
  Found non-API calls to R: 'R_CStackLimit', 'R_CleanTempDir',
    'R_DefParams', 'R_ReplDLLdo1', 'R_ReplDLLinit',
    'R_RunExitFinalizers', 'R_SetParams', 'R_SignalHandlers',
    'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  'mtcars.txt'
desmat.sanitize: no visible global function definition for 'aggregate'
dispdist: no visible global function definition for 'quantile'
dispdist: no visible global function definition for 'hist'
dispdist: no visible global function definition for 'lines'
estate: no visible global function definition for 'weighted.mean'
estate: no visible global function definition for 'lm'
genperms: no visible global function definition for 'combn'
genprobexact: no visible global function definition for 'ave'
invert.ci: no visible global function definition for 'quantile'
invert.ci: no visible global function definition for 'uniroot'
omni.ate: no visible global function definition for 'hist'
omni.ate: no visible global function definition for 'lines'
omni.ate: no visible global function definition for 'quantile'
resresplot: no visible global function definition for 'lm'
resresplot: no visible global function definition for 'symbols'
resresplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline aggregate ave combn hist lines lm quantile symbols uniroot
  weighted.mean
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "symbols")
  importFrom("stats", "aggregate", "ave", "lm", "quantile", "uniroot",
             "weighted.mean")
  importFrom("utils", "combn")
to your NAMESPACE file.
Rd file 'genperms.custom.Rd':
  \examples lines wider than 100 characters:
                     teststat <- pf(fstat[1],fstat[2],fstat[3],lower.tail=FALSE)  # extract F-test p-value

Rd file 'genprob.Rd':
  \examples lines wider than 100 characters:
                     teststat <- pf(fstat[1],fstat[2],fstat[3],lower.tail=FALSE)  # extract F-test p-value

These lines will be truncated in the PDF manual.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ipw', 'flexsurv'
Running 'test-AUC.R' [5s/6s]
  Running 'test-BinomialRegression.R' [6s/7s]
  Running 'test-BrierScore.R' [6s/8s]
  Running 'test-CauseSpecificCoxRegression.R' [6s/7s]
  Running 'test-FineGrayRegression.R' [5s/5s]
  Running 'test-ate.R' [4s/5s]
  Running 'test-boxplotScore.R' [4s/5s]
  Running 'test-iidCox.R' [6s/7s]
  Running 'test-phreg.R' [0s/1s]
  Running 'test-predictCSC.R' [27s/30s]
  Running 'test-predictCox.R' [16s/19s]
  Running 'test-predictCoxPL.R' [6s/7s]
  Running 'test-predictRisk-TD.R' [6s/7s]
  Running 'test-predictRisk.R' [9s/10s]
  Running 'test-score-bootstrap.R' [4s/5s]
  Running 'test-score.R' [22s/15s]
Running the tests in 'tests/test-ate.R' failed.
Complete output:
  > library(riskRegression)
  riskRegression version 2020.02.05
  > library(testthat)
  > library(rms)
  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 object is masked from 'package:testthat':
  
      describe
  
  The following objects are masked from 'package:base':
  
      format.pval, units
  
  Loading required package: SparseM
  
  Attaching package: 'SparseM'
  
  The following object is masked from 'package:base':
  
      backsolve
  
  > library(survival)
  > library(testthat)
  > library(data.table)
  > library(ipw)
  Error in library(ipw) : there is no package called 'ipw'
  Execution halted
KM.plot: no visible global function definition for 'lines'
SchoenSmooth: no visible global function definition for 'lm'
llCoxReg: no visible binding for global variable 'time'
risksetAUC: no visible global function definition for 'abline'
risksetROC: no visible global function definition for 'abline'
weightedKM: no visible binding for global variable 'time'
Undefined global functions or variables:
  abline lines lm time
Consider adding
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Alg2: no visible global function definition for 'uniroot'
Alg3: no visible global function definition for 'optim'
NVCopula: no visible global function definition for 'rnorm'
NVCopula: no visible global function definition for 'rgamma'
NVCopula: no visible global function definition for 'var'
NVCopula: no visible global function definition for 'cov'
NVCopula: no visible global function definition for 'qnorm'
NVCopulaMT: no visible global function definition for 'rnorm'
NVCopulaMT: no visible global function definition for 'rgamma'
NVCopulaMT: no visible global function definition for 'var'
NVCopulaMT: no visible global function definition for 'cov'
NVCopulaMT: no visible global function definition for 'qnorm'
R2X: no visible global function definition for 'write.table'
ReturnCopula: no visible global function definition for 'qt'
ReturnCopula: no visible global function definition for 'pt'
SISCopula: no visible global function definition for 'runif'
SISCopula: no visible global function definition for 'qnorm'
SISCopula: no visible global function definition for 'rnorm'
SISCopula: no visible global function definition for 'qgamma'
SISCopula: no visible global function definition for 'var'
SISCopula: no visible global function definition for 'cov'
SISCopulaMT: no visible global function definition for 'runif'
SISCopulaMT: no visible global function definition for 'qnorm'
SISCopulaMT: no visible global function definition for 'rnorm'
SISCopulaMT: no visible global function definition for 'qgamma'
SISCopulaMT: no visible global function definition for 'var'
SISCopulaMT: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optim pt qgamma qnorm qt rgamma rnorm runif uniroot var
  write.table
Consider adding
  importFrom("stats", "cov", "optim", "pt", "qgamma", "qnorm", "qt",
             "rgamma", "rnorm", "runif", "uniroot", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  'B110711CD4.CSV' 'inputparam2.txt' 'itcout0.pdf' 'itcout1.eps'
  'origin_data.csv'
Packages in Depends field not imported from:
  'compiler' 'signal'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NumConv: no visible global function definition for 'pchip'
NumConv: no visible global function definition for 'cmpfun'
NumDeconv: no visible global function definition for 'pchip'
NumDeconv : error_function: no visible global function definition for
  'pchip'
NumDeconv: no visible global function definition for 'cmpfun'
NumDeconv: no visible global function definition for 'optim'
RivivcA: no visible global function definition for 'lm'
Undefined global functions or variables:
  cmpfun lm optim pchip
Consider adding
  importFrom("stats", "lm", "optim")
to your NAMESPACE file.
Rd file 'NumConv.Rd':
  \usage lines wider than 90 characters:
     NumConv(impulse.matrix, input.matrix, conv.timescale = NULL, explicit.interpolation = 1000)

Rd file 'RivivcA.Rd':
  \examples lines wider than 100 characters:
     result<-RivivcA(input_mtx,impulse_mtx,resp_mtx,explicit.interp=accur_explic,implicit.interp=accur_implic)

These lines will be truncated in the PDF manual.
Non-standard file/directory found at top level:
  'jri'
Found the following possibly unsafe calls:
File 'rJava/R/import.R':
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File 'rJava/R/jinit.R':
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rJava/libs/rJava.so':
  Found '_exit', possibly from '_exit' (C)
  Found 'stderr', possibly from 'stderr' (C)
  Found 'stdout', possibly from 'stdout' (C)
File 'rJava/libs/rJava.so':
  Found non-API calls to R: 'R_CStackLimit', 'R_CStackStart',
    'R_GlobalContext'

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  'Barplot' 'Boxplot' 'BubblePlot' 'CircularFV' 'DataTable'
  'Dendrogram' 'DensityPlot' 'Heatmap' 'HivePlot' 'Network' 'Piechart'
  'Scatter3d' 'ScatterPlot' 'Surface3d' 'SymHeatmap' 'WordCloud'
File
  LICENSE
is not mentioned in the DESCRIPTION file.
'library' or 'require' call to 'rJava' which was already attached by Depends.
  Please remove these calls from your code.
Package vignette with placeholder title 'Vignette Title':
  'rKIN_Introduction.Rmd'
cv.coef: no visible global function definition for 'sd'
normalize.softmax: no visible global function definition for 'plogis'
plot.rknnSupport: no visible global function definition for 'dotchart'
predicted: no visible global function definition for 'influence'
predicted: no visible global function definition for 'fitted'
predicted: no visible global function definition for 'resid'
pressresid: no visible global function definition for 'influence'
pressresid: no visible global function definition for 'resid'
Undefined global functions or variables:
  dotchart fitted influence plogis resid sd
Consider adding
  importFrom("graphics", "dotchart")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'tidyr', 'highcharter', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
':::' calls which should be '::':
  'stats:::dexp' 'stats:::dgamma' 'stats:::dweibull' 'stats:::pexp'
  'stats:::pgamma' 'stats:::pweibull' 'stats:::qexp' 'stats:::qgamma'
  'stats:::qweibull' 'stats:::rexp' 'stats:::rgamma' 'stats:::rweibull'
  See the note in ?`:::` about the use of this operator.
Package suggested but not available for checking: 'tidyr'
GNU make is a SystemRequirements.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following Makefile(s) without a final LF:
  src/Makevars.in
Some 'make' programs ignore lines not ending in LF.
Found the following files/directories:
  'file.out'
Package in Depends field not imported from: 'msm'
  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:
  'EMSRb_internal' 'EM_internal' 'PD_internal'
EMSRb_internal: no visible global function definition for 'qnorm'
EM_internal: no visible global function definition for 'dnorm'
EM_internal: no visible global function definition for 'pnorm'
PD_internal: no visible global function definition for 'qtnorm'
PD_internal: no visible global function definition for 'sd'
Undefined global functions or variables:
  dnorm pnorm qnorm qtnorm sd
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
Rd file 'EMSRb_internal.Rd':
  \usage lines wider than 90 characters:
     EMSRb_internal(Fare = Fare, Mean = Mean, Var = Var, p_up = numeric(length(Fare)), cap = cap)

These lines will be truncated in the PDF manual.
ma.filter: no visible global function definition for 'par'
ma.filter: no visible global function definition for 'lines'
ma.filter: no visible global function definition for 'abline'
qn: no visible global function definition for 'lm'
qn: no visible global function definition for 'var'
qn: no visible global function definition for 'resid'
ss.filter: no visible global function definition for 'smooth.spline'
ss.filter: no visible global function definition for 'par'
ss.filter: no visible global function definition for 'lines'
ss.filter: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline lines lm par resid smooth.spline var
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "lm", "resid", "smooth.spline", "var")
to your NAMESPACE file.
Package suggested but not available for checking: 'Seurat'
Packages suggested but not available for checking: 'ggraph', 'tidygraph'
Running 'spelling.R' [0s/0s]
  Running 'testthat.R' [58s/136s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rmangal)
  > 
  > test_check("rmangal")
  -- 1. Error: expected behavior (@test-as.igraph.R#13)  -------------------------
  there is no package called 'tidygraph'
  Backtrace:
    1. testthat::expect_true("tbl_graph" %in% class(tidygraph::as_tbl_graph(mg100)))
    5. tidygraph::as_tbl_graph
    6. base::getExportedValue(pkg, name)
    7. base::asNamespace(ns)
    8. base::getNamespace(ns)
    9. base::loadNamespace(name)
   10. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   11. base:::withOneRestart(expr, restarts[[1L]])
   12. base:::doWithOneRestart(return(expr), restart)
  
  == testthat results  ===========================================================
  [ OK: 113 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: expected behavior (@test-as.igraph.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'BlackOil.Rmd' using rmarkdown
Quitting from lines 104-148 (BlackOil.Rmd) 
Error: processing vignette 'BlackOil.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'BlackOil.Rmd'

--- re-building 'DryWetGas.Rmd' using rmarkdown
Quitting from lines 92-115 (DryWetGas.Rmd) 
Error: processing vignette 'DryWetGas.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'DryWetGas.Rmd'

--- re-building 'GasCondensate.Rmd' using rmarkdown
Quitting from lines 112-228 (GasCondensate.Rmd) 
Error: processing vignette 'GasCondensate.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'GasCondensate.Rmd'

--- re-building 'Introduction.Rmd' using rmarkdown
--- finished re-building 'Introduction.Rmd'

--- re-building 'VolatileOil.Rmd' using rmarkdown
Quitting from lines 123-244 (VolatileOil.Rmd) 
Error: processing vignette 'VolatileOil.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'VolatileOil.Rmd'

SUMMARY: processing the following files failed:
  'BlackOil.Rmd' 'DryWetGas.Rmd' 'GasCondensate.Rmd' 'VolatileOil.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'merTools'
Error(s) in re-building vignettes:
  ...
--- re-building 'Combined_paper_figures.Rmd' using rmarkdown
Loading required package: pwr
Loading required package: psych
Loading required package: RColorBrewer
Loading required package: plotrix

Attaching package: 'plotrix'

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

    rescale

Loading required package: rmcorr
Loading required package: lme4
Loading required package: Matrix
Loading required package: ggplot2

Attaching package: 'ggplot2'

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

    %+%, alpha

Loading required package: merTools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'merTools'
Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat2) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat3) :
  'sub' coerced into a factor
Quitting from lines 470-519 (Combined_paper_figures.Rmd) 
Error: processing vignette 'Combined_paper_figures.Rmd' failed with diagnostics:
could not find function "predictInterval"
--- failed re-building 'Combined_paper_figures.Rmd'

SUMMARY: processing the following file failed:
  'Combined_paper_figures.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'adabag'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
CI: no visible global function definition for 'sd'
CI: no visible global function definition for 'qt'
L: no visible global function definition for 'sd'
L: no visible global function definition for 'residuals'
Qa: no visible global function definition for 'logLik'
Qb: no visible global function definition for 'residuals'
Qc: no visible global function definition for 'residuals'
Qc: no visible global function definition for 'logLik'
STDERR: no visible global function definition for 'sd'
group.UCL: no visible global function definition for 'aggregate'
lr.glover: no visible binding for global variable 'logLik'
lr.glover: no visible binding for global variable 'update'
lr.glover : nobs0: no visible binding for global variable 'nobs'
lr.glover : nobs0 : nobs2: no visible global function definition for
  'residuals'
lr.glover : tlab: no visible global function definition for 'terms'
lr.glover : name: no visible global function definition for 'formula'
lr.glover : modelUpdate: no visible global function definition for
  'as.formula'
lr.glover: no visible global function definition for 'model.frame'
lr.glover: no visible binding for global variable 'AIC'
lr.glover: no visible binding for global variable 'BIC'
summarySE : <anonymous>: no visible global function definition for 'sd'
summarySE: no visible global function definition for 'qt'
Undefined global functions or variables:
  AIC BIC aggregate as.formula formula logLik model.frame nobs qt
  residuals sd terms update
Consider adding
  importFrom("stats", "AIC", "BIC", "aggregate", "as.formula", "formula",
             "logLik", "model.frame", "nobs", "qt", "residuals", "sd",
             "terms", "update")
to your NAMESPACE file.
Combi: no visible global function definition for 'new'
barplotMixCluster: no visible global function definition for 'is'
barplotMixCluster: no visible global function definition for 'par'
barplotMixCluster: no visible global function definition for 'lines'
barplotMixCluster: no visible global function definition for 'text'
barplotMixCluster: no visible global function definition for 'title'
barplotMixCluster: no visible global function definition for 'mtext'
histMixCluster: no visible global function definition for 'is'
histMixCluster: no visible global function definition for 'par'
histMixCluster: no visible global function definition for 'dnorm'
histMixCluster: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'par'
mixmodEntPlot: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'axis'
mixmodEntPlot: no visible global function definition for 'title'
mixmodEntPlot: no visible binding for global variable 'par'
plot,MixmodCombi: no visible global function definition for 'par'
plot,MixmodCombi: no visible global function definition for 'plot.new'
plot,MixmodCombi: no visible global function definition for 'title'
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'RMixtCompUtilities', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.pLGP_qvec: no visible global function definition for 'ppois'
.qLGP_pvec: no visible global function definition for 'qpois'
.rLGP.failsafe: no visible global function definition for 'runif'
.subdmg: no visible global function definition for 'dbinom'
dnegbin: no visible global function definition for 'dnbinom'
pLGP: no visible global function definition for 'ppois'
qLGP: no visible global function definition for 'qpois'
rLGP: no visible global function definition for 'rpois'
rLGP: no visible global function definition for 'rnorm'
rLGP: no visible global function definition for 'runif'
rbinegbin: no visible global function definition for 'rnbinom'
rmanaclash: no visible global function definition for 'rbinom'
rmanaclash: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'cheatsheet.Rmd' using rmarkdown
--- finished re-building 'cheatsheet.Rmd'

--- re-building 'gff-processing.Rmd' using rmarkdown
Quitting from lines 102-131 (gff-processing.Rmd) 
Error: processing vignette 'gff-processing.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'gff-processing.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

--- re-building 'nozzle.Rmd' using rmarkdown
--- finished re-building 'nozzle.Rmd'

SUMMARY: processing the following file failed:
  'gff-processing.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following calls to attach():
File 'Rmosek/R/builder.R':
  attach(builderenv, pos, name, warn.conflicts)
See section 'Good practice' in '?attach'.
Package suggested but not available for checking: 'mice'
GNU make is a SystemRequirements.
rms.pval: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking: 'plotly', 'mice'
Package vignette with placeholder title 'Vignette Title':
  'rmtl.Rmd'
dWishartSpike: no visible global function definition for 'dnorm'
pWishartSpike: no visible global function definition for 'pnorm'
qWishartSpike: no visible global function definition for 'qnorm'
rWishartSpike: no visible global function definition for 'qnorm'
rmp: no visible global function definition for 'runif'
rtw: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'openair'
Package required but not available: 'hot.deck'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  'DESeq' 'seqinr' 'topGO'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'rnaturalearthhires'
Malformed Title field: should not end in a period.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'rdflib'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
well19937.validate: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Nnls.trimW : fun1: no visible global function definition for 'runif'
initM: no visible global function definition for 'runif'
rnmf: no visible global function definition for 'txtProgressBar'
rnmf: no visible global function definition for 'setTxtProgressBar'
see: no visible global function definition for 'heat.colors'
see: no visible global function definition for 'colorRampPalette'
see: no visible global function definition for 'grey'
see: no visible global function definition for 'par'
see: no visible global function definition for 'image'
see: no visible global function definition for 'mtext'
simtum: no visible global function definition for 'runif'
simtum: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

Packages suggested but not available for checking: 'ggmap', 'ropenaq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls in package code:
  'robustbase' 'sfsmisc'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for 'as.formula'
.BuildPartial: no visible global function definition for 'residuals'
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for 'na.omit'
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable 'median'
.PairwiseCorrelation: no visible global function definition for
  'complete.cases'
.yw: no visible global function definition for 'toeplitz'
FastQn: no visible global function definition for 'median'
FastQn: no visible global function definition for 'mad'
fqn: no visible global function definition for 'median'
fqn: no visible global function definition for 'mad'
psdcor: no visible global function definition for 'posdefify'
psdcor: no visible global function definition for 'nearcor'
robar: no visible global function definition for 'frequency'
robcor: no visible global function definition for 'covMcd'
s_FastQn: no visible global function definition for 'median'
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
RobRSVD: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Package suggested but not available for checking: 'clubSandwich'
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo' 'mgcv' 'robustbase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GIC: no visible global function definition for 'integrate'
QM.poisson: no visible global function definition for 'ppois'
QM.poisson: no visible global function definition for 'dpois'
expect.poisson: no visible global function definition for 'dpois'
expect.poisson: no visible global function definition for 'ppois'
pred.robustgam: no visible global function definition for
  'Predict.matrix'
robust.sigma: no visible global function definition for 'median'
robustgam: no visible global function definition for 's'
robustgam: no visible global function definition for
  'smooth.construct.tp.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.cr.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.ps.smooth.spec'
robustgam : w.fun: no visible global function definition for 'covMcd'
robustgam.GIC.optim: no visible global function definition for 'optim'
robustgam.crossval : w.fun: no visible global function definition for
  'covMcd'
robustgam.crossval: no visible global function definition for
  'integrate'
smooth.construct.tr.smooth.spec: no visible global function definition
  for 'quantile'
w.binomial: no visible global function definition for 'pbinom'
w.poisson: no visible global function definition for 'ppois'
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aggregateRanks: no visible binding for global variable 'median'
aggregateRanks: no visible global function definition for 'pnorm'
betaScores: no visible global function definition for 'pbeta'
correctBetaPvaluesExact: no visible binding for global variable 'qbeta'
thresholdBetaScore: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  median pbeta pnorm qbeta
Consider adding
  importFrom("stats", "median", "pbeta", "pnorm", "qbeta")
to your NAMESPACE file.
Package required but not available: 'ggpubr'

Package suggested but not available for checking: 'GEOquery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Package required but not available: 'DiagrammeR'

Package suggested but not available for checking: 'rENA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DiagrammeR', 'flexsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
NPROCwoGS: no visible global function definition for 'quantile'
NPROCwoGS : rdirichlet: no visible global function definition for
  'rgamma'
NPROCwoGS: no visible global function definition for 'rbinom'
NPROCwoGS: no visible global function definition for 'rbeta'
NPROCwoGS: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  quantile rbeta rbinom rgamma
Consider adding
  importFrom("stats", "quantile", "rbeta", "rbinom", "rgamma")
to your NAMESPACE file.
prepare_Rd: score.Rd:20-22: Dropping empty section \details
prepare_Rd: score.Rd:23-25: Dropping empty section \source
prepare_Rd: score.Rd:26-28: Dropping empty section \references
Rd file 'NPROCwoGS.Rd':
  \examples lines wider than 100 characters:
     AUC<- sum((ROC.est$T.Se[1,-1]+ROC.est$T.Se[1,-(ncutoff+2)])*(ROC.est$T.Sp[1,-1]-ROC.est$T.Sp[1,-(ncutoff+2)])/2)
     plot(1-ROC.est$T.Sp[1,],ROC.est$T.Se[1,],"l", xlab="1-Specificities",ylab="Sensitivities", main=paste("AUC=", format(AUC, digits=4),

Rd file 'ROCwoGS-package.Rd':
  \examples lines wider than 100 characters:
     AUC<- sum((ROC.est$T.Se[1,-1]+ROC.est$T.Se[1,-(ncutoff+2)])*(ROC.est$T.Sp[1,-1]-ROC.est$T.Sp[1,-(ncutoff+2)])/2)
     plot(1-ROC.est$T.Sp[1,],ROC.est$T.Se[1,],"l", xlab="1-Specificities",ylab="Sensitivities", main=paste("AUC=", format(AUC, digits=4),

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: 'tidyr'
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'RODBC'
A package should be listed in only one of these fields.
'library' or 'require' call to 'RODBC' which was already attached by Depends.
  Please remove these calls from your code.
GNU make is a SystemRequirements.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ROSE.eval: no visible global function definition for 'methods'
ROSE.eval: no visible binding for global variable 'model.frame'
ROSE.eval: no visible binding for global variable 'predict'
adj.formula: no visible global function definition for 'terms'
adj.formula: no visible global function definition for 'as.formula'
omnibus.balancing: no visible binding for global variable 'model.frame'
ou.sampl: no visible global function definition for 'rbinom'
over.sampl: no visible global function definition for 'rbinom'
roc.curve: no visible global function definition for 'lines'
roc.curve: no visible global function definition for 'abline'
rose.real: no visible binding for global variable 'sd'
rose.real: no visible global function definition for 'sd'
rose.real: no visible global function definition for 'rnorm'
rose.sampl: no visible global function definition for 'rbinom'
under.sampl: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  abline as.formula lines methods model.frame predict rbinom rnorm sd
  terms
Consider adding
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
bestFM: no visible global function definition for 'data'
gaRoth: no visible global function definition for 'data'
ros: no visible global function definition for 'na.omit'
rosunc: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Packages suggested but not available for checking: 'phylobase', 'RNeXML'
Error(s) in re-building vignettes:
  ...
--- re-building 'data_mashups.Rmd' using rmarkdown
Quitting from lines 151-155 (data_mashups.Rmd) 
Error: processing vignette 'data_mashups.Rmd' failed with diagnostics:
there is no package called 'phylobase'
--- failed re-building 'data_mashups.Rmd'

--- re-building 'meta-analysis.Rmd' using rmarkdown
--- finished re-building 'meta-analysis.Rmd'

--- re-building 'rotl.Rmd' using rmarkdown
--- finished re-building 'rotl.Rmd'

SUMMARY: processing the following file failed:
  'data_mashups.Rmd'

Error: Vignette re-building failed.
Execution halted
.computeValueReduct: no visible global function definition for 'combn'
.findAllReductsFromCore: no visible global function definition for
  'combn'
.findFirstReductsFromCore: no visible global function definition for
  'combn'
.findSmallestReductFamilyFromCore: no visible global function
  definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
royston.test: no visible global function definition for 'shapiro.test'
royston.test: no visible global function definition for 'cor'
royston.test: no visible global function definition for 'qnorm'
royston.test: no visible global function definition for 'pnorm'
royston.test: no visible global function definition for 'cov'
royston.test: no visible global function definition for 'mahalanobis'
royston.test: no visible global function definition for 'qqplot'
royston.test: no visible global function definition for 'qchisq'
royston.test: no visible global function definition for 'ppoints'
royston.test: no visible global function definition for 'abline'
royston.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
License components which are templates and need '+ file LICENSE':
  MIT
Package in Depends field not imported from: 'hash'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
P: no visible global function definition for 'has.key'
get_rand_int: no visible global function definition for 'runif'
last: no visible global function definition for 'tail'
rand_partitions: no visible global function definition for 'hash'
Undefined global functions or variables:
  has.key hash runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
evalMedian: no visible global function definition for 'xtabs'
evalMode: no visible global function definition for 'xtabs'
rpartScore: no visible global function definition for 'model.extract'
rpartScore: no visible global function definition for 'var'
rpartScore: no visible binding for global variable 'var'
splitAbs: no visible global function definition for 'xtabs'
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to 'RODBC' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
rpart.rules.push: no visible global function definition for 'sqlSave'
rpart.rules.table : <anonymous>: no visible global function definition
  for 'setNames'
rpart.subrules.table : <anonymous>: no visible global function
  definition for 'setNames'
Undefined global functions or variables:
  setNames sqlSave
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Package vignette with placeholder title 'Vignette Title':
  'codelists.Rmd'
Non-standard file/directory found at top level:
  'Read-and-delete-me'
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'survival'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'MASS' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenerateData: no visible global function definition for 'mvrnorm'
GetVarImp : FitPenalizedModel: no visible global function definition
  for 'clogit'
Undefined global functions or variables:
  clogit mvrnorm
Rd file 'GetVarImp.Rd':
  \examples lines wider than 100 characters:
     hist(MyResults, breaks=6, col="orange", xlab="Importance score", ylab="Number of features", main="Histogram of R-PCLR variable importan ... [TRUNCATED]
     ## Sort from most important (highest importance score) to least important feature (lowest importance score)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  'Rpdb.pdb'
Package required but not available: 'doBy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'mygraph.eps' 'mygraph.png' 'mygraph.tex'
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'usage.Rmd' using knitr
Quitting from lines 134-139 (usage.Rmd) 
Error: processing vignette 'usage.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'usage.Rmd'

SUMMARY: processing the following file failed:
  'usage.Rmd'

Error: Vignette re-building failed.
Execution halted
Found a 'configure.in' file: 'configure.ac' has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/libpq/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
GNU make is a SystemRequirements.
Package required but not available: 'tidyr'

Packages suggested but not available for checking:
  'flexsurv', 'flexsurvcure'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
but_last: no visible global function definition for 'head'
first: no visible global function definition for 'head'
last: no visible global function definition for 'tail'
preview_frames: no visible global function definition for 'str'
print.EprimeFrame: no visible global function definition for 'str'
print.FrameList: no visible global function definition for 'str'
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  'rpsychi-Ex.R'
Rd file 'ind.prop.Rd':
  \examples lines wider than 100 characters:
     ind.prop(y~x, data=dat, lev.count=2, ref.ind=1)    #Odds for not relapse is higher in treatment than control condition.
     ind.prop(y~x, data=dat, lev.count=1, ref.ind=1)    #Odds for relapse is lower in treatment than control condition.
     ind.prop(y~x, data=dat, lev.count=2, ref.ind=2)    #Odds for not relapse is lower in control than treatment condition.
     ind.prop(y~x, data=dat, lev.count=1, ref.ind=2)    #Odds for relapse is higher in control than treatment condition.

Rd file 'ind.prop.second.Rd':
  \examples lines wider than 100 characters:
     ind.prop.second(x=tab[,1], n = rowSums(tab))             #Risk for relapse is lower in treatment than control condition.
     ind.prop.second(x=tab[,1], n = rowSums(tab), ref.ind=2)  #Risk for relapse is higher in control than treatment condition.

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: 'ggpubr'
Error(s) in re-building vignettes:
  ...
--- re-building 'Rpvt.Rmd' using rmarkdown
Quitting from lines 115-172 (Rpvt.Rmd) 
Error: processing vignette 'Rpvt.Rmd' failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building 'Rpvt.Rmd'

SUMMARY: processing the following file failed:
  'Rpvt.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'DiagrammeR'
Found the following files/directories:
  'HL_H0.pdf' 'pi0infer.pdf' 'rate.txt' 'summary.txt'
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'RelativePermeability.Rmd' using rmarkdown
Quitting from lines 29-78 (RelativePermeability.Rmd) 
Error: processing vignette 'RelativePermeability.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'RelativePermeability.Rmd'

SUMMARY: processing the following file failed:
  'RelativePermeability.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'mvoutlier'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'test.bpl' 'test.cr' 'test.ct'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'robustbase' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.computekappa: no visible global function definition for 'pnorm'
.computekappa: no visible global function definition for 'dnorm'
.initmethod : <anonymous>: no visible global function definition for
  'median'
.initmethod: no visible global function definition for 'model.matrix'
.mspe: no visible global function definition for 'rnorm'
.mspe : <anonymous>: no visible global function definition for 'rnorm'
makedata: no visible global function definition for 'rnorm'
makedata : addraneff: no visible global function definition for 'rnorm'
plot.meanssaemodel: no visible global function definition for 'par'
plot.meanssaemodel: no visible global function definition for 'lines'
plot.meanssaemodel: no visible global function definition for 'axis'
plot.meanssaemodel: no visible global function definition for 'grid'
plot.meanssaemodel: no visible global function definition for 'box'
plot.meanssaemodel: no visible global function definition for 'legend'
plot.meanssaemodel: no visible global function definition for 'arrows'
saemodel: no visible global function definition for 'model.frame'
saemodel: no visible global function definition for 'model.response'
saemodel: no visible global function definition for 'model.matrix'
summary.fitsaemodel: no visible global function definition for 'pt'
summary.fitsaemodel: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'plotly'
Package required but not available: 'tidyr'

Packages suggested but not available for checking: 'recipes', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'qgraph'
stripslash: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
convexhull: no visible global function definition for 'chull'
convexhull: no visible global function definition for 'rnorm'
drawcompletegraph: no visible global function definition for 'segments'
getbag: no visible global function definition for 'chull'
getbag: no visible global function definition for 'polygon'
getbag: no visible global function definition for 'points'
inflate: no visible global function definition for 'rnorm'
rsmed: no visible global function definition for 'runif'
rsplot: no visible global function definition for 'chull'
rsplot: no visible global function definition for 'polygon'
rsplot: no visible global function definition for 'points'
rsrings: no visible global function definition for 'chull'
rsrings: no visible global function definition for 'polygon'
rsrings: no visible global function definition for 'points'
rstinterval: no visible global function definition for 'runif'
rstinterval: no visible global function definition for 'rnorm'
rstinterval: no visible global function definition for 'chull'
rstinterval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  chull points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'Rcompression'
Non-standard files/directories found at top level:
  'aclocal.m4' 'clients' 'clients.txt' 'version'
GNU make is a SystemRequirements.
Note: information on .o files is not available
File '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rserve/libs/Rserve.so':
  Found 'exit', possibly from 'exit' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'random', possibly from 'random' (C)
  Found 'srandom', possibly from 'srandom' (C)
File 'Rserve/libs/Rserve.so':
  Found non-API call to R: 'R_TempDir'

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
addNoisyCopies: no visible global function definition for 'rnorm'
eta: no visible global function definition for 'var'
gaussClassifier: no visible global function definition for 'runif'
getSigma: no visible global function definition for 'sd'
getSigma: no visible binding for global variable 'sd'
sfaClassify: no visible global function definition for 'rainbow'
sfaClassify: no visible global function definition for 'par'
sfaClassify: no visible global function definition for 'points'
sfaClassify: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines par points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'aire.zmvm', 'ggmap', 'tidyr'
Package suggested but not available for checking: 'NeuralNetTools'
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'INLA'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
negbin.pow : negbin.disp: no visible global function definition for
  'rpois'
negbin.pow : negbin.disp: no visible global function definition for
  'rnbinom'
negbin.pow : inner.fcn: no visible global function definition for
  'na.omit'
negbin.pow : inner.fcn: no visible global function definition for
  'quantile'
negbin.pow: no visible global function definition for 'txtProgressBar'
negbin.pow: no visible global function definition for
  'setTxtProgressBar'
poiss.pow : inner.fcn: no visible global function definition for
  'rpois'
poiss.pow : inner.fcn: no visible global function definition for
  'quantile'
poiss.pow: no visible global function definition for 'txtProgressBar'
poiss.pow: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  na.omit quantile rnbinom rpois setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "quantile", "rnbinom", "rpois")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package required but not available: 'GMMAT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'Database' 'rSQM.yaml' 'rSQM_Sample_Project' 'sample_script.R'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Packages required but not available: 'tidyr', 'broom'

Package suggested but not available for checking: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package vignette with placeholder title 'Vignette Title':
  'main-vignette.Rmd'
Malformed Title field: should not end in a period.
Found the following files/directories:
  'Rplots.svg'
Found the following files/directories:
  'svgplot1.svg' 'svgplot10.svg' 'svgplot11.svg' 'svgplot12.svg'
  'svgplot13.svg' 'svgplot2.svg' 'svgplot3.svg' 'svgplot4.svg'
  'svgplot5.svg' 'svgplot6.svg' 'svgplot7.svg' 'svgplot8.svg'
  'svgplot9.svg'
Package vignette with placeholder title 'Vignette Title':
  'vignette.Rmd'
Found the following files/directories:
  'mapCH2017.rda'
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab

Found the following assignments to the global environment:
File 'rSymPy/R/sympy.R':
  assign(".Jython", .jnew("org.python.util.PythonInterpreter"), 
    .GlobalEnv)
  assign(".Jython", rJython(modules = system.file("Lib", package = "rSymPy")), 
    .GlobalEnv)
Malformed Title field: should not end in a period.
barplot.rtconnect: no visible global function definition for 'rainbow'
barplot.rtconnect: no visible global function definition for 'text'
plot.rtconnect: no visible global function definition for 'par'
plot.rtconnect: no visible global function definition for 'axis.Date'
rtconnect: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis.Date par rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'reanalysis_rr98.Rmd' using rmarkdown
Loading required package: rtdists
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
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'tidyr'
Loading required package: purrr
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: binom
`summarise()` regrouping output by 'id', 'instruction' (override with `.groups` argument)
Quitting from lines 57-75 (reanalysis_rr98.Rmd) 
Error: processing vignette 'reanalysis_rr98.Rmd' failed with diagnostics:
could not find function "nest"
--- failed re-building 'reanalysis_rr98.Rmd'

SUMMARY: processing the following file failed:
  'reanalysis_rr98.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'explor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
plotGLCM: no visible global function definition for 'points'
Undefined global functions or variables:
  points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
Found the following files/directories:
  'test_addPageBreak.doc' 'test_addPlot.doc' 'test_addSessionInfo.doc'
  'test_addTable.doc'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'sjPlot'
Error(s) in re-building vignettes:
  ...
--- re-building 'coupled_oscillator_V05.Rmd' using rmarkdown
--- finished re-building 'coupled_oscillator_V05.Rmd'

--- re-building 'inertia_coordination_V05.Rmd' using rmarkdown
--- finished re-building 'inertia_coordination_V05.Rmd'

--- re-building 'overview_data_prep_V05.Rmd' using rmarkdown
--- finished re-building 'overview_data_prep_V05.Rmd'

--- re-building 'sysVar_inOut_V05.Rmd' using rmarkdown
Quitting from lines 63-64 (sysVar_inOut_V05.Rmd) 
Error: processing vignette 'sysVar_inOut_V05.Rmd' failed with diagnostics:
there is no package called 'sjPlot'
--- failed re-building 'sysVar_inOut_V05.Rmd'

SUMMARY: processing the following file failed:
  'sysVar_inOut_V05.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyr', 'timetk', 'tidyquant', 'feasts', 'plotly', 'fabletools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Package required but not available: 'alfred'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'Tsttwalk.dat'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'parsnip', 'tidyr'

Package suggested but not available for checking: 'xrf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'choroplethr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'results'
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Rd file 'Runiversal-package.Rd':
  \examples lines wider than 100 characters:
     #Getting estimates from regression object as Java variables that be directly interpretable by Bean Shell.

These lines will be truncated in the PDF manual.
Found the following files/directories:
  'somefile.xml'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mixOmics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
HapMendlianCheck: no visible global function definition for
  'write.table'
rvPDT.test.sub: no visible global function definition for 'pnorm'
whap.prehap: no visible global function definition for 'write.table'
whap.prehap: no visible global function definition for 'read.table'
Undefined global functions or variables:
  pnorm read.table write.table
Consider adding
  importFrom("stats", "pnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'pixmap' which was already attached by Depends.
  Please remove these calls from your code.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  'par'
rvideopoker : showBack: no visible global function definition for
  'title'
rvideopoker : showCardsInitially: no visible global function definition
  for 'title'
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: 'gpuR'
Package suggested but not available for checking: 'ggraph'
Running examples in 'rvinecopulib-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.rvine_structure
> ### Title: Plotting R-vine structures
> ### Aliases: plot.rvine_structure plot.rvine_matrix
> 
> ### ** Examples
> 
> plot(cvine_structure(1:5))
Error in plot.vinecop_dist(vinecop_dist(pcs, x), ...) : 
  The 'ggraph' package must be installed to plot.
Calls: plot -> plot.rvine_structure -> plot.vinecop_dist
Execution halted
Running 'testthat.R' [7s/8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rvinecopulib)
  > 
  > test_check("rvinecopulib")
  -- 1. Error: plot functions work (@test_rvine_structure.R#40)  -----------------
  The 'ggraph' package must be installed to plot.
  Backtrace:
   1. base::plot(vc)
   2. rvinecopulib:::plot.vinecop_dist(vc)
  
  -- 2. Error: plot functions work (@test_vinecop_dist.R#85)  --------------------
  The 'ggraph' package must be installed to plot.
  Backtrace:
    1. testthat::expect_silent(...)
   10. rvinecopulib:::plot.vinecop_dist(...)
  
  == testthat results  ===========================================================
  [ OK: 255 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: plot functions work (@test_rvine_structure.R#40) 
  2. Error: plot functions work (@test_vinecop_dist.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following notes/warnings:
  Non-staged installation was used
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RVowpalWabbit.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
lc_TDT: no visible global function definition for 'pchisq'
rvTDT: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  dbeta pchisq
Consider adding
  importFrom("stats", "dbeta", "pchisq")
to your NAMESPACE file.
LASSO: no visible global function definition for 'lm'
LASSO: no visible global function definition for 'anova'
LASSO: no visible global function definition for 'glm'
LASSO: no visible global function definition for 'pchisq'
LASSO : <anonymous>: no visible global function definition for
  'extractAIC'
PCR : <anonymous>: no visible global function definition for 'cor'
PLS : <anonymous>: no visible global function definition for 'cor'
RR : RRscore: no visible binding for global variable 'sd'
SPLS: no visible global function definition for 'lm'
SPLS: no visible global function definition for 'anova'
SPLS : <anonymous>: no visible global function definition for
  'extractAIC'
VTWOD : getScores: no visible global function definition for 'sd'
VTWOD : getScores: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
check_ISO_code: no visible binding for global variable 'NoAm_country'
check_ISO_code: no visible binding for global variable 'SoAm_country'
check_ISO_code: no visible binding for global variable 'Oceana_country'
check_ISO_code: no visible binding for global variable 'Africa_country'
check_ISO_code: no visible binding for global variable 'Asia_country'
check_ISO_code: no visible binding for global variable 'Eur_country'
climate_map: no visible binding for global variable 'data'
date_correct: no visible global function definition for 'tail'
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for 'na.omit'
RWBP.default: no visible global function definition for 'kmeans'
RWBP.formula: no visible global function definition for 'model.extract'
predict.RWBP: no visible global function definition for 'head'
Undefined global functions or variables:
  head kmeans model.extract na.omit
Consider adding
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
weblogo: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Found the following files/directories:
  'RWebLogo.pdf' 'RWebLogo.png'
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Malformed Title field: should not end in a period.
.dwt: no visible global function definition for 'median'
.udwt: no visible global function definition for 'median'
plotSignalTransformation: no visible global function definition for
  'box'
plotSignalTransformation: no visible global function definition for
  'axis'
plotSignalTransformation: no visible global function definition for
  'lines'
plotSignalTransformation: no visible global function definition for
  'legend'
Undefined global functions or variables:
  axis box legend lines median
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines")
  importFrom("stats", "median")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'SnakeCharmR', 'tidyr', 'installr'
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'googleAnalyticsR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
flemming.plot: no visible global function definition for 'par'
flemming.plot: no visible global function definition for 'segments'
flemming.plot: no visible global function definition for 'text'
flemming.plot : triax.segments: no visible global function definition
  for 'segments'
legend.bubbles: no visible global function definition for 'quantile'
legend.bubbles: no visible global function definition for 'legend'
other.methods: no visible global function definition for 'quantile'
pejrup.plot: no visible global function definition for 'par'
pejrup.plot: no visible global function definition for 'segments'
pejrup.plot: no visible global function definition for 'text'
pejrup.plot : triax.segments: no visible global function definition for
  'segments'
pejrup.plot: no visible global function definition for 'legend'
rysgran.plot: no visible global function definition for 'par'
rysgran.plot: no visible global function definition for 'text'
rysgran.plot: no visible global function definition for 'points'
rysgran.plot: no visible global function definition for 'abline'
rysgran.plot: no visible global function definition for 'mtext'
rysgran.ternary: no visible global function definition for 'par'
rysgran.ternary: no visible global function definition for 'points'
rysgran.ternary: no visible global function definition for 'text'
shepard.plot: no visible global function definition for 'par'
shepard.plot: no visible global function definition for 'segments'
shepard.plot: no visible global function definition for 'text'
shepard.plot : triax.segments: no visible global function definition
  for 'segments'
shepard.plot: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend mtext par points quantile segments text
Consider adding
  importFrom("graphics", "abline", "legend", "mtext", "par", "points",
             "segments", "text")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package required but not available: 'biclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
calculate.summary: no visible global function definition for 'sd'
detect.saccades: no visible global function definition for 'median'
diagnostic.plot: no visible global function definition for 'dev.new'
diagnostic.plot: no visible global function definition for 'par'
diagnostic.plot: no visible global function definition for 'recordPlot'
diagnostic.plot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.new dev.off median par recordPlot sd
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
CV.Epidemic.Vn: no visible global function definition for 'uniroot'
CV.Epidemic.Wn: no visible global function definition for 'uniroot'
G.alfa: no visible global function definition for 'dchisq'
Graf.Diagnostic: no visible global function definition for 'stepfun'
Graf.Diagnostic: no visible global function definition for 'title'
Graf.Diagnostic: no visible global function definition for 'quantile'
Graf.Diagnostic: no visible global function definition for 'legend'
Graf.Diagnostic: no visible global function definition for 'arrows'
Graf.Diagnostic: no visible global function definition for 'par'
Plot.ll: no visible global function definition for 'segments'
Plot.ll: no visible global function definition for 'axis'
SemiparChangePoint: no visible global function definition for 'glm'
SemiparChangePoint: no visible binding for global variable 'binomial'
SemiparChangePoint: no visible global function definition for
  'glm.control'
SemiparChangePoint: no visible global function definition for 'coef'
Sn.alfa : tempfun: no visible global function definition for 'dchisq'
Sn.alfa : d.tempfun: no visible global function definition for 'dchisq'
Zn.alfa : tempfun: no visible global function definition for 'dchisq'
Zn.alfa : d.tempfun: no visible global function definition for 'dchisq'
cumsum.test: no visible global function definition for 'var'
p.OneChange : tempfun: no visible global function definition for
  'dchisq'
p.OneChange: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  arrows axis binomial coef dchisq glm glm.control legend par quantile
  segments stepfun title uniroot var
Consider adding
  importFrom("graphics", "arrows", "axis", "legend", "par", "segments",
             "title")
  importFrom("stats", "binomial", "coef", "dchisq", "glm", "glm.control",
             "quantile", "stepfun", "uniroot", "var")
to your NAMESPACE file.
prepare_Rd: BootsModelTest.Rd:28-29: Dropping empty section \details
prepare_Rd: BootsModelTest.Rd:43: Dropping empty section \note
prepare_Rd: CriticalValues.Rd:38: Dropping empty section \note
prepare_Rd: Pvalues.Rd:24-25: Dropping empty section \details
prepare_Rd: Pvalues.Rd:38: Dropping empty section \note
prepare_Rd: cumsum.test.Rd:16-17: Dropping empty section \details
prepare_Rd: cumsum.test.Rd:28: Dropping empty section \note
fit.saery.AR1: no visible global function definition for 'qnorm'
fit.saery.MA1: no visible global function definition for 'qnorm'
fit.saery.indep: no visible global function definition for 'qnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'write.table'
plot.saery: no visible global function definition for 'devAskNewPage'
plot.saery: no visible global function definition for 'par'
plot.saery: no visible global function definition for 'abline'
plot.saery: no visible global function definition for 'title'
plot.saery: no visible global function definition for 'axis'
plot.saery: no visible global function definition for 'lines'
plot.saery: no visible global function definition for 'legend'
pvalue: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par pnorm qnorm rnorm title
  write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package in Depends field not imported from: 'lpSolveAPI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable 'gaussian'
glm: no visible global function definition for 'glm.control'
glm: no visible global function definition for 'model.response'
glm: no visible global function definition for 'is.empty.model'
glm: no visible global function definition for 'model.matrix'
glm: no visible global function definition for 'model.weights'
glm: no visible global function definition for 'model.offset'
glm: no visible global function definition for 'model.extract'
glm: no visible global function definition for 'glm.fit'
glm: no visible global function definition for '.getXlevels'
separator: no visible global function definition for 'make.lp'
separator: no visible global function definition for 'set.column'
separator: no visible global function definition for 'set.rhs'
separator: no visible global function definition for 'set.constr.type'
separator: no visible global function definition for 'set.objfn'
separator: no visible global function definition for 'set.bounds'
separator: no visible global function definition for 'lp.control'
separator: no visible global function definition for 'get.variables'
separator: no visible global function definition for 'set.basis'
separator: no visible global function definition for
  'get.dual.solution'
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Rd file 'mudiff.acc.Rd':
  \usage lines wider than 90 characters:
     mudiff.acc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, equal = TRUE, m = 10000, mcs = 3)

Rd file 'mudiff.alc.Rd':
  \usage lines wider than 90 characters:
     mudiff.alc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, equal = TRUE, m = 10000, mcs = 3)

Rd file 'mudiff.mblmodwoc.Rd':
  \usage lines wider than 90 characters:
     mudiff.mblmodwoc(len, alpha1, beta1, alpha2, beta2, level = 0.95, worst.level = 0.95, m = 50000, mcs = 3)

Rd file 'mudiff.mblmodwoc.equalvar.Rd':
  \usage lines wider than 90 characters:
     mudiff.mblmodwoc.equalvar(len, alpha, beta, level = 0.95, worst.level = 0.95, m = 50000, mcs = 3)

Rd file 'mudiff.modwoc.Rd':
  \usage lines wider than 90 characters:
     mudiff.modwoc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, worst.level = 0.95, equal = TRUE, m = 50000, mcs = 3)

Rd file 'mudiff.modwoc.equalvar.Rd':
  \usage lines wider than 90 characters:
     mudiff.modwoc.equalvar(len, alpha, beta, n01, n02, level = 0.95, worst.level = 0.95, equal = TRUE)

These lines will be truncated in the PDF manual.
propdiff.acc: no visible global function definition for 'rbeta'
propdiff.acc: no visible global function definition for 'rbinom'
propdiff.acc: no visible global function definition for 'pbeta'
propdiff.alc: no visible global function definition for 'rbeta'
propdiff.alc: no visible global function definition for 'rbinom'
propdiff.alc: no visible global function definition for 'qbeta'
propdiff.freq: no visible global function definition for 'qnorm'
propdiff.mblacc: no visible global function definition for 'rbeta'
propdiff.mblacc: no visible global function definition for 'rbinom'
propdiff.mblacc: no visible global function definition for 'pbeta'
propdiff.mblalc: no visible global function definition for 'rbeta'
propdiff.mblalc: no visible global function definition for 'rbinom'
propdiff.mblalc: no visible global function definition for 'qbeta'
propdiff.mblmodwoc: no visible global function definition for 'qchisq'
propdiff.mblmodwoc: no visible global function definition for 'pbeta'
propdiff.mblwoc: no visible global function definition for 'pbeta'
propdiff.modwoc: no visible global function definition for 'qchisq'
propdiff.modwoc: no visible global function definition for 'pbeta'
propdiff.woc: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
GraphBinaryForestPlot: no visible global function definition for
  'abline'
GraphBinaryForestPlot: no visible global function definition for 'text'
GraphContinuousForestPlot: no visible global function definition for
  'abline'
GraphContinuousForestPlot: no visible global function definition for
  'text'
ImputeBinaryEvents: no visible global function definition for 'rbinom'
ImputeSMD: no visible global function definition for 'rnorm'
funnelplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
generate.sample.core: no visible global function definition for
  'predict'
mdh: no visible global function definition for 'model.frame'
mdh: no visible binding for global variable 'na.fail'
mdh: no visible global function definition for '.getXlevels'
mdh: no visible global function definition for 'quantile'
mdh: no visible global function definition for 'hist'
predict.mdh: no visible global function definition for 'model.frame'
samur: no visible global function definition for 'predict'
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: 'geepack'
Errors in running code in vignettes:
when running code in 'sandwich-CL.Rnw'
  ...

> library("sandwich")

> library("geepack")

  When sourcing 'sandwich-CL.R':
Error: there is no package called 'geepack'
Execution halted

  'sandwich-CL.Rnw'... failed
  'sandwich-OOP.Rnw'... [4s/4s] OK
  'sandwich.Rnw'... [1s/2s] OK
Error(s) in re-building vignettes:
  ...
--- re-building 'sandwich-CL.Rnw' using Sweave

Error: processing vignette 'sandwich-CL.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("geepack") : there is no package called 'geepack'

--- failed re-building 'sandwich-CL.Rnw'

--- re-building 'sandwich-OOP.Rnw' using Sweave
Loading required package: car
Loading required package: carData
Loading required package: lmtest
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: survival
--- finished re-building 'sandwich-OOP.Rnw'

--- re-building 'sandwich.Rnw' using Sweave

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

--- finished re-building 'sandwich.Rnw'

SUMMARY: processing the following file failed:
  'sandwich-CL.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'openair'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'tidyverse'
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for 'download.file'
generate.sas7bdat.source: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
parse.SAScii: no visible binding for global variable 'end'
parse.SAScii: no visible binding for global variable 'start'
read.SAScii: no visible global function definition for 'download.file'
read.SAScii: no visible global function definition for 'unzip'
read.SAScii: no visible global function definition for 'read.fwf'
read.SAScii: no visible global function definition for 'capture.output'
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
Rd file 'read.SAScii.Rd':
  \usage lines wider than 90 characters:
     read.SAScii( fn, sas_ri, beginline = 1, buffersize = 50, zipped = F , n = -1 , intervals.to.print = 1000 , lrecl = NULL , skip.decimal. ... [TRUNCATED]
  \examples lines wider than 100 characters:
                     paste( "http://smpbff2.dsd.census.gov/pub/sipp/2004/l04puw" , i , ".zip" , sep = "" )

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
SASPECT: no visible global function definition for 'dbinom'
my.SOnePro: missing arguments not allowed in calls to 'c'
my.ttest: no visible global function definition for 'var'
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
Found the following files/directories:
  'SASPECT.result.txt'
GNU make is a SystemRequirements.
Found the following files/directories:
  'stateLung-R01.pdf' 'stateLung-R01.txt'
loads: no visible global function definition for 'untar'
saves: no visible global function definition for 'tar'
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
K: no visible global function definition for 'dnorm'
sBF: no visible global function definition for 'density'
sBF: no visible global function definition for 'txtProgressBar'
sBF: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package required but not available: 'factoextra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Malformed Description field: should contain one or more complete sentences.
fitSBSA: no visible binding for global variable 'var'
fitSBSA: no visible global function definition for 'var'
fitSBSA: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
Non-standard file/directory found at top level:
  'src-java'
GNU make is a SystemRequirements.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.scair: no visible global function definition for 'par'
plot.scair: no visible global function definition for 'points'
plot.scar: no visible global function definition for 'par'
plot.scar: no visible global function definition for 'points'
predict.scair: no visible global function definition for 'approx'
predict.scar: no visible global function definition for 'approx'
scair: no visible global function definition for 'gaussian'
scair: no visible global function definition for 'runif'
scair: no visible global function definition for 'rnorm'
scar: no visible global function definition for 'gaussian'
scar: no visible global function definition for 'glm.fit'
scar: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx gaussian glm.fit par points rnorm runif
Consider adding
  importFrom("graphics", "par", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package vignette with placeholder title 'Vignette Title':
  'buildtree.Rmd'
Packages required but not available: 'tidygraph', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
prime.factor: no visible global function definition for 'data'
prime.factor: no visible binding for global variable 'primlist'
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File 'schoolmath/R/prime.factor.R':
  data(primlist)
See section 'Good practice' in '?data'.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'QUIC'
Error(s) in re-building vignettes:
  ...
--- re-building 'scLink-vignette.Rmd' using rmarkdown
Quitting from lines 40-41 (scLink-vignette.Rmd) 
Error: processing vignette 'scLink-vignette.Rmd' failed with diagnostics:
Please make sure the package QUIC is installed!
--- failed re-building 'scLink-vignette.Rmd'

SUMMARY: processing the following file failed:
  'scLink-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Seurat', 'gprofiler2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'alakazam', 'shazam', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
score.GGUM: no visible global function definition for 'dnorm'
score.GGUM: no visible global function definition for 'hist'
score.GGUM: no visible global function definition for 'write.table'
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  'EAP_est1.txt'
CreatePssm: no visible binding for global variable 'training'
Undefined global functions or variables:
  training
Packages required but not available: 'dynwrap', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
License components which are templates and need '+ file LICENSE':
  MIT License
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  'RCurl' 'XML'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for 'getURLAsynchronous'
scrape: no visible global function definition for 'runif'
scrape: no visible global function definition for 'capture.output'
scrape: no visible binding for global variable 'xmlParse'
scrape: no visible binding for global variable 'htmlParse'
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Package suggested but not available for checking: 'oligoClasses'
Found the following calls to attach():
File 'scriptests/R/source.pkg.R':
  attach(NULL, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
  attach(envir, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
See section 'Good practice' in '?attach'.
Package required but not available: 'TPEA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'case-study.Rmd' using rmarkdown
Quitting from lines 53-60 (case-study.Rmd) 
Error: processing vignette 'case-study.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'case-study.Rmd'

--- re-building 'replicating-basque.Rmd' using rmarkdown
--- finished re-building 'replicating-basque.Rmd'

SUMMARY: processing the following file failed:
  'case-study.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
lahiri.design: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
estimateTimeToComputeTargetDefinition: no visible global function
  definition for 'flush.console'
estimateTimeToComputeTargetDefinition: no visible global function
  definition for 'combn'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'flush.console'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'combn'
initialize,sdcTargetDefinitionClass: no visible global function
  definition for 'quantile'
initialize,sdcTargetMatrixClass: no visible global function definition
  for 'flush.console'
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
Found the following files/directories:
  'result.txt'
prepare_Rd: sdd.Rd:46-47: Dropping empty section \seealso
prepare_Rd: sddpack-package.Rd:31-32: Dropping empty section \seealso
prepare_Rd: sddsolve.Rd:29-30: Dropping empty section \references
prepare_Rd: sddsolve.Rd:38-39: Dropping empty section \seealso
prepare_Rd: sddsolve.Rd:40-41: Dropping empty section \examples
.ACF.compute: no visible global function definition for 'pnorm'
.ACF.compute: no visible global function definition for 'qnorm'
.ACF.compute: no visible global function definition for 'pchisq'
.ACF.plot: no visible global function definition for 'abline'
.ADF.compute: no visible global function definition for 'qnorm'
.ADF.compute: no visible global function definition for 'chisq.test'
.ADF.compute: no visible global function definition for 'qchisq'
.ADF.compute: no visible global function definition for 'pchisq'
.ADF.plot: no visible global function definition for 'abline'
.CADF.plot: no visible global function definition for 'points'
.DeltaADF.plot: no visible global function definition for 'abline'
.RPADF.compute: no visible global function definition for 'pchisq'
.RPADF.compute: no visible global function definition for 'qchisq'
.RPADF.plot: no visible global function definition for 'abline'
.RPADF.plot: no visible global function definition for 'rect'
.fmin: no visible global function definition for 'optimize'
.fobj: no visible global function definition for 'pchisq'
.gen.plot: no visible global function definition for 'axis'
.gen.plot: no visible global function definition for 'box'
.gen.plot: no visible global function definition for 'abline'
.lcv: no visible global function definition for 'bw.nrd0'
.lcv: no visible global function definition for 'nlm'
ADF: no visible binding for global variable 'p.adjust.methods'
ADF: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  abline axis box bw.nrd0 chisq.test nlm optimize p.adjust
  p.adjust.methods pchisq pnorm points qchisq qnorm rect
Consider adding
  importFrom("graphics", "abline", "axis", "box", "points", "rect")
  importFrom("stats", "bw.nrd0", "chisq.test", "nlm", "optimize",
             "p.adjust", "p.adjust.methods", "pchisq", "pnorm", "qchisq",
             "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  'MC p-value.ps' 'Output.csv' 'Rh.ps' 'Th.ps' 'dataratio .Rdata'
  'featuresRmax.csv' 'featuresT.csv'
Packages required but not available: 'ggsn', 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dimplot: no visible global function definition for 'par'
dimplot: no visible global function definition for 'barplot'
dimplot: no visible global function definition for 'axis'
find.traj: no visible global function definition for 'flush.console'
nullprob: no visible global function definition for 'pbinom'
pbox: no visible global function definition for 'rect'
pbox: no visible global function definition for 'par'
prim.traj: no visible global function definition for 'flush.console'
prim.trajauto: no visible global function definition for
  'flush.console'
resampstats: no visible binding for global variable 'sd'
scatterbox: no visible binding for global variable 'box'
sd.start: no visible global function definition for 'read.csv'
sd.start: no visible global function definition for 'par'
sd.start: no visible global function definition for 'graphics.off'
sd.start: no visible global function definition for 'hist'
sd.start: no visible global function definition for 'plot.ecdf'
sd.start: no visible global function definition for 'write.csv'
sd.start: no visible global function definition for 'flush.console'
trajplot: no visible global function definition for 'points'
trajplot: no visible global function definition for 'flush.console'
trajplot: no visible global function definition for 'lm'
trajplot: no visible global function definition for 'predict.lm'
trajplot: no visible global function definition for 'identify'
Undefined global functions or variables:
  axis barplot box flush.console graphics.off hist identify lm par
  pbinom plot.ecdf points predict.lm read.csv rect sd write.csv
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "axis", "barplot", "box", "hist", "identify",
             "par", "points", "rect")
  importFrom("stats", "lm", "pbinom", "plot.ecdf", "predict.lm", "sd")
  importFrom("utils", "flush.console", "read.csv", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  'demofile.txt'
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.
sealasso: no visible global function definition for 'lars'
weight.calc: no visible global function definition for 'lars'
Undefined global functions or variables:
  lars
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'createTree.Rd':
  \usage lines wider than 90 characters:
     createTree(data, treeType = "quad", dataType = "point", columns = if (dataType=="point") 1:2 else 1:4, ...)

These lines will be truncated in the PDF manual.
adx: no visible global function definition for 'abline'
adx: no visible global function definition for 'legend'
dx: no visible global function definition for 'abline'
dx: no visible global function definition for 'legend'
maxd: no visible global function definition for 'abline'
maxd: no visible global function definition for 'legend'
pc: no visible global function definition for 'rainbow'
pc: no visible global function definition for 'abline'
pc: no visible global function definition for 'legend'
pc: no visible global function definition for 'points'
pcu: no visible global function definition for 'rainbow'
pcu: no visible global function definition for 'abline'
pcu: no visible global function definition for 'legend'
pcu: no visible global function definition for 'points'
rmsd: no visible global function definition for 'abline'
rmsd: no visible global function definition for 'legend'
rsd: no visible global function definition for 'abline'
rsd: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "points")
to your NAMESPACE file.
Package vignette with placeholder title 'Vignette Title':
  'seastests-vignette.Rmd'
Package in Depends field not imported from: 'JM'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SEchart: no visible global function definition for 'rect'
SEchart: no visible global function definition for 'par'
SEchart: no visible global function definition for 'grid'
SEchart: no visible global function definition for 'axis'
SEchart: no visible global function definition for 'text'
SEchart: no visible global function definition for 'lines'
SEchart: no visible global function definition for 'heat.colors'
SEchart: no visible global function definition for 'topo.colors'
SEchart: no visible global function definition for 'cm.colors'
SEchart: no visible global function definition for 'terrain.colors'
SEchart: no visible global function definition for 'gray.colors'
SEchart: no visible global function definition for 'rainbow'
SEchart: no visible global function definition for 'points'
SEchart: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par points
  rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "points", "rect", "text")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
fdc2s: no visible global function definition for 'lm'
fdc3s: no visible global function definition for 'lm'
fds2s: no visible global function definition for 'lm'
fds3s: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Package required but not available: 'phylobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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).
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'rsbml'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
.read.SeerStatTXT: no visible global function definition for
  'read.table'
.write.SeerStatTXT: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
prepare_Rd: SEER2RTestdata.Rd:77-78: Dropping empty section \source
Rd file 'SEER2R-package.Rd':
  \examples lines wider than 100 characters:
     #load testing data: there are three data objects, i.e. SEER2RTestData1,SEER2RTestData2,SEER2RTestData3 
     dicinfoused = write.SeerStat(SEER2RTestData2, DICfileName = "testrun1.dic",UseVarLabelsInTxtFile=FALSE);

Rd file 'read.SeerStat.Rd':
  \usage lines wider than 90 characters:
     read.SeerStat(DICfileName, TXTfileName = NULL, UseVarLabelsInData = FALSE,ReadHeaderOnly=FALSE,...)
  \examples lines wider than 100 characters:
     #load testing data: there are three data objects, i.e. SEER2RTestData1,SEER2RTestData2,SEER2RTestData3 
     dicinfoused = write.SeerStat(SEER2RTestData2, DICfileName = "testrun1.dic",UseVarLabelsInTxtFile=FALSE);

Rd file 'write.SeerStat.Rd':
  \usage lines wider than 90 characters:
     write.SeerStat(myData, DICfileName, TXTfileName = NULL, UseVarLabelsInTxtFile = TRUE, LabVarsNames = NULL,...)
  \examples lines wider than 100 characters:
     #load testing data: there are three data objects, i.e. SEER2RTestData1,SEER2RTestData2,SEER2RTestData3 
     dicinfoused = write.SeerStat(SEER2RTestData2, DICfileName = "testrun1.dic",UseVarLabelsInTxtFile=FALSE);

These lines will be truncated in the PDF manual.
Found the following files/directories:
  'testrun1.dic' 'testrun1.txt' 'testrun2.dic' 'testrun2.txt'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggraph', 'tidygraph', 'tidyr'
Package suggested but not available for checking: 'tidyr'
Package suggested but not available for checking: 'moveHMM'
Package suggested but not available for checking: 'tidyr'
get.infectiousness: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Packages required but not available: 'tidyr', 'factoextra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'mixOmics'
get_statistics_from_file: no visible global function definition for
  'read.csv'
glm_anova: no visible global function definition for 'aov'
glm_anova: no visible global function definition for 'glm'
glm_anova: no visible global function definition for 'gaussian'
glm_anova: no visible global function definition for 'anova'
glm_anova: no visible global function definition for 'quasipoisson'
glm_anova: no visible global function definition for 'sd'
glm_anova: no visible global function definition for 'p.adjust'
ttest_cohens_d: no visible global function definition for 't.test'
ttest_cohens_d: no visible global function definition for 'sd'
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  'expression.csv' 'group.csv'
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable 'dbeta'
getbinPost: no visible binding for global variable 'pbeta'
getbinPost : fu: no visible global function definition for 'dbinom'
getbinPost : fu: no visible global function definition for 'predict'
getbinPost: no visible global function definition for 'integrate'
getbinPost: no visible global function definition for 'splinefun'
int.funct: no visible global function definition for 'integrate'
int.funct2: no visible global function definition for 'integrate'
min.abs: no visible global function definition for 'uniroot'
print.SEL: no visible global function definition for 'integrate'
print.summary.SEL : foo1: no visible global function definition for
  'predict'
print.summary.SEL : foo2: no visible global function definition for
  'predict'
print.summary.SEL: no visible global function definition for
  'integrate'
quantSEL: no visible global function definition for 'predict'
quantSEL: no visible global function definition for 'splinefun'
rvSEL: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbeta dbinom integrate pbeta predict runif splinefun uniroot
Consider adding
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: 'sem'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'semdiag.Rd':
  \usage lines wider than 90 characters:
     semdiag(x,  EQSmodel, varphi=0.1, EQSdata='data.txt', D='E', delete=integer(0), max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial= ... [TRUNCATED]

Rd file 'semdiag.robfit.Rd':
  \usage lines wider than 90 characters:
     semdiag.robfit(lisrel0, x, q, varphi, EQSmodel, EQSdata, max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial=1234)
     semdiag.robfit1(lisrel0, x, q, varphi, EQSmodel, EQSdata, max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial=1234)

These lines will be truncated in the PDF manual.
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'Rprof.out'
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChiSquaredLRTest: no visible global function definition for 'na.omit'
ChiSquaredLRTest: no visible global function definition for 'cov'
ChiSquaredLRTest: no visible global function definition for 'dmvnorm'
ChiSquaredLRTest: no visible global function definition for 'pchisq'
NormalTheoryLRTest: no visible global function definition for 'na.omit'
NormalTheoryLRTest: no visible global function definition for 'cov'
NormalTheoryLRTest: no visible global function definition for 'dmvnorm'
NormalTheoryLRTest: no visible global function definition for 'sd'
NormalTheoryLRTest: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  cov dmvnorm na.omit pchisq pnorm sd
Consider adding
  importFrom("stats", "cov", "na.omit", "pchisq", "pnorm", "sd")
to your NAMESPACE file.
Packages required but not available: 'NetworkToolbox', 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls in package code:
  'XML' 'boot' 'sem'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'boot:::const' 'stats:::AIC.logLik' 'stats:::BIC.logLik'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'addPath.plsm' 'endogenous' 'predecessors' 'qSquared' 'reorder'
  'resempls' 'residuals.sempls'
Package suggested but not available for checking: 'DiagrammeR'
Package vignette with placeholder title 'Vignette Title':
  'introduction-to-package-SEMrushR-.Rmd'
Package suggested but not available for checking: 'mice'
Running examples in 'semTools-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: combinequark
> ### Title: Combine the results from the quark function
> ### Aliases: combinequark
> 
> ### ** Examples
> 
> 
> set.seed(123321)
> dat <- HolzingerSwineford1939[,7:15]
> misspat <- matrix(runif(nrow(dat) * 9) < 0.3, nrow(dat))
> dat[misspat] <- NA
> dat <- cbind(HolzingerSwineford1939[,1:3], dat)
> 
> quark.list <- quark(data = dat, id = c(1, 2))
Data Check Passed.
ID Check Passed.
Loading required namespace: mice
Failed with error:  'there is no package called 'mice''
The quark function requires the "mice" package to be installed.
> 
> final.data <- combinequark(quark = quark.list, percent = 80)
Error in if (pct[i] >= percent) { : argument is of length zero
Calls: combinequark
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.plot_attachment: no visible global function definition for 'dev.off'
.update_list: no visible global function definition for 'modifyList'
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'
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'rtiff' which was already attached by Depends.
  Please remove these calls from your code.
Rd file 'addDefault.Rd':
  \examples lines wider than 100 characters:
     plot.calls = c("boxplot(count ~ spray, data = InsectSprays, col = 'lightgray')", "plot(1:3,1:3, col='blue', xlab='', ylab=''); points(1 ... [TRUNCATED]
     plt.extras=list(figure1= "rect(xleft=c(3,1), ytop=c(25,5),xright=c(4,2),  ybottom=c(20,0));title(main='A', cex=3)", figure2="polygon(x= ... [TRUNCATED]
     Splot = addDefault(Splot, data=c("This is default", "data2"), data.labels=c("label", "d2"), links=c("http://www.buffalo.edu, http://www ... [TRUNCATED]

Rd file 'sendplot.Rd':
  \examples lines wider than 100 characters:
     plot.calls = c("plot(x,y,col='green', pch=3)","plot(0,0, col='purple',pch=22,bg='purple')","plot(1:3,1:3, type='b',pch=21,bg='red',col= ... [TRUNCATED]
         "plot(0,0, col='purple',pch=22,bg='purple')","plot(1:3,1:3, type='b',pch=21,bg='red',col='red')","curve(x^3-3*x,-2,2, col='blue')")

These lines will be truncated in the PDF manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
gconv: no visible global function definition for 'convolve'
sens.analysis.aberrant.rank: no visible global function definition for
  'pnorm'
sens.analysis.mh: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
mscorev: no visible global function definition for 'quantile'
senmwCI : funcCI: no visible global function definition for 'qnorm'
senmwCI : funcCI2: no visible global function definition for 'qnorm'
separable1k: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for 'gray'
sensitivitySGD: no visible global function definition for 'tail'
sensitivitySGL: no visible global function definition for 'tail'
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package required but not available: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lexicon', 'syuzhet', 'textclean'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'assocpointpair_result.csv' 'foundereffectfinder_result.csv'
  'getfreqs_result.csv' 'getfreqs_result.png' 'orPlot.pdf1_1.pdf'
  'orPlot.pdf2_1.pdf' 'orPlot.pdf3_1.pdf' 'orPlot.pdf4_1.pdf'
  'orPlot.pdf5_1.pdf' 'orPlot.pdf6_1.pdf' 'orPlot.pdf7_1.pdf'
  'orPlot.pdf8_1.pdf' 'q-values_result.csv' 'rewritetuple_result.csv'
  'tartan_plot.pdf' 'vispair_plot.pdf' 'vispairfeat_plot.pdf'
  'volcano_plot.pdf'
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
plotenz : addmark: no visible global function definition for 'par'
plotenz : addmark: no visible global function definition for 'text'
plotenz : addmark: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'text'
plotenz: no visible global function definition for 'layout'
plotenz: no visible global function definition for 'text'
plotenz: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new layout par segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "segments", "text")
to your NAMESPACE file.
Rd file 'plotenz.Rd':
  \usage lines wider than 90 characters:
     plotenz(sequences, enznames, enzdata, side = TRUE, type = c("RFLP", "TRFLP"), Terminal = c("T5", "T3"))

These lines will be truncated in the PDF manual.
Found the following files/directories:
  'total'
Package suggested but not available for checking: 'biclust'
Malformed Title field: should not end in a period.
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible global function definition for 'dev.list'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.

Found the following calls to attach():
File 'session/R/session.R':
  attach(sub("file:", "", i))
See section 'Good practice' in '?attach'.
Found the following files/directories:
  'RSession.Rda'
setpath: no visible global function definition for 'cov'
setpath: no visible global function definition for 'median'
setpath: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for 'runif'
random.number.test: no visible global function definition for 'rnorm'
setRNG: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package required but not available: 'plotly'

Package suggested but not available for checking: 'loomR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'graphics' which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for 'qnorm'
severity: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
L_exp: no visible global function definition for 'pnorm'
L_hNV: no visible global function definition for 'pnorm'
L_trunc: no visible global function definition for 'pnorm'
L_trunc_mufest: no visible global function definition for 'pnorm'
dgp: no visible global function definition for 'runif'
dgp: no visible global function definition for 'rnorm'
eff.sfa: no visible global function definition for 'predict'
fitted.sfa: no visible global function definition for 'predict'
predict.sfa: no visible global function definition for 'coef'
print.sfa: no visible global function definition for 'coef'
residuals.sfa: no visible global function definition for 'fitted'
sfa: no visible global function definition for 'model.frame'
sfa: no visible global function definition for 'model.response'
sfa.fit: no visible global function definition for 'lm'
sfa.fit: no visible global function definition for 'resid'
sfa.fit: no visible global function definition for 'var'
sfa.fit: no visible global function definition for 'optim'
summary.sfa: no visible global function definition for 'logLik'
summary.sfa: no visible global function definition for 'pchisq'
te.eff.sfa: no visible global function definition for 'residuals'
te.eff.sfa: no visible global function definition for 'pnorm'
u.sfa: no visible global function definition for 'residuals'
u.sfa: no visible global function definition for 'dnorm'
u.sfa: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'sf1.Rmd' using rmarkdown
--- finished re-building 'sf1.Rmd'

--- re-building 'sf2.Rmd' using rmarkdown
--- finished re-building 'sf2.Rmd'

--- re-building 'sf3.Rmd' using rmarkdown
--- finished re-building 'sf3.Rmd'

--- re-building 'sf4.Rmd' using rmarkdown
--- finished re-building 'sf4.Rmd'

--- re-building 'sf5.Rmd' using rmarkdown
Quitting from lines 183-190 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'sf5.Rmd'

--- re-building 'sf6.Rmd' using rmarkdown
--- finished re-building 'sf6.Rmd'

--- re-building 'sf7.Rmd' using rmarkdown
--- finished re-building 'sf7.Rmd'

SUMMARY: processing the following file failed:
  'sf5.Rmd'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Encoding: UTF-8
> 
> ### Name: AsciiToInt
> ### Title: Character to and from Integer Codes Conversion
> ### Aliases: AsciiToInt ichar chars8bit strcodes
> ### Keywords: manip
> 
> ### ** Examples
> 
> chars8bit(65:70)#-> "A" "B" .. "F"
[1] "A" "B" "C" "D" "E" "F"
> stopifnot(identical(LETTERS,   chars8bit(65:90)),
+           identical(AsciiToInt(LETTERS), 65:90))
> 
> ## may only work in ISO-latin1 locale (not in UTF-8):
> <ERROR: re-encoding failure from encoding 'latin1'>
try( strcodes(c(a= "ABC", ch="1234", place = "ZÃ...
+ ## in "latin-1" gives  {otherwise should give NA instead of 252}:
Error: unexpected symbol in:
"try( strcodes(c(a= "ABC", ch="1234", place = "ZÃ...
## in "latin"
Execution halted
Malformed Description field: should contain one or more complete sentences.
.computePStar: no visible global function definition for 'uniroot'
plotBoundary: no visible global function definition for
  'scale_y_continuous'
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'SGP'
Error(s) in re-building vignettes:
  ...
--- re-building 'SGPdata.Rmd' using rmarkdown
Quitting from lines 2-11 (SGPdata.Rmd) 
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
there is no package called 'toOrdinal'
--- failed re-building 'SGPdata.Rmd'

SUMMARY: processing the following file failed:
  'SGPdata.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'mixOmics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
amse: no visible global function definition for 'na.omit'
arb: no visible global function definition for 'na.omit'
rdatagen: no visible global function definition for 'qnorm'
rdatagen: no visible global function definition for 'pbinom'
rdatagen: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'foreign' which was already attached by Depends.
  Please remove these calls from your code.
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'hydromad'
Packages required but not available: 'alakazam', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
popify: no visible global function definition for 'runif'
tipify: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package required but not available: 'bupaR'

Package suggested but not available for checking: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'heatmaply', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package vignette with placeholder title 'Vignette Title':
  'SI.Rmd'
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'highcharter'
Running examples in 'shinyjqui-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Interactions
> ### Title: Mouse interactions
> ### Aliases: Interactions jqui_draggabled jqui_droppabled jqui_resizabled
> ###   jqui_selectabled jqui_sortabled jqui_draggable jqui_droppable
> ###   jqui_resizable jqui_selectable jqui_sortable
> 
> ### ** Examples
> 
> library(shiny)
> library(highcharter)
Error in library(highcharter) : there is no package called 'highcharter'
Execution halted
Packages required but not available: 'plotly', 'sparklyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'recipes', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  '.shiny_run' 'shinyShortcut.desktop'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
shrink.estim: no visible global function definition for 'cov'
shrink.estim: no visible global function definition for 'cor'
shrink.estim: no visible global function definition for 'cov2cor'
targetCor: no visible global function definition for 'cor.test'
targetCor: no visible global function definition for 'cor'
targetCor: no visible global function definition for 'sd'
targetCor: no visible global function definition for 'cov'
targetD: no visible binding for global variable 'var'
targetF: no visible global function definition for 'cov'
targetF: no visible global function definition for 'cor'
targetG: no visible global function definition for 'cor'
targetG: no visible global function definition for 'sd'
targetG: no visible global function definition for 'cov'
targetGpos: no visible global function definition for 'cor'
targetGpos: no visible global function definition for 'sd'
targetGpos: no visible global function definition for 'cov'
targetGstar: no visible global function definition for 'cor'
targetGstar: no visible global function definition for 'sd'
targetGstar: no visible global function definition for 'cov'
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building 'sprint-corrections.Rmd' using rmarkdown
Quitting from lines 33-50 (sprint-corrections.Rmd) 
Error: processing vignette 'sprint-corrections.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'sprint-corrections.Rmd'

SUMMARY: processing the following file failed:
  'sprint-corrections.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'mvoutlier'
Depends: includes the non-default packages:
  'hdrcde', 'coda', 'MASS', 'bayesm', 'mnormt', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'MASS' 'bayesm' 'coda' 'hdrcde' 'mnormt' 'spatstat'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'siarmcmcdirichletv4.Rd':
  \usage lines wider than 90 characters:
     siarmcmcdirichletv4(data, sources, corrections = 0, concdep = 0, iterations=200000, burnin=50000, howmany=10000, thinby=15, prior = rep ... [TRUNCATED]

Rd file 'siarplotdata.Rd':
  \usage lines wider than 90 characters:
     siarplotdata(siardata, siarversion = 0, grp=1:siardata$numgroups,panel=NULL,isos=c(0,0),leg=1)

Rd file 'siarproportionbygroupplot.Rd':
  \usage lines wider than 90 characters:
     siarproportionbygroupplot(siardata, siarversion=0,probs=c(95,75,50),xlabels=NULL, grp=NULL, type="boxes",clr=gray((9:1)/10),scl=1,xspc= ... [TRUNCATED]

Rd file 'siarproportionbysourceplot.Rd':
  \usage lines wider than 90 characters:
     siarproportionbysourceplot(siardata, siarversion=0,probs=c(95,75,50),xlabels=NULL, grp=NULL, type="boxes",clr=gray((9:1)/10),scl=1,xspc ... [TRUNCATED]

Rd file 'siarsolomcmcv4.Rd':
  \usage lines wider than 90 characters:
     siarsolomcmcv4(data, sources, corrections = 0, concdep = 0, iterations=200000, burnin=50000, howmany=10000, thinby=15, prior = rep(1, n ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'ade4' 'corpcor'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filter.PCA.default: no visible global function definition for
  'princomp'
filter.mRMR.default: no visible global function definition for
  'discretize'
gaussian.default: no visible global function definition for 'cov'
gaussian.default: no visible global function definition for
  'cov.shrink'
plot.verify.cv: no visible global function definition for 'points'
plot.verify.ho: no visible global function definition for 'points'
plot.verify.loo: no visible global function definition for 'points'
predict.dpa1: no visible global function definition for 'cor'
predict.filter.PCA: no visible global function definition for 'predict'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'is.struct'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'var'
simulator.Simple1: no visible global function definition for 'rnorm'
verify.ho.default: no visible global function definition for 'predict'
verify.loo.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct points predict princomp rnorm
  var
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
Rd file 'plot.verify.ho.Rd':
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[129:256,],Yval=key[129:256],nbreV ... [TRUNCATED]

Rd file 'sideChannelAttack-package.Rd':
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[129:256,],Yval=key[129:256],nbreV ... [TRUNCATED]

Rd file 'verify.ho.Rd':
  \usage lines wider than 90 characters:
     verify.ho(model, filter, Xlearn, Ylearn, Xval, Yval, nbreVarX, param.model=list(), param.fs=list(), ...)
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[128:256,],Yval=key[128:256],nbreV ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package required but not available: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dSepAdji: no visible global function definition for 'as'
dag2cpdagAdj: no visible global function definition for 'as'
randomDAG: no visible global function definition for 'rbinom'
structIntervDist: no visible global function definition for 'as'
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  'MM.csv' 'Simul.csv' 'catalytic.csv'
.cluster: no visible global function definition for 'kmeans'
.plot.sigclust: no visible global function definition for 'par'
.plot.sigclust: no visible global function definition for 'density'
.plot.sigclust: no visible global function definition for 'runif'
.plot.sigclust: no visible global function definition for 'dnorm'
.plot.sigclust: no visible global function definition for 'lines'
.plot.sigclust: no visible global function definition for 'points'
.plot.sigclust: no visible global function definition for 'title'
.plot.sigclust: no visible global function definition for 'text'
.plot.sigclust: no visible global function definition for 'qnorm'
.plot.sigclust: no visible global function definition for 'abline'
.plot.sigclust: no visible global function definition for 'quantile'
.plot.sigclust: no visible global function definition for 'legend'
.simnull: no visible global function definition for 'rnorm'
.vareigen: no visible global function definition for 'mad'
.vareigen: no visible global function definition for 'cov'
sigclust: no visible global function definition for 'sd'
sigclust: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Package vignette with placeholder title 'Vignette Title':
  'getting-started.Rmd'
Packages required but not available: 'ggpubr', 'tidyr'

Package suggested but not available for checking: 'ggalluvial'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Seurat', 'tidyr'

Package suggested but not available for checking: 'chromVAR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
signmedian.test: no visible global function definition for 'median'
signmedian.test: no visible global function definition for 'binom.test'
signmedian.test: no visible global function definition for 'pbinom'
signmedian.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'ggraph'
Package required but not available: 'biclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'phylobase', 'phyext2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls in package code:
  'gdata' 'splines'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.SII: no visible global function definition for 'lines'
plot.SII: no visible global function definition for 'abline'
plot.SII: no visible global function definition for 'legend'
sii : approx.l: no visible global function definition for 'approx'
sii.excel: no visible global function definition for 'predict'
sii.excel : approx.l: no visible global function definition for
  'approx'
Undefined global functions or variables:
  abline approx legend lines predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Package suggested but not available for checking: 'robCompositions'
getFormula: no visible global function definition for 'as.formula'
internalSimXyplot : f: no visible global function definition for
  'median'
runSimulation: no visible global function definition for 'runif'
setup: no visible global function definition for 'runif'
clusterSetup,ANY-data.frame-SampleControl: no visible binding for
  global variable 'cnam'
clusterSetup,ANY-data.frame-TwoStageControl: no visible binding for
  global variable 'cnam'
initialize,DCARContControl: no visible binding for global variable
  'rnorm'
initialize,DataControl: no visible binding for global variable 'rnorm'
Undefined global functions or variables:
  as.formula cnam median rnorm runif
Consider adding
  importFrom("stats", "as.formula", "median", "rnorm", "runif")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building 'simFrame-eusilc.Rnw' using Sweave
Loading required package: Rcpp
Loading required package: lattice
Loading required package: parallel
--- finished re-building 'simFrame-eusilc.Rnw'

--- re-building 'simFrame-intro.Rnw' using Sweave
Loading required package: Rcpp
Loading required package: lattice
Loading required package: parallel

Error: processing vignette 'simFrame-intro.Rnw' failed with diagnostics:
 chunk 23 
Error in library("robCompositions") : 
  there is no package called 'robCompositions'

--- failed re-building 'simFrame-intro.Rnw'

SUMMARY: processing the following file failed:
  'simFrame-intro.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'broom'

Packages suggested but not available for checking: 'tidyr', 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'database.csv' 'output.csv' 'output_clst.csv'
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Running examples in 'simITS-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adjust_data
> ### Title: Adjust an outcome time series based on the group weights.
> ### Aliases: adjust_data
> 
> ### ** Examples
> 
> data( "meck_subgroup" )
> head( meck_subgroup )
# A tibble: 6 x 5
# Groups:   month [2]
  month n.cases n.bail pbail category
  <dbl>   <int>  <dbl> <dbl> <fct>   
1   -29     550    349 0.635 felony  
2   -29    1316    699 0.531 misdem  
3   -29     305    174 0.570 traffic 
4   -28     549    378 0.689 felony  
5   -28    1338    708 0.529 misdem  
6   -28     334    193 0.578 traffic 
> pis = calculate_group_weights( "category", Nname="n.cases", 
+                                meck_subgroup, t_min=0, t_max= max( meck_subgroup$month ) )
> pis
# A tibble: 3 x 3
  category     N pi_star
  <fct>    <int>   <dbl>
1 felony   11055   0.325
2 misdem   18521   0.544
3 traffic   4443   0.131
> 
> agg = aggregate_data( meck_subgroup, 
+                       outcomename="pbail", groupname="category", Nname="n.cases", 
+                       is_count=FALSE,
+                       rich = TRUE, covariates = NULL )
Error in loadNamespace(name) : there is no package called 'tidyr'
Calls: aggregate_data ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'simple_ITS_example.Rmd' using rmarkdown
Quitting from lines 97-103 (simple_ITS_example.Rmd) 
Error: processing vignette 'simple_ITS_example.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'simple_ITS_example.Rmd'

SUMMARY: processing the following file failed:
  'simple_ITS_example.Rmd'

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
Packages required but not available: 'DiagrammeR', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'simmer.plot'
Found the following files/directories:
  'res_mutation.tsv' 'res_mutationCounts.txt'
  'res_processContribution.txt' 'res_processes.txt'
cumallcausehr: no visible global function definition for 'integrate'
plotbe: no visible global function definition for 'lines'
plotbe: no visible global function definition for 'legend'
plotcph: no visible global function definition for 'confint'
plotcph: no visible global function definition for 'abline'
plotcph: no visible global function definition for 'axis'
plotcph: no visible global function definition for 'polygon'
plotcph: no visible global function definition for 'lines'
simCR: no visible global function definition for 'rnorm'
simEBMT: no visible global function definition for 'model.matrix'
simexit: no visible global function definition for 'runif'
simexitinner: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix polygon rnorm
  runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
Found the following files/directories:
  'simu.pheno' 'usedpars.txt'
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  'HISTORY'
Packages required but not available: 'janitor', 'plotly', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Non-standard file/directory found at top level:
  'COPYRIGHTS'
Copyright information should be in file inst/COPYRIGHTS
Package in Depends field not imported from: 'mclust'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for 'Mclust'
Simpsons: no visible global function definition for 'lm'
Simpsons: no visible global function definition for 'abline'
Simpsons: no visible global function definition for 'par'
Simpsons: no visible global function definition for 'legend'
Simpsons: no visible global function definition for 'txtProgressBar'
Simpsons: no visible global function definition for 'setTxtProgressBar'
Simpsons: no visible global function definition for 'quantile'
plot.Simpson: no visible global function definition for 'lm'
plot.Simpson: no visible global function definition for 'abline'
plot.Simpson: no visible global function definition for 'par'
plot.Simpson: no visible global function definition for 'legend'
Undefined global functions or variables:
  Mclust abline legend lm par quantile setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following files/directories:
  'SimRAD-exampleRefSeq-Fasta.fa' 'SimRAD-exampleRefSeq.fa'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'moveHMM'
Package suggested but not available for checking: 'vcfR'
Found the following files/directories:
  'crop_device.pdf'
Package suggested but not available for checking: 'tidyr'
Running examples in 'simstandard-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_factor_scores
> ### Title: Add factor scores to observed data
> ### Aliases: add_factor_scores
> 
> ### ** Examples
> 
> library(simstandard)
> # lavaan model
> m = "
+ X =~ 0.9 * X1 + 0.8 * X2 + 0.7 * X3
+ "
> 
> # Make data.frame for two cases
> d <- data.frame(
+   X1 = c(1.2, -1.2),
+   X2 = c(1.5, -1.8),
+   X3 = c(1.8, -1.1))
> 
> # Compute factor scores for two cases
> add_factor_scores(d, m)
Error in loadNamespace(name) : there is no package called 'tidyr'
Calls: add_factor_scores ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'simstandard_tutorial.Rmd' using rmarkdown
Quitting from lines 16-38 (simstandard_tutorial.Rmd) 
Error: processing vignette 'simstandard_tutorial.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'simstandard_tutorial.Rmd'

SUMMARY: processing the following file failed:
  'simstandard_tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'abind' 'svUnit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for 'abind'
simSummary_unitTests: no visible global function definition for
  'clearLog'
simSummary_unitTests: no visible global function definition for
  'runTest'
simSummary_unitTests: no visible global function definition for
  'svSuite'
simSummary_unitTests: no visible global function definition for 'Log'
simSummary_unitTests: no visible global function definition for 'stats'
simSummary_unitTests: no visible global function definition for
  'metadata'
simSummary_unitTests: no visible global function definition for
  'errorLog'
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
Package suggested but not available for checking: 'flexsurv'
Error(s) in re-building vignettes:
  ...
--- re-building 'simsurv_technical.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'simsurv_technical.Rmd'

--- re-building 'simsurv_usage.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 15-23 (simsurv_usage.Rmd) 
Error: processing vignette 'simsurv_usage.Rmd' failed with diagnostics:
there is no package called 'flexsurv'
--- failed re-building 'simsurv_usage.Rmd'

SUMMARY: processing the following file failed:
  'simsurv_usage.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Seurat'
plotBGpvalues: no visible global function definition for 'par'
plotBGpvalues: no visible global function definition for 'title'
plotBGpvalues: no visible global function definition for 'axis'
plotBGpvalues: no visible binding for global variable 'abline'
plotBGpvalues: no visible global function definition for 'box'
plotCGpvalues: no visible global function definition for 'par'
plotCGpvalues: no visible global function definition for 'title'
plotCGpvalues: no visible global function definition for 'axis'
plotCGpvalues: no visible binding for global variable 'abline'
plotCGpvalues: no visible global function definition for 'box'
plotDAGpvalues: no visible global function definition for 'par'
plotDAGpvalues: no visible global function definition for 'title'
plotDAGpvalues: no visible global function definition for 'axis'
plotDAGpvalues: no visible binding for global variable 'abline'
plotDAGpvalues: no visible global function definition for 'box'
plotUGpvalues: no visible global function definition for 'par'
plotUGpvalues: no visible global function definition for 'title'
plotUGpvalues: no visible global function definition for 'axis'
plotUGpvalues: no visible binding for global variable 'abline'
plotUGpvalues: no visible global function definition for 'box'
simpvalueVec: no visible binding for global variable 'pnorm'
sinBG: no visible global function definition for 'cov2cor'
sinCG : sinAMP: no visible global function definition for 'cov2cor'
sinCG : sinLWF: no visible global function definition for 'cov2cor'
sinDAG: no visible global function definition for 'cov2cor'
sinUG: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  abline axis box cov2cor par pnorm title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "par", "title")
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
Package required but not available: 'multicolor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'miceadds'
Packages required but not available: 'tidyr', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rsample', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  'helicopter.pdf'
Package suggested but not available for checking: 'sjPlot'
Packages suggested but not available for checking:
  'mice', 'sjPlot', 'sjstats', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'design_philosophy.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 'design_philosophy.Rmd'

--- re-building 'exploringdatasets.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 104-111 (exploringdatasets.Rmd) 
Error: processing vignette 'exploringdatasets.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'exploringdatasets.Rmd'

--- re-building 'recodingvariables.Rmd' using rmarkdown
--- finished re-building 'recodingvariables.Rmd'

SUMMARY: processing the following file failed:
  'exploringdatasets.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'sjstats', 'tidyr'

Package suggested but not available for checking: 'clubSandwich'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'modelr', 'tidyr'

Package suggested but not available for checking: 'sjPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
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.
cvskda: no visible global function definition for 'detectCores'
cvskda: no visible global function definition for 'makeCluster'
cvskda: no visible global function definition for 'clusterApplyLB'
cvskda: no visible global function definition for 'mclapply'
cvskda: no visible global function definition for 'stopCluster'
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
Package required but not available: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dskt: no visible global function definition for 'dt'
pskt: no visible global function definition for 'pt'
qskt: no visible global function definition for 'qt'
rskt: no visible global function definition for 'runif'
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
slcestimates: no visible global function definition for 'par'
slcestimates: no visible global function definition for 'abline'
slcestimates: no visible global function definition for 'lines'
slcestimates: no visible global function definition for 'axis'
slcestimates: no visible global function definition for 'points'
slcestimates: no visible global function definition for 'title'
Undefined global functions or variables:
  abline axis lines par points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "points",
             "title")
to your NAMESPACE file.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mosaic'
Package suggested but not available for checking: 'mosaic'
Package suggested but not available for checking: 'caret'
Running 'spelling.R' [0s/1s]
  Running 'testthat.R' [24s/28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SLOPE)
  > 
  > test_check("SLOPE")
  -- 1. Error: model training with caret works (@test-caret-training.R#4)  -------
  there is no package called 'caret'
  Backtrace:
   1. base::library(caret)
  
  == testthat results  ===========================================================
  [ OK: 90 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: model training with caret works (@test-caret-training.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'weights'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Packages required but not available:
  'mice', 'MVN', 'NoiseFiltersR', 'missMDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File 'smco/R/smco.R':
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

smco: no visible global function definition for 'runif'
smco: no visible global function definition for 'rnorm'
smco: no visible global function definition for 'qnorm'
smco: no visible global function definition for 'pnorm'
smco: no visible global function definition for 'optim'
Undefined global functions or variables:
  optim pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "optim", "pnorm", "qnorm", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  'etc'
File 'SMC/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("##\n", "## Sequential Monte Carlo Package (SMC)\n",     "##\n", "## Functionality: sequential Monte Carlo (SMC) or sequential importance\n",     "## sampling (SIS) or hidden Markov models (HMM), particle filter (PF)\n",     "## and auxiliary particle filter (APF)\n", "##\n", "## Use: \"help(package = SMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

See section 'Good practice' in '?.onAttach'.

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for 'runif'
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for 'runif'
MarkovSwitchingFuncGenerator: no visible global function definition for
  'rnorm'
MarkovSwitchingFuncGenerator: no visible global function definition for
  'runif'
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for 'dnorm'
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for 'dnorm'
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for 'runif'
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
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.
em: no visible global function definition for 'coxph'
em: no visible global function definition for 'optim'
plotpredictsmcure: no visible global function definition for 'matplot'
plotpredictsmcure: no visible global function definition for 'lines'
smcure: no visible binding for global variable 'na.omit'
smcure: no visible global function definition for 'model.frame'
smcure: no visible global function definition for 'model.extract'
smcure: no visible global function definition for 'model.matrix'
smcure: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'survreg'
smcure: no visible binding for global variable 'var'
smcure: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
Package required but not available: 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Grad.sph: no visible global function definition for 'dist'
IMDS: no visible global function definition for 'cmdscale'
IMDS: no visible global function definition for 'as.dist'
IMDS: no visible global function definition for 'runif'
IMDS: no visible global function definition for 'optim'
idistSph: no visible global function definition for 'dist'
obj.sph: no visible global function definition for 'dist'
plot.imds: no visible binding for global variable 'lines'
plot.imds: no visible global function definition for 'text'
plot.imds: no visible global function definition for 'rect'
Undefined global functions or variables:
  as.dist cmdscale dist lines optim rect runif text
Consider adding
  importFrom("graphics", "lines", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'ggplot2' 'reshape'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'corpcor' 'ggplot2' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: 'weights'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
lines.SmithWilsonYieldCurve: no visible global function definition for
  'lines'
points.SmithWilsonYieldCurve: no visible global function definition for
  'points'
Undefined global functions or variables:
  lines points
Consider adding
  importFrom("graphics", "lines", "points")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

Package suggested but not available for checking: 'rPython'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Fourier2d: no visible global function definition for 'fft'
kernel2dsmooth: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Found the following files/directories:
  'my_new_social_media_plot.png'
Malformed Description field: should contain one or more complete sentences.
dNMR: no visible global function definition for 'pnorm'
dNMR: no visible global function definition for 'dnorm'
pNMR: no visible global function definition for 'pnorm'
pNMR: no visible global function definition for 'dnorm'
rMR: no visible global function definition for 'rnorm'
rMR: no visible global function definition for 'rchisq'
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
SMVar.paired : <anonymous>: no visible global function definition for
  'var'
SMVar.paired: no visible global function definition for 'var'
SMVar.paired: no visible global function definition for 'pt'
SMVar.paired: no visible global function definition for 'p.adjust'
SMVar.paired: no visible global function definition for 'write.table'
SMVar.unpaired : <anonymous>: no visible global function definition for
  'var'
SMVar.unpaired: no visible global function definition for 'var'
SMVar.unpaired: no visible global function definition for 'pt'
SMVar.unpaired: no visible global function definition for 'p.adjust'
SMVar.unpaired: no visible global function definition for 'write.table'
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'SMVar.paired.Rd':
  \usage lines wider than 90 characters:
     SMVar.paired(geneNumbers, logratio, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)

Rd file 'SMVar.unpaired.Rd':
  \usage lines wider than 90 characters:
     SMVar.unpaired(geneNumbers, listcond, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)

These lines will be truncated in the PDF manual.
Package required but not available: 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'plotly'
Malformed Title field: should not end in a period.
Package in Depends field not imported from: 'snow'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KS.test: no visible global function definition for 'quantile'
KS.test : Fgaus: no visible global function definition for 'pnorm'
KS.test: no visible global function definition for 'setNames'
cs.test: no visible global function definition for 'pbinom'
cs.test: no visible global function definition for 'pnorm'
cs.test: no visible global function definition for 'setNames'
kde: no visible global function definition for 'quantile'
kde : Fgaus: no visible global function definition for 'pnorm'
kde: no visible global function definition for 'par'
kre: no visible global function definition for 'quantile'
kre: no visible global function definition for 'lines'
ns.test: no visible global function definition for 'complete.cases'
ns.test: no visible global function definition for 'qnorm'
ns.test: no visible global function definition for 'pnorm'
ns.test: no visible global function definition for 'pchisq'
ns.test: no visible global function definition for 'setNames'
ns.test: no visible global function definition for 'qt'
quant.test: no visible global function definition for 'complete.cases'
quant.test: no visible global function definition for 'pbinom'
quant.test: no visible global function definition for 'pnorm'
quant.test: no visible global function definition for 'setNames'
quant.test: no visible global function definition for 'quantile'
quant.test: no visible global function definition for 'phyper'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'setNames'
runs.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
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.
Found the following files/directories:
  'geneSet.set' 'snplistdb.sqlite'
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'mvtnorm' 'combinat'
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for 'chisq.test'
maxsel: no visible global function definition for 'complete.cases'
maxsel.asymp.test: no visible global function definition for
  'complete.cases'
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  'colorspace' 'snpStats'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.args: no visible global function definition for 'is'
write.sbams: no visible global function definition for 'as'
write.sbams: no visible global function definition for 'write.table'
Undefined global functions or variables:
  as is write.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following calls to attach():
File 'SOAR/R/SOAR.R':
  attach(NULL, pos, basename(directory))
See section 'Good practice' in '?attach'.
Found the following files/directories:
  '.R_Test'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
calculate.areas: no visible global function definition for 'runif'
calculate.gradedareas: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages required but not available: 'mice', 'tidycensus', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Warning: no function found corresponding to methods exports from 'SoDA' 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.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: 'base::WHAT'
Call with DUP:
   .Fortran("GEODISTV", as.double(lat1), as.double(lon1), as.double(lat2), 
       as.double(lon2), dist = double(nok), as.integer(nok), DUP = DUP, 
       PACKAGE = "SoDA")
DUP is no longer supported and will be ignored.
Malformed Description field: should contain one or more complete sentences.
Ssimpute.als: no visible global function definition for 'rnorm'
Ssvd.als: no visible global function definition for 'rnorm'
cs.default: no visible binding for global variable 'weighted.mean'
simpute.als: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
compileDatabase: no visible global function definition for 'use_data'
Undefined global functions or variables:
  use_data
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

Package suggested but not available for checking: 'Sojourn.Data'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mvoutlier'
Running examples in 'solitude-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: isolationForest
> ### Title: Fit an Isolation Forest
> ### Aliases: isolationForest
> 
> ### ** Examples
> 
> data("humus", package = "mvoutlier")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'mvoutlier'
Calls: data -> find.package
Execution halted
Malformed Description field: should contain one or more complete sentences.
Package vignette with placeholder title 'Vignette Title':
  'SolveRationalMatrixEquation.Rmd'
soma: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
bm: no visible global function definition for 'rnorm'
bm: no visible global function definition for 'ts'
fbm: no visible global function definition for 'fft'
fbm: no visible global function definition for 'rnorm'
fbm: no visible global function definition for 'ts'
gbm: no visible global function definition for 'rnorm'
gbm: no visible global function definition for 'ts'
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for 'pbinom'
kfweOrd: no visible global function definition for 'qnbinom'
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'someMTP' 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.
Package in Depends field not imported from: 'methods'
  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 'hexbin' which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for 'quantile'
hexbinpie: no visible global function definition for 'polygon'
hexbinpie: no visible global function definition for 'text'
makehexbinplot: no visible global function definition for 'rainbow'
makehexbinplot: no visible global function definition for 'col2rgb'
makehexbinplot: no visible global function definition for 'edit'
makehexbinplot: no visible global function definition for 'dev.new'
makehexbinplot: no visible global function definition for 'plot.new'
makehexbinplot: no visible global function definition for 'plot.window'
makehexbinplot: no visible global function definition for 'box'
makehexbinplot: no visible global function definition for 'axis'
makehexbinplot: no visible global function definition for 'legend'
som.plot: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
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.
Malformed Title field: should not end in a period.
License components which are templates and need '+ file LICENSE':
  MIT
Non-standard files/directories found at top level:
  'README.markdown' 'build_package.sh' 'upload.sh'
Found the following files/directories:
  'asc.gif' 'bg.gif' 'desc.gif' 'jquery-1.4.2.js'
  'jquery.tablesorter.js' 'sample.html' 'style.css'
convert_municipality_names: no visible global function definition for
  'read.csv'
regression_plot: no visible binding for global variable 'loess'
regression_plot: no visible global function definition for
  'colorRampPalette'
regression_plot: no visible global function definition for
  'loess.control'
regression_plot: no visible global function definition for 'predict'
regression_plot : <anonymous>: no visible global function definition
  for 'quantile'
regression_plot : <anonymous>: no visible global function definition
  for 'pnorm'
regression_plot: no visible global function definition for
  'flush.console'
regression_plot: no visible global function definition for 'density'
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  'splineSearch.xls'
Package suggested but not available for checking: 'SciencesPo'

Package which this enhances but not available for checking: 'RecordLinkage'
Package required but not available: 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
License components which are templates and need '+ file LICENSE':
  MIT
Package suggested but not available for checking: 'r2cytoscape'
exploreSP23Design: no visible global function definition for
  'txtProgressBar'
exploreSP23Design: no visible global function definition for
  'setTxtProgressBar'
generateClinicalTrialData : <anonymous>: no visible global function
  definition for 'runif'
generateClinicalTrialData: no visible global function definition for
  'rbinom'
generateClinicalTrialData: no visible global function definition for
  'rexp'
mHP.b : crossingProbDiff: no visible global function definition for
  'pnorm'
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.b: no visible global function definition for 'qnorm'
mHP.b: no visible global function definition for 'uniroot'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c: no visible global function definition for 'uniroot'
mHP.c: no visible global function definition for 'qnorm'
performInterimLook: no visible global function definition for 'optim'
performInterimLook: no visible global function definition for
  'constrOptim'
performInterimLook: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  Miwa constrOptim optim pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Rd file 'space.joint.Rd':
  \examples lines wider than 100 characters:
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))

Rd file 'space.neighbor.Rd':
  \examples lines wider than 100 characters:
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: 'DiagrammeR'
Missing link or links in documentation object 'SpaDES.core-package.Rd':
  '[reproducible]{cache}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
Running 'test-all.R' [275s/320s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'SpaDES.core'
  
  The following objects are masked from 'package:stats':
  
      end, start
  
  The following object is masked from 'package:utils':
  
      citation
  
  -- 1. Failure: test checkpointing with disk-backed raster (@test-checkpoint.R#11
  `simA` not equal to `simB`.
  Component "caribouMovement": Component "Par": Component ".plotInitialTime": Modes: logical, numeric
  Component "caribouMovement": Component "Par": Component ".plotInitialTime": target is logical, current is numeric
  Component "randomLandscapes": Component "Par": Component ".plotInitialTime": Modes: logical, numeric
  Component "randomLandscapes": Component "Par": Component ".plotInitialTime": target is logical, current is numeric
  
  Error in header[["Content-Length"]] : subscript out of bounds
  -- 2. Failure: saveSimList does not work correctly (@test-save.R#199)  ---------
  all.equal(mySim, sim) isn't true.
  
  == testthat results  ===========================================================
  [ OK: 538 | SKIPPED: 11 | WARNINGS: 4 | FAILED: 2 ]
  1. Failure: test checkpointing with disk-backed raster (@test-checkpoint.R#112) 
  2. Failure: saveSimList does not work correctly (@test-save.R#199) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'ffbase'
Missing or unexported object: 'pomp::gillespie.hl.sim'
hausman: no visible global function definition for 'pchisq'
span.formula: no visible global function definition for 'model.frame'
span.formula: no visible global function definition for 'model.matrix'
span.formula: no visible global function definition for
  'model.response'
spbe: no visible global function definition for 'cor'
spbe: no visible global function definition for 'pt'
spfe: no visible global function definition for 'cor'
spfe: no visible global function definition for 'pt'
sprandom: no visible global function definition for 'cor'
sprandom: no visible global function definition for 'pt'
summary.span: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyr'
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sparklyr', 'sparklyr.nested'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'RCurl' 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  'URLencode'
SPARQL: no visible binding for global variable 'getURL'
SPARQL: no visible global function definition for 'URLencode'
SPARQL: no visible binding for global variable 'xmlParse'
SPARQL: no visible global function definition for 'getNodeSet'
SPARQL: no visible global function definition for 'xpathApply'
SPARQL: no visible binding for global variable 'postForm'
get_attr: no visible global function definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'xmlDoc'
get_value: no visible global function definition for 'xmlDoc'
get_value: no visible global function definition for 'xpathSApply'
get_value: no visible binding for global variable 'xmlValue'
get_value: no visible global function definition for 'xpathApply'
get_value: no visible binding for global variable 'xmlGetAttr'
readCSVstring: no visible global function definition for 'read.csv'
readTSVstring: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
f.I2.cont: no visible global function definition for 'combn'
f.I2.dich: no visible global function definition for 'combn'
f.pstar.cont: no visible global function definition for 'combn'
f.pstar.dich: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyverse'
Malformed Description field: should contain one or more complete sentences.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/MatrixAddons.h
  inst/include/sparseLTSEigen.h
Some Unix compilers require LF line endings.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'sparseMVN.Rnw' using knitr
Quitting from lines 534-548 (sparseMVN.Rnw) 
Error: processing vignette 'sparseMVN.Rnw' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'sparseMVN.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Package vignette with placeholder title 'Vignette Title':
  'Starting.Rmd'
Package suggested but not available for checking: 'RStoolbox'
Package suggested but not available for checking: 'INLA'
Checking should be performed on sources prepared by 'R CMD build'.
Found the following sources/headers not terminated with a newline:
  src/calc.c
Some compilers warn on such files.
Package suggested but not available for checking: 'INLA'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following sources/headers not terminated with a newline:
  inst/include/STCXEM.h
  inst/include/STCXEMnonspatial.h
  inst/include/STCXEMspatial.h
  inst/include/STCdata.h
  inst/include/STCmodel.h
  inst/include/STCparam.h
  inst/include/STCtune.h
Some compilers warn on such files.
GNU make is a SystemRequirements.
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  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).
Package suggested but not available for checking: 'broom'
GenerateCliquesCovariance: 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: 'spDataLarge'
Malformed Title field: should not end in a period.
bartlett: no visible global function definition for 'pchisq'
local.rbfdot: no visible binding for global variable 'sd'
local.rbfdot: no visible global function definition for 'dist'
local.rbfdot : <anonymous>: no visible global function definition for
  'median'
speccalt: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
ChaoBunge: no visible global function definition for 'qnorm'
ChaoLee1992: no visible global function definition for 'qnorm'
Pmix: no visible global function definition for 'dpois'
PmixSCon: no visible global function definition for 'dbeta'
bootPCG: no visible global function definition for 'flush.console'
bootPCG: no visible global function definition for 'quantile'
bootPnpmle: no visible global function definition for 'flush.console'
bootPnpmle: no visible global function definition for 'quantile'
bootUnpmle: no visible global function definition for 'flush.console'
bootUnpmle: no visible global function definition for 'quantile'
chao1984: no visible global function definition for 'qnorm'
jackknife: no visible global function definition for 'dbinom'
jackknife: no visible global function definition for 'qnorm'
pcg: no visible global function definition for 'flush.console'
unpmle: no visible global function definition for 'flush.console'
untrunPmix: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyverse'
Package required but not available: 'caret'

Packages suggested but not available for checking:
  'qdap', 'MAIT', 'xcms', 'rcytoscapejs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'ggraph', 'tidyr'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'caret'
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'leaps' which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for 'glm'
modSearch: no visible binding for global variable 'binomial'
modSearch: no visible global function definition for 'na.omit'
modSearch: no visible global function definition for 'as.formula'
speff: no visible binding for global variable 'na.pass'
speff: no visible global function definition for 'model.matrix'
speff: no visible global function definition for 'terms'
speff: no visible global function definition for 'model.response'
speff: no visible global function definition for 'as.formula'
speff: no visible global function definition for 'predict'
speff: no visible global function definition for 'na.omit'
speff: no visible global function definition for 'glm'
speff: no visible binding for global variable 'na.omit'
speffSurv: no visible global function definition for 'model.matrix'
speffSurv: no visible global function definition for 'terms'
speffSurv: no visible global function definition for 'model.response'
speffSurv: no visible global function definition for 'as.formula'
speffSurv: no visible global function definition for 'uniroot'
summary.speff: no visible global function definition for 'qnorm'
summary.speff: no visible global function definition for 'pnorm'
summary.speffSurv: no visible global function definition for 'qnorm'
summary.speffSurv: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
Found the following files/directories:
  '.neig'
Malformed Description field: should contain one or more complete sentences.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'caret'
Package in Depends field not imported from: 'rgl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for 'runif'
rgl.sphMW: no visible global function definition for 'plot3d'
rgl.sphcirc: no visible global function definition for 'rotate3d'
rgl.sphcirc: no visible global function definition for 'lines3d'
rgl.sphgrid: no visible global function definition for 'open3d'
rgl.sphgrid: no visible global function definition for 'plot3d'
rgl.sphgrid: no visible global function definition for 'lines3d'
rgl.sphgrid: no visible global function definition for 'text3d'
rgl.sphpoints: no visible global function definition for 'points3d'
rgl.sphsun: no visible global function definition for 'plot3d'
rgl.sphtext: no visible global function definition for 'text3d'
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package vignette with placeholder title 'Vignette Title':
  'spiders.Rmd'
Found the following files/directories:
  'AlphaGA_3.txt' 'AlphaML_3.txt' 'BetaGA_3.txt' 'BetaML_3.txt'
  'Performance_GA_ML_ 3 .pdf' 'SPIGA_3Pmon.Pm_St1.pdf'
  'SPIGA_3Pmon.Pm_St2.pdf' 'SPI_AG_3.txt' 'SPI_ML_3.txt'
  'SPI_ML_3Pm_St1.pdf' 'SPI_ML_3Pm_St2.pdf' 'SPI_ML_3Pm_St3.pdf'
  'SPI_ML_3Pm_St4.pdf' 'SPI_PARAM_3.txt' 'SPI_PARAM_3Pm_St1.pdf'
  'SPI_PARAM_3Pm_St2.pdf' 'SPI_PARAM_3Pm_St3.pdf'
  'SPI_PARAM_3Pm_St4.pdf'
Packages in Depends field not imported from:
  'lars' 'parallel' 'randomForest'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'quadprog' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for 'density'
SPIn: no visible global function definition for 'quantile'
SPIn: no visible global function definition for 'solve.QP'
bootSPIn: no visible global function definition for 'runif'
plot.SPIn: no visible global function definition for 'hist'
plot.SPIn: no visible global function definition for 'lines'
plot.SPIn: no visible global function definition for 'text'
plot.SPIn: no visible global function definition for 'quantile'
plot.SPIn: no visible global function definition for 'legend'
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
spi: no visible global function definition for 'read.table'
spi: no visible global function definition for 'ecdf'
spi: no visible global function definition for 'qnorm'
spi: no visible global function definition for 'colorRampPalette'
spi: no visible global function definition for 'filled.contour'
spi: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
prepare_Rd: spi.Rd:117-119: Dropping empty section \note
prepare_Rd: spi.Rd:123-125: Dropping empty section \seealso
Rd file 'spi.Rd':
  \examples lines wider than 100 characters:
     spi(7,"spi.txt",1963,2010,"Standardized Precipitation Index - Rio Grande do Norte State",1,"years","months")

These lines will be truncated in the PDF manual.
Found the following files/directories:
  'spi.txt'
Package required but not available: 'mosaic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'antaresViz'
Package required but not available: 'biomod2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
R2.global: no visible global function definition for 'var'
calculer.var.exp: no visible global function definition for 'var'
creer.noeud: no visible global function definition for 'var'
ponderer.classe: no visible global function definition for 'var'
ponderer.classe: no visible global function definition for 'cov'
spodt: no visible global function definition for 'model.frame'
spodt.tree: no visible global function definition for 'plot.new'
spodt.tree: no visible global function definition for 'par'
spodt.tree: no visible global function definition for 'plot.window'
spodt.tree: no visible global function definition for 'text'
spodt.tree: no visible global function definition for 'segments'
test.spodt: no visible global function definition for 'model.frame'
test.spodt: no visible global function definition for 'hist'
test.spodt: no visible global function definition for 'abline'
tracer.noeud: no visible global function definition for 'text'
tracer.noeud: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
Ell.Theta: no visible global function definition for 'ell.theta'
confid.int.theta: no visible global function definition for 'qchisq'
confid.int.theta : sim.c: no visible global function definition for
  'runif'
confid.int.theta: no visible global function definition for 'quantile'
dd.est: no visible global function definition for 'ecdf'
ks.sporm : Simul: no visible global function definition for 'runif'
ks.stat: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'ecdf'
test.theta: no visible global function definition for 'ecdf'
test.theta : sim: no visible global function definition for 'runif'
Undefined global functions or variables:
  ecdf ell.theta qchisq quantile runif
Consider adding
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
prepare_Rd: H.Binv.Rd:48-50: Dropping empty section \note
prepare_Rd: V.theta.Rd:28-30: Dropping empty section \details
prepare_Rd: V.theta.Rd:43-45: Dropping empty section \note
prepare_Rd: V.theta.Rd:49-51: Dropping empty section \seealso
prepare_Rd: V.theta.Rd:52-53: Dropping empty section \examples
prepare_Rd: confid.int.theta.Rd:62-64: Dropping empty section \note
prepare_Rd: dd.est.Rd:39-41: Dropping empty section \note
prepare_Rd: dd.est.Rd:45-47: Dropping empty section \seealso
prepare_Rd: ell.theta.Rd:60-62: Dropping empty section \note
prepare_Rd: ell.theta.Rd:69-70: Dropping empty section \examples
prepare_Rd: grad.hessinv.Rd:47-49: Dropping empty section \note
prepare_Rd: ks.sporm.Rd:43-45: Dropping empty section \note
prepare_Rd: ks.stat.Rd:39-41: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:66-68: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:72-74: Dropping empty section \seealso
prepare_Rd: newton.theta.Rd:47-49: Dropping empty section \note
prepare_Rd: phi.Rd:32-38: Dropping empty section \value
prepare_Rd: phi.Rd:48-50: Dropping empty section \note
prepare_Rd: plotor.Rd:26-32: Dropping empty section \value
prepare_Rd: plotor.Rd:42-44: Dropping empty section \note
prepare_Rd: plotor.Rd:48-50: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:55-56: Dropping empty section \examples
prepare_Rd: test.theta.Rd:54-56: Dropping empty section \note
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fetch_NBAPlayerStatistics: 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.
Packages required but not available: 'smoof', 'SPOT', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/sppmix.h
Some Unix compilers require LF line endings.
Package vignette with placeholder title 'Vignette Title':
  'spreadr_vignette.Rmd'
Package required but not available: 'swfscMisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Rd file 'SlrArd.Rd':
  \usage lines wider than 90 characters:
     SlrArd(T, X, bias = TRUE, method = c("VB", "VBMacKay", "PX-VB"), control = list(), check.lb=TRUE, a0 = 0, b0 = 0, mu0 = 0, xi0 = 1)

These lines will be truncated in the PDF manual.
plot.SPRT: no visible global function definition for 'par'
plot.SPRT: no visible global function definition for 'abline'
print.SPRT: no visible global function definition for 'head'
Undefined global functions or variables:
  abline head par
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("utils", "head")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
sGda : <anonymous>: no visible global function definition for 'cov'
sortgene: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  'RJDBC' 'RMySQL' 'RODBC' 'RPostgreSQL' 'RSQLite' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for 'read.csv'
cacheQuery: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable 'median'
SQN: no visible global function definition for 'quantile'
SQN.demo.data: no visible global function definition for 'rnorm'
mix.qn: no visible global function definition for 'ecdf'
mix.qn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Packages required but not available: 'tidyr', 'naniar', 'janitor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
File 'sROC/R/onload.R':
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

See section 'Good practice' in '?.onAttach'.

AUC : TrapezInt: no visible global function definition for 'approx'
AUC : SimpsonInt: no visible global function definition for 'approx'
CI.CDF: no visible global function definition for 'qnorm'
bw.CDF: no visible global function definition for 'sd'
bw.CDF: no visible global function definition for 'IQR'
bw.CDF.pi: no visible global function definition for 'sd'
bw.CDF.pi: no visible global function definition for 'bw.nrd0'
bw.CDF.pi: no visible global function definition for 'bw.nrd'
bw.CDF.pi: no visible global function definition for 'bw.ucv'
bw.CDF.pi: no visible global function definition for 'bw.bcv'
bw.CDF.pi: no visible global function definition for 'bw.SJ'
bw.CDF.pi: no visible global function definition for 'IQR'
plot.CDF: no visible global function definition for 'plot.default'
plot.CDF: no visible global function definition for 'lines'
plot.CDF: no visible global function definition for 'polygon'
plot.ROC: no visible global function definition for 'plot.default'
plot.ROC: no visible global function definition for 'abline'
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
Rd file 'CI.CDF.Rd':
  \examples lines wider than 100 characters:
     curve(pnorm(x, mean=-2, sd=1)/2 + pnorm(x, mean=3, sd=0.8)/2, from =-6, to=6, add=TRUE, lty=2, col="blue")

Rd file 'kCDF.Rd':
  \examples lines wider than 100 characters:
     curve(pnorm(x, mean=-2, sd=1)/2 + pnorm(x, mean=3, sd=0.8)/2, from =-6, to=6, add=TRUE, lty=2, col="blue")

Rd file 'kROC.Rd':
  \usage lines wider than 90 characters:
     kROC(x, y, bw.x="pi_ucv", bw.y="pi_ucv", adjust=1, kernel=c("normal", "epanechnikov"), xgrid, 

These lines will be truncated in the PDF manual.
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.
Package suggested but not available for checking: 'caret'
Running examples in 'ssc-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coBC
> ### Title: CoBC method
> ### Aliases: coBC
> 
> ### ** Examples
> 
> 
> library(ssc)
> 
> ## Load Wine data set
> data(wine)
> 
> cls <- which(colnames(wine) == "Wine")
> x <- wine[, -cls] # instances without classes
> y <- wine[, cls] # the classes
> x <- scale(x) # scale the attributes
> 
> ## Prepare data
> set.seed(20)
> # Use 50% of instances for training
> tra.idx <- sample(x = length(y), size = ceiling(length(y) * 0.5))
> xtrain <- x[tra.idx,] # training instances
> ytrain <- y[tra.idx]  # classes of training instances
> # Use 70% of train instances as unlabeled set
> tra.na.idx <- sample(x = length(tra.idx), size = ceiling(length(tra.idx) * 0.7))
> ytrain[tra.na.idx] <- NA # remove class information of unlabeled instances
> 
> # Use the other 50% of instances for inductive testing
> tst.idx <- setdiff(1:length(y), tra.idx)
> xitest <- x[tst.idx,] # testing instances
> yitest <- y[tst.idx] # classes of testing instances
> 
> ## Example: Training from a set of instances with 1-NN as base classifier.
> set.seed(1)
> m1 <- coBC(x = xtrain, y = ytrain, 
+            learner = caret::knn3, 
+            learner.pars = list(k = 1),
+            pred = "predict")
Error in loadNamespace(name) : there is no package called 'caret'
Calls: coBC ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'SingleCaseES'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ssd : correction_method_D: no visible global function definition for
  'rnorm'
ssd : generate_bootstrap: no visible global function definition for
  'rmultinom'
ssd : bootstrap_method: no visible global function definition for
  'median'
ssd : bootstrap_method: no visible global function definition for
  'quantile'
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for 'rmultinom'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'median'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'quantile'
ssd: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'distributions.Rmd' using rmarkdown

Attaching package: 'ssdtools'

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

    dgamma, dlnorm, dweibull, pgamma, plnorm, pweibull, qgamma, qlnorm,
    qweibull, rgamma, rlnorm, rweibull

--- finished re-building 'distributions.Rmd'

--- re-building 'exposure-plots.Rmd' using rmarkdown

Attaching package: 'ssdtools'

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

    dgamma, dlnorm, dweibull, pgamma, plnorm, pweibull, qgamma, qlnorm,
    qweibull, rgamma, rlnorm, rweibull

--- finished re-building 'exposure-plots.Rmd'

--- re-building 'faqs.Rmd' using rmarkdown

Attaching package: 'ssdtools'

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

    dgamma, dlnorm, dweibull, pgamma, plnorm, pweibull, qgamma, qlnorm,
    qweibull, rgamma, rlnorm, rweibull

Quitting from lines 39-49 (faqs.Rmd) 
Error: processing vignette 'faqs.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'faqs.Rmd'

--- re-building 'small-sample-bias-ref.Rmd' using rmarkdown
--- finished re-building 'small-sample-bias-ref.Rmd'

--- re-building 'ssdtools.Rmd' using rmarkdown

Attaching package: 'ssdtools'

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

    dgamma, dlnorm, dweibull, pgamma, plnorm, pweibull, qgamma, qlnorm,
    qweibull, rgamma, rlnorm, rweibull

--- finished re-building 'ssdtools.Rmd'

--- re-building 'small-sample-bias.pdf.asis' using asis
--- finished re-building 'small-sample-bias.pdf.asis'

SUMMARY: processing the following file failed:
  'faqs.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'MESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
L_hNV: no visible global function definition for 'pnorm'
L_hNV_rho: no visible global function definition for 'pnorm'
eff.ssfa: no visible global function definition for 'pnorm'
plot_fitted: no visible global function definition for 'lines'
plot_moran: no visible global function definition for 'residuals'
print.summary.ssfa: no visible global function definition for
  'printCoefmat'
ssfa: no visible global function definition for 'model.frame'
ssfa: no visible global function definition for 'model.response'
ssfa.fit: no visible global function definition for 'lm'
ssfa.fit: no visible global function definition for 'var'
ssfa.fit: no visible global function definition for 'logLik'
summary.ssfa: no visible global function definition for 'pnorm'
summary.ssfa: no visible global function definition for 'logLik'
summary.ssfa: no visible global function definition for 'pchisq'
summary.ssfa: no visible binding for global variable 'df'
u.ssfa: no visible global function definition for 'dnorm'
u.ssfa: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'survey'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for 'hadamard'
Undefined global functions or variables:
  hadamard
Malformed Title field: should not end in a period.
mem.usage: 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.
Packages required but not available: 'parsnip', 'RSSL'

Packages suggested but not available for checking:
  'caret', 'tidymodels', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
map.world: no visible global function definition for 'par'
map.world: no visible global function definition for 'plot.new'
map.world: no visible global function definition for 'plot.window'
map.world: no visible global function definition for 'lines'
map.world: no visible global function definition for 'title'
map.world: no visible global function definition for 'axis'
map.world: no visible global function definition for 'box'
plot.smooth.sspline: no visible global function definition for
  'predict'
plot.smooth.sspline: no visible global function definition for
  'filled.contour'
plot.smooth.sspline: no visible binding for global variable
  'terrain.colors'
plot.smooth.sspline: no visible global function definition for 'title'
plot.smooth.sspline: no visible global function definition for 'axis'
station: no visible binding for global variable 'WTdiff'
station: no visible global function definition for 'points'
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'scanstatistics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
error.est : <anonymous>: no visible global function definition for
  'median'
holm.robust: no visible global function definition for 'pnorm'
holm.robust: no visible global function definition for 'median'
holm.robust: no visible global function definition for 'mad'
huberize: no visible global function definition for 'quantile'
ssvd.initial: no visible global function definition for 'mad'
ssvd.iter.thresh: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
Packages required but not available: 'ggfortify', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'QUIC'
Unknown package 'QUIC' in Rd xrefs
genericPlot: no visible global function definition for 'dev.new'
genericPlot: no visible global function definition for 'par'
genericPlot: no visible global function definition for 'rainbow'
genericPlot: no visible global function definition for 'lines'
genericPlot: no visible global function definition for 'legend'
genericPlot: no visible global function definition for 'dev.copy2pdf'
genericPlot: no visible global function definition for 'dev.copy2eps'
genericPlot: no visible global function definition for 'dev.print'
genericPlot: no visible binding for global variable 'png'
genericPlot: no visible binding for global variable 'tiff'
plotStrains: no visible global function definition for 'rainbow'
plotStrains: no visible global function definition for 'dev.new'
plotStrains: no visible global function definition for 'par'
plotStrains: no visible global function definition for 'lines'
plotStrains: no visible global function definition for 'legend'
plotStrains: no visible global function definition for 'dev.copy2pdf'
plotStrains: no visible global function definition for 'dev.copy2eps'
plotStrains: no visible global function definition for 'dev.print'
plotStrains: no visible binding for global variable 'png'
plotStrains: no visible binding for global variable 'tiff'
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par")
to your NAMESPACE file.
Found the following files/directories:
  'Rplot001.pdf'
Non-standard file/directory found at top level:
  'Licence'
'library' or 'require' calls to packages already attached by Depends:
  'np' 'sp'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'np' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.

Found the following calls to attach():
File 'stam/R/stkde.sig.r':
  attach(samdata)
See section 'Good practice' in '?attach'.
Rd file 'stkde.sig.rd':
  \examples lines wider than 100 characters:
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=1))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=2))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken

These lines will be truncated in the PDF manual.
find.names: no visible global function definition for 'na.omit'
generate.names: no visible global function definition for 'na.omit'
standardize.countrynames: no visible global function definition for
  'data'
standardize.names: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Rd file 'standardize.countrynames.Rd':
  \usage lines wider than 90 characters:
     standardize.countrynames(input, input.column = NULL, standard = "default", standard.column = NULL, only.names = FALSE, na.rm = FALSE, s ... [TRUNCATED]

Rd file 'standardize.text.Rd':
  \usage lines wider than 90 characters:
     standardize.text(input, input.column = NULL, standard, standard.column = NULL, regex = NULL, codes = NULL, match = FALSE, only.names =  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Packages required but not available: 'tidyr', 'cdom'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'Zelig'
'library' or 'require' call to 'codetools' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'codetools' 'gss'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ncdfgeom', 'ncmeta', 'starsdata'
Error(s) in re-building vignettes:
  ...
--- re-building 'stars1.Rmd' using rmarkdown
Quitting from lines 183-185 (stars1.Rmd) 
Error: processing vignette 'stars1.Rmd' failed with diagnostics:
package ncmeta required, please install it first
--- failed re-building 'stars1.Rmd'

--- re-building 'stars2.Rmd' using rmarkdown
--- finished re-building 'stars2.Rmd'

--- re-building 'stars3.Rmd' using rmarkdown
--- finished re-building 'stars3.Rmd'

--- re-building 'stars4.Rmd' using rmarkdown
--- finished re-building 'stars4.Rmd'

--- re-building 'stars5.Rmd' using rmarkdown
--- finished re-building 'stars5.Rmd'

SUMMARY: processing the following file failed:
  'stars1.Rmd'

Error: Vignette re-building failed.
Execution halted
Unexported objects imported by ':::' calls:
  's2dverification:::.KnownLatNames' 's2dverification:::.KnownLonNames'
  See the note in ?`:::` about the use of this operator.
Package required but not available: 'psycho'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'testmat.sdml' 'testmat2.sdml'
Package suggested but not available for checking: 'asreml'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
actvspred: no visible global function definition for 'quantile'
actvspred: no visible global function definition for 'aggregate'
actvspred: no visible global function definition for 'par'
actvspred: no visible global function definition for 'lines'
auc: no visible global function definition for 'par'
decile: no visible global function definition for 'quantile'
dqcontinuous : numoutliers: no visible global function definition for
  'quantile'
dqcontinuous : <anonymous>: no visible global function definition for
  'sd'
dqcontinuous : <anonymous>: no visible global function definition for
  'quantile'
gini: no visible global function definition for 'par'
gini: no visible global function definition for 'abline'
iv: no visible global function definition for 'quantile'
iv: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'par'
ks: no visible global function definition for 'lines'
outliers: no visible global function definition for 'quantile'
outliers: no visible global function definition for 'na.omit'
pentile: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline aggregate lines na.omit par quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
inspect: no visible global function definition for 'par'
inspect: no visible global function definition for 'abline'
inspect: no visible global function definition for 'lines'
inspect: no visible global function definition for 'points'
plotfit: no visible global function definition for 'dev.off'
plotfit: no visible global function definition for 'par'
plotfit: no visible global function definition for 'lines'
plotfit: no visible global function definition for 'points'
plotfit: no visible global function definition for 'legend'
plothill: no visible global function definition for 'par'
plothill: no visible global function definition for 'abline'
plothill: no visible global function definition for 'points'
plotmultifit: no visible global function definition for 'par'
plotmultifit: no visible global function definition for 'lines'
plotmultifit: no visible global function definition for 'points'
plotmultifit: no visible global function definition for 'pexp'
plotmultifit: no visible global function definition for 'plnorm'
plotmultifit: no visible global function definition for 'ppois'
plotmultifit: no visible global function definition for 'legend'
plotols: no visible global function definition for 'dev.off'
plotols: no visible global function definition for 'lm'
plotols: no visible global function definition for 'par'
plotols: no visible global function definition for 'abline'
plotols: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
Package required but not available: 'psycho'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Packages required but not available:
  'broomExtra', 'ipmisc', 'tidyBF', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggfortify', 'factoextra', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'openair'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
getStp: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'axis'
plot.steeptest: no visible global function definition for 'box'
plot.steeptest: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'abline'
plot.steeptest: no visible global function definition for 'legend'
plot.steeptest: no visible global function definition for
  'as.graphicsAnnot'
steeptest: no visible global function definition for 'lm'
summary.steeptest: no visible global function definition for 'var'
summary.steeptest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Stem.Bootstrap: no visible global function definition for 'runif'
filtering: no visible global function definition for 'is.ts'
filtering: no visible global function definition for 'ts'
filtering: no visible global function definition for 'start'
filtering: no visible global function definition for 'end'
filtering: no visible global function definition for 'frequency'
kalman: no visible global function definition for 'ts'
smoothing: no visible global function definition for 'is.ts'
smoothing: no visible global function definition for 'ts'
smoothing: no visible global function definition for 'start'
smoothing: no visible global function definition for 'end'
smoothing: no visible global function definition for 'frequency'
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  DataLR.cpp:131:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
  DataLR.cpp:132:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/stepR.Rcheck/00install.out' for details.
Found the following files/directories:
  'corrviz.html'
Packages required but not available: 'tidygraph', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Rd file 'calc.stoich.coef.Rd':
  \usage lines wider than 90 characters:
     calc.stoich.coef(alpha, name, subst, subst.norm, nu.norm = 1, constraints = list(), eps = 1e-5, verbose = TRUE)

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
StratPhyloCongruence: no visible global function definition for 'runif'
StratPhyloCongruence: no visible global function definition for
  'txtProgressBar'
StratPhyloCongruence: no visible global function definition for
  'setTxtProgressBar'
StratPhyloCongruence: no visible global function definition for 'pnorm'
StratPhyloCongruence: no visible global function definition for 'sd'
geoscalePhylo: no visible global function definition for 'data'
geoscalePhylo: no visible global function definition for 'par'
geoscalePhylo: no visible global function definition for 'text'
geoscalePhylo: no visible global function definition for 'segments'
geoscalePhylo: no visible global function definition for 'rect'
geoscalePhylo: no visible global function definition for 'rgb'
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following files/directories:
  'myNewStrat.R'
Package suggested but not available for checking: 'StrathE2E2examples'
Package suggested but not available for checking: 'tidyverse'
Package required but not available: 'ggtree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Missing or unexported object: 'limma::ebayes'
Malformed Title field: should not end in a period.
Package suggested but not available for checking: 'caret'
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'STRaitRazoR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
Warning: no function found corresponding to methods exports from 'stsm.class' 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.
stsm.model: no visible global function definition for 'is.ts'
stsm.model: no visible global function definition for 'var'
stsm.model: no visible global function definition for 'frequency'
stsm.model: no visible global function definition for 'na.omit'
stsm.model: no visible global function definition for 'fft'
stsm.model: no visible global function definition for 'new'
stsm.sgf: no visible global function definition for 'frequency'
char2numeric,stsm: no visible global function definition for
  'frequency'
set.cpar,stsm: no visible global function definition for 'validObject'
set.nopars,stsm: no visible global function definition for
  'validObject'
set.pars,stsm: no visible global function definition for 'validObject'
transPars,stsm: no visible global function definition for 'var'
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'tidyr', 'skimr', 'visdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'EmiStatR_output' 'ExamplePlot-event.pdf' 'ExamplePlot-season.pdf'
  'Output1_MC-uncertainty_360min-event.pdf'
  'Output1_MC-uncertainty_360min-season.pdf' 'gof.RData' 'gof.csv'
  'gofGoF_results.RData' 'gofGoF_results.csv' 'mc.RData' 'sim1.RData'
  'summ.RData' 'variance.RData'
identifyGraph: no visible global function definition for 'phyper'
mytriangle: no visible global function definition for 'symbols'
plotGraph: no visible global function definition for 'par'
updateOrgEnvir: no visible global function definition for 'read.table'
Undefined global functions or variables:
  par phyper read.table symbols
Consider adding
  importFrom("graphics", "par", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'ROCR' 'penalized'
  Please remove these calls from your code.
ELF: no visible global function definition for 'pt'
ELF: no visible global function definition for 'qnorm'
ELF: no visible global function definition for 'lm'
ELF: no visible global function definition for 'lowess'
ELF: no visible global function definition for 'dnorm'
ELF: no visible global function definition for 'approx'
subtype: no visible global function definition for 'runif'
subtype: no visible global function definition for 'hclust'
subtype: no visible global function definition for 'dist'
subtype: no visible global function definition for 'cutree'
subtype: no visible global function definition for 'pt'
subtype: no visible global function definition for 'heatmap'
test_subtype_only: no visible global function definition for 'pt'
test_subtype_only: no visible global function definition for 'survdiff'
test_subtype_only: no visible global function definition for 'survfit'
test_subtype_only: no visible global function definition for 'title'
ufun: no visible global function definition for 'dnorm'
ufun: no visible global function definition for 'lowess'
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
Rd file 'subtype.Rd':
  \usage lines wider than 90 characters:
     subtype(GEset, outcomeLabels, treatment=NULL, Npermutes=10, Nchunks = 25, minClusterSizeB = 20, NclustersASet = 100, FDRpermutation = T ... [TRUNCATED]
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

Rd file 'summary.Rd':
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Packages required but not available: 'tidyr', 'naniar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'tkrplot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
playSudoku : replot: no visible global function definition for 'par'
playSudoku : replot: no visible global function definition for
  'segments'
playSudoku : replot: no visible global function definition for 'text'
playSudoku: no visible global function definition for 'tktoplevel'
playSudoku: no visible global function definition for 'tkwm.title'
playSudoku: no visible global function definition for 'tkrplot'
playSudoku: no visible global function definition for 'tktext'
playSudoku: no visible global function definition for 'tkscrollbar'
playSudoku : <anonymous>: no visible global function definition for
  'tkyview'
playSudoku: no visible global function definition for 'tkconfigure'
playSudoku : <anonymous>: no visible global function definition for
  'tkset'
playSudoku: no visible global function definition for 'tkpack'
playSudoku: no visible global function definition for 'tcl'
playSudoku: no visible global function definition for 'tkcget'
playSudoku : showz: no visible global function definition for
  'tkrreplot'
playSudoku : type: no visible global function definition for 'tkinsert'
playSudoku : type: no visible global function definition for 'tksee'
playSudoku : kb: no visible global function definition for 'tkdestroy'
playSudoku: no visible global function definition for
  'getGraphicsEvent'
playSudoku: no visible global function definition for 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
Undefined global functions or variables:
  getGraphicsEvent par segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "segments", "text")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
SUE.fitted.values: no visible global function definition for
  'model.frame'
SUE.lm: no visible global function definition for 'model.frame'
SUE.lm: no visible global function definition for 'lm'
SUE.lm: no visible global function definition for 'anova'
SUE.residuals: no visible global function definition for 'model.frame'
parameters : para2: no visible global function definition for 'uniroot'
parameters: no visible global function definition for 'optimize'
parameters: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  anova lm model.frame optimize uniroot
Consider adding
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
Rd file 'SUE.lm.Rd':
  \examples lines wider than 100 characters:
     ##We analysis the well known stackloss data by using ordinary linear method and the subsampling method. 
     ##proportion of outliers in the data. The subsample size is chosen to be the default size of ns = 11.
     plot(SUE.fitted.values(a2),SUE.residuals(a2),xlab="(b) fitted values",ylab="residuals",ylim=c(-12,12))
     plot(SUE.fitted.values(a3),SUE.residuals(a3),xlab="(c) fitted values",ylab="residuals",ylim=c(-12,12))

These lines will be truncated in the PDF manual.
Packages suggested but not available for checking: 'plotly', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'frame-calendar.Rmd' using rmarkdown
Quitting from lines 31-37 (frame-calendar.Rmd) 
Error: processing vignette 'frame-calendar.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'frame-calendar.Rmd'

SUMMARY: processing the following file failed:
  'frame-calendar.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  'CFH.scores.full.vcf'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'INLA'
Package required but not available: 'd3r'

Package suggested but not available for checking: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
MCMCCV: no visible global function definition for 'rnorm'
MLCVGauss: no visible global function definition for 'runif'
MLCVGauss: no visible global function definition for 'optim'
SimSunderData: no visible global function definition for 'runif'
SimSunderData: no visible global function definition for 'dist'
SimSunderData: no visible global function definition for 'rnorm'
SimSunderData: no visible global function definition for 'qgamma'
SimSunderData: no visible global function definition for 'pnorm'
SimSunderData: no visible global function definition for 'rmultinom'
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.
Malformed Description field: should contain one or more complete sentences.
sunter: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  'rgamma'
supcluster : itgamma: no visible global function definition for
  'dgamma'
supcluster : itgamma: no visible global function definition for 'runif'
supcluster : itbeta: no visible global function definition for 'rnorm'
supcluster : itbeta: no visible global function definition for 'runif'
supcluster : itj: no visible global function definition for 'dmultinom'
supcluster: no visible global function definition for 'kmeans'
tab1: no visible global function definition for 'image'
tab1: no visible global function definition for 'gray'
tab1: no visible global function definition for 'var'
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
Call with DUP:
   .C(R_clusterer, E = as.double(E), X = as.double(X), W = as.double(W), 
       P = as.double(P), y = as.double(y), prob = as.double(prob), 
       theta = as.double(theta), lambda = as.double(lambda * n), 
       n = as.integer(n), g = as.integer(g), m = as.integer(m), 
       p = as.integer(p), critflag = as.integer(critflag), penflag = as.integer(penflag), 
       blockflag = as.integer(blockflag), valiflag = as.integer(valiflag), 
       traceflag = as.integer(trace), genliste = integer(lSize), 
       kriterium = double(lSize), DUP = FALSE)
DUP is no longer supported and will be ignored.
.p.1gen: warning in formatC(id, wid = 6): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(s, wid = 4): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'dig' to
  'digits'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'wid' to
  'width'
predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)]
  %*% koeff))))), nc = 1): partial argument match of 'nc' to 'ncol'
ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr =
  ncol(X)): partial argument match of 'nr' to 'nrow'
aggtrees: no visible global function definition for 'predict'
coef.pelora: no visible global function definition for 'fitted'
dlda: no visible binding for global variable 'var'
logreg: no visible global function definition for 'glm'
logreg: no visible binding for global variable 'binomial'
logreg: no visible global function definition for 'predict'
plot.pelora: no visible global function definition for 'text'
plot.wilma: no visible global function definition for 'fitted'
plot.wilma: no visible global function definition for 'text'
predict.pelora: no visible global function definition for 'fitted'
predict.pelora: no visible global function definition for 'coef'
predict.wilma: no visible global function definition for 'fitted'
print.wilma: no visible global function definition for 'fitted'
ridge.coef: no visible binding for global variable 'var'
sign.change: no visible binding for global variable 'cov'
standardize.genes: no visible binding for global variable 'sd'
Undefined global functions or variables:
  binomial coef cov fitted glm predict sd text var
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "binomial", "coef", "cov", "fitted", "glm",
             "predict", "sd", "var")
to your NAMESPACE file.
Package required but not available: 'biclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'boa' 'coda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for 'as.mcmc.list'
superdiag: no visible global function definition for 'as.mcmc'
superdiag: no visible global function definition for 'runif'
superdiag: no visible global function definition for 'geweke.diag'
superdiag: no visible global function definition for 'heidel.diag'
superdiag: no visible global function definition for 'raftery.diag'
superdiag: no visible global function definition for 'gelman.diag'
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'caret'
'library' or 'require' call to 'gam' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
TrainSuperMDS: no visible global function definition for 'rnorm'
TrainSuperMDSOnce: no visible global function definition for 'cmdscale'
TrainSuperMDSOnce: no visible global function definition for 'quantile'
distmat: no visible global function definition for 'dist'
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'caret'
Running examples in 'superml-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GridSearchCV
> ### Title: Grid Search CV
> ### Aliases: GridSearchCV
> 
> ### ** Examples
> 
> 
> ## ------------------------------------------------
> ## Method `GridSearchCV$new`
> ## ------------------------------------------------
> 
> rf <- RFTrainer$new()
> gst <-GridSearchCV$new(trainer = rf,
+                       parameters = list(n_estimators = c(100),
+                                         max_depth = c(5,2,10)),
+                                         n_folds = 3,
+                                         scoring = c('accuracy','auc'))
> 
> ## ------------------------------------------------
> ## Method `GridSearchCV$fit`
> ## ------------------------------------------------
> 
> rf <- RFTrainer$new()
> gst <-GridSearchCV$new(trainer = rf,
+                       parameters = list(n_estimators = c(100),
+                                         max_depth = c(5,2,10)),
+                                         n_folds = 3,
+                                         scoring = c('accuracy','auc'))
> data("iris")
> gst$fit(iris, "Species")
[1] "entering grid search"
[1] "In total, 3 models will be trained"
Error in loadNamespace(name) : there is no package called 'caret'
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: 'mosaic'
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
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.
Running examples in 'superpc-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: superpc.cv
> ### Title: Cross-validation for supervised principal components
> ### Aliases: superpc.cv
> ### Keywords: regression survival
> 
> ### ** Examples
> 
> set.seed(332)
> x<-matrix(rnorm(1000*40),ncol=40)
> y<-10+svd(x[1:60,])$v[,1]+ .1*rnorm(40)
> censoring.status<- sample(c(rep(1,30),rep(0,10)))
> 
> featurenames <- paste("feature",as.character(1:1000),sep="")
> data<-list(x=x,y=y, censoring.status=censoring.status, featurenames=featurenames)
> 
> 
> a<- superpc.train(data, type="survival")
> aa<-superpc.cv(a,data)

fold= 1
12345678910111213141516Error in svd(x, LINPACK = TRUE) : 
  the LINPACK argument has been defunct since R 3.1.0
Calls: superpc.cv -> mysvd -> svd
Execution halted
Package required but not available: 'logistf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'flexsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
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.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for 'lines'
plot.survErr: no visible global function definition for 'lines'
schemper: no visible global function definition for 'predict'
schemper: no visible global function definition for 'survfit'
schemper: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx lines predict survfit
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "approx", "predict")
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.
Est.PH: no visible global function definition for 'coxph'
Inf.Cval: no visible global function definition for 'rexp'
Inf.Cval: no visible global function definition for 'var'
Inf.Cval.Delta: no visible global function definition for 'rexp'
Inf.Cval.Delta: no visible global function definition for 'var'
cvC: no visible global function definition for 'coxph'
cvC: no visible global function definition for 'weighted.mean'
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
pearson: no visible global function definition for 'cor'
plot.survcorr: no visible global function definition for 'pnorm'
plot.survcorr: no visible global function definition for 'par'
plot.survcorr: no visible global function definition for 'points'
survcorr: no visible global function definition for 'model.frame'
survcorr: no visible global function definition for 'qnorm'
survcorr: no visible global function definition for 'runif'
survcorr: no visible global function definition for 'pnorm'
survcorr: no visible global function definition for 'var'
survcorr: no visible global function definition for 'qt'
Undefined global functions or variables:
  cor model.frame par pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
Package suggested but not available for checking: 'INLA'
Malformed Description field: should contain one or more complete sentences.
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.
AER: no visible binding for global variable 'survexp.fr'
AER: no visible global function definition for 'na.omit'
AER: no visible global function definition for 'survexp'
AER: no visible global function definition for 'poisson'
AER: no visible global function definition for 'glm'
AER: no visible global function definition for 'qnorm'
LR: no visible binding for global variable 'survexp.fr'
LR: no visible global function definition for 'na.omit'
LR: no visible global function definition for 'survexp'
LR: no visible global function definition for 'pchisq'
SMR: no visible binding for global variable 'survexp.fr'
SMR: no visible global function definition for 'na.omit'
SMR: no visible global function definition for 'survexp'
SMR: no visible global function definition for 'qnorm'
SMR: no visible global function definition for 'pchisq'
SMR: no visible global function definition for 'glm'
SMR: no visible binding for global variable 'poisson'
survexp_plot: no visible binding for global variable 'survexp.fr'
survexp_plot: no visible global function definition for 'na.omit'
survexp_plot: no visible global function definition for 'par'
survexp_plot: no visible global function definition for 'survfit'
survexp_plot: no visible global function definition for 'survexp'
survexp_plot: no visible global function definition for 'lines'
survexp_plot: no visible global function definition for 'legend'
survexp_plot: no visible global function definition for 'curve'
survexp_plot: no visible global function definition for 'arrows'
survexp_plot: no visible global function definition for 'points'
Undefined global functions or variables:
  arrows curve glm legend lines na.omit par pchisq points poisson qnorm
  survexp survexp.fr survfit
Consider adding
  importFrom("graphics", "arrows", "curve", "legend", "lines", "par",
             "points")
  importFrom("stats", "glm", "na.omit", "pchisq", "poisson", "qnorm")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
Survgini: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Package required but not available: 'flexsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'flexsurv'

Package suggested but not available for checking: 'INLA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'survC1' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for 'coxph'
Est.HR.FUN: no visible global function definition for 'basehaz'
Est.HR.FUN: no visible global function definition for 'approx'
Ghat.FUN: no visible global function definition for 'survfit'
IDI.INF: no visible global function definition for 'kmcens'
IDI.INF: no visible global function definition for 'quantile'
IDI.INF.GRAPH: no visible global function definition for 'lines'
IDI.INF.GRAPH: no visible global function definition for 'abline'
IDI.INF.GRAPH: no visible global function definition for 'points'
IDI.INF.GRAPH: no visible global function definition for 'title'
PTB.IDI.FUN: no visible global function definition for 'rexp'
shade: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines points polygon quantile rexp
  survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "points", "polygon", "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
Rd file 'IDI.INF.GRAPH.Rd':
  \usage lines wider than 90 characters:
     IDI.INF.GRAPH(x, main = NULL, xlab = NULL, ylab = NULL, cex.main = NULL, cex.lab = NULL, ...)

Rd file 'IDI.INF.Rd':
  \usage lines wider than 90 characters:
     IDI.INF(indata, covs0, covs1, t0, npert = 300, npert.rand = NULL, seed1 = NULL, alpha = 0.05)

These lines will be truncated in the PDF manual.
Packages required but not available: 'tidyr', 'survminer', 'tidytidbits'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'ggpubr', 'broom', 'tidyr'

Package suggested but not available for checking: 'flexsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Calls with DUP:
   .C("myInversion", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, DUP = FALSE, PACKAGE = "svcm")
   .C("myTrace", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, BBenv$diag, BBenv$env, BBenv$xenv, BBenv$N, 
       BBenv$Nenv, BBenv$Nplus1, ED = ED, DUP = FALSE, PACKAGE = "svcm")
   .C("dsC2env", N, A@x, as.integer(A@i), as.integer(A@p), diagvec = diagvec, 
       env = env, xenv = as.integer(xenv), DUP = FALSE)
DUP is no longer supported and will be ignored.
Malformed Description field: should contain one or more complete sentences.
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
svd3dplot: no visible global function definition for 'wireframe'
svd3dplot: no visible global function definition for 'levelplot'
Undefined global functions or variables:
  levelplot wireframe
Malformed Description field: should contain one or more complete sentences.
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for 'localeToCharset'
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
.onAttach : svBrowser: no visible global function definition for
  'browseURL'
.onAttach: no visible global function definition for 'loadhistory'
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'doBy'
svycox.calibrate: no visible global function definition for 'quantile'
svycox.calibrate: no visible binding for global variable 'median'
svycox.calibrate: no visible global function definition for
  'as.formula'
svycox.calibrate: no visible global function definition for 'arrows'
svycox.calibrate: no visible global function definition for 'abline'
svycox.nomogram: no visible global function definition for 'predict'
svycox.nomogram: no visible global function definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'formula'
Undefined global functions or variables:
  abline arrows as.formula formula median predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
additional_comp: no visible global function definition for 'aggregate'
additional_compPV : <anonymous>: no visible global function definition
  for 'aggregate'
cor.aux.func : <anonymous>: no visible global function definition for
  'cov.wt'
eta.func : <anonymous>: no visible global function definition for 'lm'
eta.func : <anonymous>: no visible global function definition for
  'anova'
glm.dummy.no.std: no visible global function definition for
  'as.formula'
pv_by: no visible binding for global variable 'var'
pv_perc: no visible binding for global variable 'var'
pv_quantile: no visible binding for global variable 'var'
svyPVcor: no visible global function definition for 'update'
svyPVcor: no visible global function definition for 'var'
svyPVeta: no visible global function definition for 'update'
svyPVeta: no visible global function definition for 'var'
svyPVglm: no visible global function definition for 'gaussian'
svyPVglm: no visible binding for global variable 'as.formula'
svyPVglm: no visible binding for global variable 'var'
svyPVglm: no visible global function definition for 'pt'
svyPVttest: no visible binding for global variable 'as.formula'
svyPVttest: no visible global function definition for 'var'
svyPVttest: no visible global function definition for 'pt'
svyPVttest: no visible binding for global variable 'var'
t.test.aux: no visible global function definition for 'as.formula'
t.test.aux: no visible global function definition for 'complete.cases'
Undefined global functions or variables:
  aggregate anova as.formula complete.cases cov.wt gaussian lm pt
  update var
Consider adding
  importFrom("stats", "aggregate", "anova", "as.formula",
             "complete.cases", "cov.wt", "gaussian", "lm", "pt",
             "update", "var")
to your NAMESPACE file.
Packages required but not available: 'broom', 'tidyr', 'timetk'

Packages suggested but not available for checking: 'tidyquant', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'swephRdata'
Packages required but not available: 'swfscMisc', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggpubr'
Error(s) in re-building vignettes:
  ...
--- re-building 'SWIM-vignette.Rmd' using rmarkdown
Warning: Computation failed in `stat_ecdf()`:
there is no package called 'spatstat'
Warning: Computation failed in `stat_ecdf()`:
there is no package called 'spatstat'
Warning: Computation failed in `stat_ecdf()`:
there is no package called 'spatstat'
Warning: Computation failed in `stat_ecdf()`:
there is no package called 'spatstat'
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'loading-packages'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 405-408 (SWIM-vignette.Rmd) 
Error: processing vignette 'SWIM-vignette.Rmd' failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building 'SWIM-vignette.Rmd'

SUMMARY: processing the following file failed:
  'SWIM-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'MASS' 'fda' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for 'getbasismatrix'
fj_pl: no visible global function definition for 'create.bspline.basis'
fj_pl: no visible global function definition for 'getbasispenalty'
forward_backward.quantities : <anonymous>: no visible global function
  definition for 'dnorm'
function_cases1AND2: no visible global function definition for 'dnorm'
function_cases3AND4: no visible global function definition for 'dnorm'
pij_iid: no visible global function definition for 'dnorm'
pilj: no visible global function definition for 'dnorm'
updateLambda: no visible global function definition for 'optimize'
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SWMPr', 'broom', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggmap', 'openair', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
symbol: no visible global function definition for 'plot.new'
symbol: no visible global function definition for 'plot.window'
symbol: no visible global function definition for 'axis'
symbol: no visible global function definition for 'box'
symbol: no visible global function definition for 'title'
symbol: no visible global function definition for 'rainbow'
symbol: no visible global function definition for 'hsv'
symbol: no visible global function definition for 'rect'
symbol: no visible global function definition for 'polygon'
symbol: no visible global function definition for 'lines'
symbol: no visible global function definition for 'text'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
Rd file 'symbol.Rd':
  \usage lines wider than 90 characters:
     symbol(df, type="star", colin=NULL, colout=NULL, colin2=NA, colout2=1, ssize=NULL, labels=0, labelsize=0.6,
            scheme=1, sortby=0, descending=FALSE, coorx=NULL, coory=NULL, lty=1, main=NULL, sub=NULL, xlab=NULL, ylab=NULL,
            add=FALSE, xlim=NULL, ylim=NULL, facew=0.5, faceh=0.5, eyes=0.5, eyed=0.5, mouthw=0.5, mouthc=0.5, brows=0.5,
            browp=0.5, nosel=0.5, nosew=0.5, ears=0.5, pupils=0.5, body=0.5, limb1=0.5, limb2=0.5, limb3=0.5, limb4=0.5, defcol=NA)

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: 'mpoly'
Package in Depends field not imported from: 'fields'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for 'fft'
cwt_iw: no visible global function definition for 'fft'
est_riskshrink_thresh: no visible global function definition for
  'median'
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  'doc'
'library' or 'require' calls to packages already attached by Depends:
  'tcltk' 'tkrplot'
  Please remove these calls from your code.
Rd file 'acshgral.rd':
  \examples lines wider than 100 characters:
       #Display relationships into a parenthetical notation. You can track the indices of the species in the

Rd file 'gridinfer.rd':
  \examples lines wider than 100 characters:
       #are nested inside it. In a network analysis this kind of element will behave as intermediary node.  

Rd file 'reweight.rd':
  \examples lines wider than 100 characters:
       plot(unlist(ej),unlist(reweight(ej)), xlab = "Input matrix", ylab = "Reweighted matrix", main = "First reweighting")

These lines will be truncated in the PDF manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
mainNetFunction: no visible global function definition for 'png'
mainNetFunction: no visible global function definition for 'lines'
mainNetFunction: no visible global function definition for 'legend'
mainNetFunction: no visible global function definition for 'dev.off'
plotROC: no visible global function definition for 'lines'
simulatedData: no visible global function definition for 'rpois'
simulatedData : <anonymous>: no visible global function definition for
  'rpois'
simulatedData : rlognormpois: no visible global function definition for
  'rnorm'
simulatedData : rlognormpois: no visible global function definition for
  'rpois'
Undefined global functions or variables:
  dev.off legend lines png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'LowRankQP' 'rgenoud'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for 'LowRankQP'
gaps.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'lines'
path.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'legend'
synth: no visible binding for global variable 'sd'
synth: no visible binding for global variable 'var'
synth: no visible global function definition for 'LowRankQP'
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Found the following files/directories:
  'test.csv'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.checkDimAndTest: no visible global function definition for
  'chisq.test'
.checkDimAndTest: no visible global function definition for
  'fisher.test'
plotTable1Heatmap: no visible global function definition for 'par'
plotTable1Heatmap: no visible global function definition for 'image'
plotTable1Heatmap: no visible global function definition for 'abline'
plotTable1Heatmap: no visible global function definition for 'axis'
plotTable1Heatmap: no visible global function definition for 'text'
plotTable1Heatmap: no visible global function definition for 'legend'
plotTable1Heatmap: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
Found the following files/directories:
  '.xls' 'attenu.xls' 'chick1.xls' 'chick2.xls' 'generic1.xls'
  'hands.xls' 'table1.xls'
Found the following files/directories:
  'myhtmlcode.html'
Package suggested but not available for checking: 'geepack'
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'grid' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'perturb' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for 'grid.rect'
cellgram: no visible global function definition for 'gpar'
cellgram: no visible global function definition for 'grid.segments'
cellgram: no visible global function definition for 'grid.circle'
cellgram: no visible global function definition for 'grid.polygon'
cellgram: no visible global function definition for 'grid.text'
cellgram: no visible global function definition for 'unit'
compare: no visible global function definition for 'sd'
tableplot.colldiag: no visible global function definition for
  'colldiag'
tableplot.colldiag: no visible global function definition for 'xtabs'
tableplot.default: no visible global function definition for
  'grid.newpage'
tableplot.default: no visible global function definition for
  'grid.layout'
tableplot.default: no visible global function definition for 'unit'
tableplot.default: no visible global function definition for
  'pushViewport'
tableplot.default: no visible global function definition for 'viewport'
tableplot.default: no visible global function definition for
  'grid.text'
tableplot.default: no visible global function definition for
  'upViewport'
tableplot.default: no visible global function definition for 'gpar'
tableplot.default: no visible global function definition for
  'grid.rect'
tableplot.default: no visible global function definition for
  'popViewport'
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
Rd file 'Linehan.Rd':
  \examples lines wider than 100 characters:
             cell.specs=list(list(0,"grey50",1,1,"red",1,"white","grey90",2,.7,"black",FALSE,"black",99)),
             cell.specs=list(list(0,c("black","blue"),1,1,c("black","blue"),1,"white","grey80",2,.7,"black",FALSE,"black",99))

Rd file 'cellgram.Rd':
  \usage lines wider than 90 characters:
     cellgram(cell, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape.lty.neg = 1, cell.fill = "whi ... [TRUNCATED]

Rd file 'congruence.array.Rd':
  \usage lines wider than 90 characters:
     congruence.array(X, FUN = congruence.coef, stat.name = "phi", round = FALSE, scale = 1, ref = "last")

Rd file 'make.specs0.Rd':
  \usage lines wider than 90 characters:
     make.specs0(n = NULL, as.data.frame = FALSE, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape ... [TRUNCATED]
     cell.fill = "white", back.fill = "white", label = 0, label.size = 0.7, label.col = "black", ref.lines = FALSE, ref.col = "gray80",  sca ... [TRUNCATED]

Rd file 'tableplot.Rd':
  \usage lines wider than 90 characters:
             v.parts = 0, h.parts = 0, gap = 2, text.m = 0, empty.text.size = 0.8, empty.text.col = "grey30", 
             title = NULL, table.label = TRUE, label.size = 0.8, side.rot = 0, left.space = 10, top.space = 10+10*(!is.null(title)), ...)
  \examples lines wider than 100 characters:
             cell.specs = list(list(0,"grey50",1,0,"red",1,"white","grey80",1,0.7,"black",FALSE,"black",93)),

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: 'echarts4r'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'pixiedust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pmatch'
Package suggested but not available for checking: 'tidyverse'
Package required but not available: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'miceadds'
Error(s) in re-building vignettes:
  ...
--- re-building 'deidentification.Rmd' using rmarkdown
Loading required package: sp
Warning in `dim<-`(`*tmp*`, value = c(nr, nc)) :
  NAs introduced by coercion to integer range
Quitting from lines 146-152 (deidentification.Rmd) 
Error: processing vignette 'deidentification.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building 'deidentification.Rmd'

SUMMARY: processing the following file failed:
  'deidentification.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  'spruce.taper.pars.rdata'
'library' or 'require' calls in package code:
  'gdata' 'ggplot2' 'grid' 'lattice' 'xtable'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'tashudata'
Package suggested but not available for checking: 'tidyr'
Packages suggested but not available for checking: 'MonetDBLite', 'duckdb'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'taxa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'nameNode.sqlite'
License components which are templates and need '+ file LICENSE':
  MIT
BootTree: no visible global function definition for 'hclust'
BootTree: no visible global function definition for 'dist'
BootTree: no visible global function definition for 'as.dist'
BootTree: no visible global function definition for 'cor'
BootTree: no visible binding for global variable 'var'
Pgpd: no visible global function definition for 'optim'
Pgpd : <anonymous>: no visible global function definition for 'optim'
Pgpd: no visible global function definition for 'var'
Pgpd: no visible global function definition for 'rnorm'
Pgpd: no visible global function definition for 'quantile'
Pvalue: no visible global function definition for 'rnorm'
SigTree: no visible global function definition for 'data'
TreeStat: no visible global function definition for 'hclust'
TreeStat: no visible global function definition for 'as.dist'
TreeStat: no visible global function definition for 'dist'
TreeStat: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'hclust'
plot.best: no visible global function definition for 'as.dist'
plot.best: no visible global function definition for 'dist'
plot.best: no visible global function definition for 'cor'
treetext: no visible global function definition for 'par'
treetext: no visible global function definition for 'text'
Undefined global functions or variables:
  as.dist cor data dist hclust optim par quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'ggalt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'GEOquery'
Malformed Description field: should contain one or more complete sentences.
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for 'hist'
mapper1D: no visible global function definition for 'dist'
mapper1D: no visible global function definition for 'as.dist'
mapper1D: no visible global function definition for 'hclust'
mapper1D: no visible global function definition for 'cutree'
mapper2D: no visible global function definition for 'dist'
mapper2D: no visible global function definition for 'as.dist'
mapper2D: no visible global function definition for 'hclust'
mapper2D: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RSEIS' 'pracma' 'signal'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CalcCorners: no visible global function definition for 'abline'
ConvDiffCoef: no visible global function definition for 'pascal'
ConvolveTrace: no visible global function definition for 'filter'
DeconTrace: no visible global function definition for 'as.Zpg'
DeconTrace: no visible global function definition for 'butter'
DeconTrace: no visible global function definition for 'filter'
GetDPZ: no visible global function definition for 'data'
MakeDPZ: no visible global function definition for 'bilinear'
MakeDPZ: no visible global function definition for 'fft'
MakeDPZ: no visible global function definition for 'lines'
MakeDPZ: no visible global function definition for 'legend'
MatchCoefDPZ : CalcMisfit: no visible global function definition for
  'fft'
MatchCoefDPZ : CalcMisfit: no visible global function definition for
  'filter'
MatchCoefDPZ : generate: no visible global function definition for
  'runif'
MatchCoefDPZ : generate: no visible global function definition for
  'rnorm'
MatchCoefDPZ: no visible global function definition for 'fft'
MatchCoefDPZ: no visible global function definition for 'filter'
MatchCoefDPZ: no visible global function definition for 'Zpg'
MatchCoefDPZ: no visible global function definition for 'lines'
MatchCoefDPZ: no visible global function definition for 'abline'
Metropolis: no visible global function definition for 'runif'
PZ2Coef: no visible global function definition for 'Poly'
PlotResp: no visible global function definition for 'fft'
PlotResp: no visible global function definition for 'filter'
PlotResp: no visible global function definition for 'lines'
Undefined global functions or variables:
  Poly Zpg abline as.Zpg bilinear butter data fft filter legend lines
  pascal rnorm runif
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "fft", "filter", "rnorm", "runif")
  importFrom("utils", "data")
to your NAMESPACE file.
Packages required but not available: 'SPOT', 'adabag'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'DiagrammeR', 'plotly', 'tidyr'
Package suggested but not available for checking: 'R2wd'
Package suggested but not available for checking: 'tidyr'
Running examples in 'tealeaves-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tleaves
> ### Title: 'tleaves': find leaf temperatures for multiple parameter sets
> ### Aliases: tleaves tleaf
> 
> ### ** Examples
> 
> # tleaf for single parameter set:
> 
> leaf_par <- make_leafpar()
> enviro_par <- make_enviropar()
> constants <- make_constants()
> tleaf(leaf_par, enviro_par, constants)

Solving for T_leaf ... done
        T_leaf         value convergence            R_abs              S_r
1 301.4181 [K] -2.122124e-08           0 1363.813 [W/m^2] 907.9499 [W/m^2]
                 H                L                      E          Ar       Gr
1 107.3552 [W/m^2] 348.5078 [W/m^2] 0.00794791 [mol/m^2/s] 0.004827203 788182.4
        Re       g_bw
1 12778.08 0.02972824
> 
> # tleaves for multiple parameter set:
> 
> enviro_par <- make_enviropar(
+   replace = list(
+     T_air = set_units(c(293.15, 298.15), K)
+   )
+ )
> tleaves(leaf_par, enviro_par, constants)
Error in loadNamespace(name) : there is no package called 'tidyr'
Calls: tleaves ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R' [7s/8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tealeaves)
  Loading required package: units
  udunits system database from /usr/share/xml/udunits
  > 
  > test_check("tealeaves")
  -- 1. Error: benchmarks haven't changed (@test-benchmarks.R#14)  ---------------
  there is no package called 'tidyr'
  Backtrace:
   1. tidyr::crossing
   2. base::getExportedValue(pkg, name)
   3. base::asNamespace(ns)
   4. base::getNamespace(ns)
   5. base::loadNamespace(name)
   6. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7. base:::withOneRestart(expr, restarts[[1L]])
   8. base:::doWithOneRestart(return(expr), restart)
  
  -- 2. Error: tleaves output has correct dimensions (@test-tleaves-crossing.R#12)
  there is no package called 'tidyr'
  Backtrace:
    1. tealeaves::tleaves(...)
    2. pars %<>% purrr::map_if(~inherits(.x, "units"), drop_units)
   10. tealeaves:::make_parameter_sets(.)
    4. pars %<>% names()
    4. glue::glue("{x} = pars${x}", x = .)
    4. stringr::str_c(., collapse = ", ")
    4. glue::glue("tidyr::crossing({x})", x = .)
    4. base::parse(text = .)
    4. base::eval(.)
   11. purrr::transpose(.)
   21. base::getExportedValue(pkg, name)
   22. base::asNamespace(ns)
   23. base::getNamespace(ns)
   24. base::loadNamespace(name)
   25. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   26. base:::withOneRestart(expr, restarts[[1L]])
   27. base:::doWithOneRestart(return(expr), restart)
  
  == testthat results  ===========================================================
  [ OK: 80 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: benchmarks haven't changed (@test-benchmarks.R#14) 
  2. Error: tleaves output has correct dimensions (@test-tleaves-crossing.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'parameter-functions.Rmd' using rmarkdown
--- finished re-building 'parameter-functions.Rmd'

--- re-building 'tealeaves-intermediate.Rmd' using rmarkdown
--- finished re-building 'tealeaves-intermediate.Rmd'

--- re-building 'tealeaves-introduction.Rmd' using rmarkdown
Loading required package: units
udunits system database from /usr/share/xml/udunits
Quitting from lines 95-123 (tealeaves-introduction.Rmd) 
Error: processing vignette 'tealeaves-introduction.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'tealeaves-introduction.Rmd'

SUMMARY: processing the following file failed:
  'tealeaves-introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'arulesViz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Calls with DUP:
   .C(tensoraCmulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.complex(X[xtidx]), as.complex(Y[ytidx]), 
       erg = complex(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
   .C(tensoramulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.numeric(X[xtidx]), as.numeric(Y[ytidx]), 
       erg = numeric(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
DUP is no longer supported and will be ignored.
S3 methods shown with full name in documentation object 'mean.tensor':
  'mean.tensor'

S3 methods shown with full name in documentation object 'solve.tensor':
  'solve.tensor'

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: 'tfestimators'
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for global variable 'ID'
TER.deesc.1.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B: no visible binding for global variable 'ID'
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A3.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A2.f: no visible binding for global variable 'ID'
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : B1.f: no visible binding for global variable 'ID'
TER.deesc.A.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B: no visible binding for global variable 'ID'
Undefined global functions or variables:
  ID
Found the following files/directories:
  'ExtinctionRateChanges.txt' 'ExtinctionRates.txt'
  'MassExtinctionTimes.txt' 'SpeciationRateChanges.txt'
  'SpeciationRates.txt' 'SurvivalProbabilities.txt' 'analysis_conifer'
  'input_tree.tre' 'run_1' 'run_2' 'samples_numCategories.txt'
Package required but not available: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gurobi'
Packages required but not available: 'caret', 'tidyr'

Package suggested but not available for checking: 'AnthropMMD'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Running 'testthat.R' [17s/18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(texPreview)
  > test_check("texPreview")
  -- 1. Error: (unknown) (@test-tex.R#115)  --------------------------------------
  R: delegate failed `'potrace' --svg --output '%o' '%i'' @ error/delegate.c/InvokeDelegate/1952
  Backtrace:
    1. testthat::describe(...)
    2. [ base::eval(...) ] with 1 more call
    5. texPreview:::tex_preview.xtable(...)
    7. texPreview:::tex_preview.character(...)
    8. texPreview:::tex_preview.default(...)
    9. texPreview:::tex_image(obj, stem, write_flag, overwrite)
   10. magick::image_write(imgOut, tex_path(fileDir, stem, dev = imgFormat))
   11. magick:::magick_image_write(...)
  
  TLPDB: not a directory, not loading: /home/hornik/lib/texmf/
  tlmgr: running in usermode, did you call `tlmgr init-usertree'?
  == testthat results  ===========================================================
  [ OK: 36 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test-tex.R#115) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'broom'

Packages which this enhances but not available for checking:
  'miceadds', 'Zelig'
Unknown package 'Zelig' in Rd xrefs
Package required but not available: 'lexicon'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
phyper_right: no visible global function definition for 'dhyper'
progression: no visible global function definition for 'density'
progression: no visible global function definition for 'points'
progression: no visible global function definition for 'legend'
progression: no visible global function definition for 'text'
specificities.distribution.plot: no visible global function definition
  for 'dhyper'
specificities.distribution.plot: no visible global function definition
  for 'Axis'
specificities.distribution.plot: no visible global function definition
  for 'arrows'
specificities.distribution.plot: no visible global function definition
  for 'text'
specificities.distribution.plot: no visible global function definition
  for 'title'
specificities.probabilities.vector: no visible global function
  definition for 'phyper'
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "points", "text",
             "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
Packages suggested but not available for checking: 'qgraph', 'ggraph'
Error(s) in re-building vignettes:
  ...
--- re-building 'textplot-examples.Rnw' using knitr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggraph'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggraph'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggraph'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggraph'
Downloading udpipe model from https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.4/master/inst/udpipe-ud-2.4-190531/dutch-alpino-ud-2.4-190531.udpipe to /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/textplot.Rcheck/vign_test/textplot/vignettes/dutch-alpino-ud-2.4-190531.udpipe
Visit https://github.com/jwijffels/udpipe.models.ud.2.4 for model license details
trying URL 'https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.4/master/inst/udpipe-ud-2.4-190531/dutch-alpino-ud-2.4-190531.udpipe'
Content type 'application/octet-stream' length 16963783 bytes (16.2 MB)
==================================================
downloaded 16.2 MB

Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggraph'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggraph'
Quitting from lines 175-184 (textplot-examples.Rnw) 
Error: processing vignette 'textplot-examples.Rnw' failed with diagnostics:
could not find function "textplot_bar"
--- failed re-building 'textplot-examples.Rnw'

SUMMARY: processing the following file failed:
  'textplot-examples.Rnw'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'textreuse'
Running examples in 'textrank-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: textrank_candidates_lsh
> ### Title: Use locality-sensitive hashing to get combinations of sentences
> ###   which contain words which are in the same minhash bucket
> ### Aliases: textrank_candidates_lsh
> 
> ### ** Examples
> 
> library(textreuse)
Error in library(textreuse) : there is no package called 'textreuse'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'textrank.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 142-151 (textrank.Rmd) 
Error: processing vignette 'textrank.Rmd' failed with diagnostics:
there is no package called 'textreuse'
--- failed re-building 'textrank.Rmd'

SUMMARY: processing the following file failed:
  'textrank.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'recipes', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lexicon', 'textclean'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tfdatasets'
Package required but not available: 'tfestimators'

Package suggested but not available for checking: 'rsample'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'modelr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tfestimators', 'recipes'
Package required but not available: 'tfdatasets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'tmp.test.data.csv'
Package suggested but not available for checking: 'tfdatasets'
ParseTrueFX: no visible global function definition for 'read.csv'
TrueFXRef: no visible global function definition for 'download.file'
TrueFXRef: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
Package required but not available: 'smacof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'recipes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Thinknum: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
coef_traceplot: no visible global function definition for 'rainbow'
coef_traceplot: no visible global function definition for 'abline'
coef_traceplot : <anonymous>: no visible global function definition for
  'lines'
coef_traceplot: no visible global function definition for 'text'
ee.GEE.aux : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  abline combn lines rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for 'printCoefmat'
threesls: no visible global function definition for 'cor'
threesls: no visible global function definition for 'pt'
tsls.formula: no visible global function definition for 'model.matrix'
tsls.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'extending.Rmd' using rmarkdown
--- finished re-building 'extending.Rmd'

--- re-building 'invariants.Rmd' using rmarkdown
--- finished re-building 'invariants.Rmd'

--- re-building 'tibble.Rmd' using rmarkdown
--- finished re-building 'tibble.Rmd'

--- re-building 'types.Rmd' using rmarkdown
Quitting from lines 11-18 (types.Rmd) 
Error: processing vignette 'types.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'types.Rmd'

SUMMARY: processing the following file failed:
  'types.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'broom', 'tidyr'
.LoadTickDataHK: no visible global function definition for 'read.csv'
.LoadTickDataSHSZ: no visible global function definition for 'read.csv'
DrawDown: no visible global function definition for 'na.omit'
PerformanceReport: no visible global function definition for
  'aggregate'
PerformanceReport: no visible global function definition for 'sd'
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyr'
Malformed Title field: should not end in a period.
Malformed Title field: should not end in a period.
newTiddler: no visible global function definition for 'new'
twImage: no visible global function definition for 'new'
twLink: no visible global function definition for 'new'
twList: no visible global function definition for 'new'
twTable: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'ggdist', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'dotwhisker', 'modelr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ipmisc', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'modelr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'tidycwl-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_edges
> ### Title: Get edges in a CWL workflow into a data frame
> ### Aliases: get_edges
> 
> ### ** Examples
> 
> # edges represented by a dictionary
> flow <- system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>% read_cwl_json()
> get_edges(
+   flow %>% parse_outputs(),
+   flow %>% parse_steps()
+ ) %>% str()
'data.frame':	62 obs. of  5 variables:
 $ from     : chr  "Salmon_Quant___Reads" "Salmon_Quant___Reads" "reads" "max_number_of_parallel_jobs" ...
 $ to       : chr  "SBG_Create_Expression_Matrix___Transcripts" "SBG_Create_Expression_Matrix___Genes" "SBG_Pair_FASTQs_by_Metadata_1" "SBG_Pair_FASTQs_by_Metadata_1" ...
 $ port_from: chr  "quant_sf" "quant_genes_sf" NA NA ...
 $ port_to  : chr  NA NA NA NA ...
 $ type     : chr  "step_to_step" "step_to_step" "input_to_step" "input_to_step" ...
> 
> # edges represented by a list
> flow <- system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>% read_cwl_yaml()
Warning in readLines(file) :
  invalid input found on input connection '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/tidycwl/cwl/sbg/workflow/rnaseq-salmon.cwl'
Warning in readLines(file) :
  incomplete final line found on '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/tidycwl/cwl/sbg/workflow/rnaseq-salmon.cwl'
> get_edges(
+   flow %>% parse_outputs(),
+   flow %>% parse_steps()
+ ) %>% str()
Error in obj[sapply(obj, is.null)] <- NA : invalid subscript type 'list'
Calls: %>% ... get_el_from_list -> sapply -> lapply -> get_el_from_list
Execution halted
Package suggested but not available for checking: 'explore'
Error(s) in re-building vignettes:
  ...
--- re-building 'tidydice.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.

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 32-35 (tidydice.Rmd) 
Error: processing vignette 'tidydice.Rmd' failed with diagnostics:
there is no package called 'explore'
--- failed re-building 'tidydice.Rmd'

SUMMARY: processing the following file failed:
  'tidydice.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'tidyr'
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'benchmark.Rmd' using rmarkdown
Warning: Some expressions had a GC in every iteration; so filtering is disabled.
Warning: Some expressions had a GC in every iteration; so filtering is disabled.
--- finished re-building 'benchmark.Rmd'

--- re-building 'chinese_tutorial.Rmd' using rmarkdown
--- finished re-building 'chinese_tutorial.Rmd'

--- re-building 'english_tutorial.Rmd' using rmarkdown
--- finished re-building 'english_tutorial.Rmd'

--- re-building 'example1_intro.Rmd' using rmarkdown
--- finished re-building 'example1_intro.Rmd'

--- re-building 'example2_join.Rmd' using rmarkdown
--- finished re-building 'example2_join.Rmd'

--- re-building 'example3_reshape.Rmd' using rmarkdown
Quitting from lines 18-20 (example3_reshape.Rmd) 
Error: processing vignette 'example3_reshape.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'example3_reshape.Rmd'

--- re-building 'example4_nest.Rmd' using rmarkdown
--- finished re-building 'example4_nest.Rmd'

--- re-building 'example5_fst.Rmd' using rmarkdown
--- finished re-building 'example5_fst.Rmd'

--- re-building 'example6_dt.Rmd' using rmarkdown
--- finished re-building 'example6_dt.Rmd'

SUMMARY: processing the following file failed:
  'example3_reshape.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'fuzzyjoin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'factoextra', 'plotly', 'broom', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'parsnip', 'recipes', 'rsample', 'tidyr', 'tune',
  'workflows'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ncmeta', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'europepmc'
Packages required but not available: 'rsample', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'parsnip'
Error(s) in re-building vignettes:
  ...
--- re-building 'cubist.Rmd' using rmarkdown
--- finished re-building 'cubist.Rmd'

--- re-building 'glm.Rmd' using rmarkdown
--- finished re-building 'glm.Rmd'

--- re-building 'lm.Rmd' using rmarkdown
Quitting from lines 11-19 (lm.Rmd) 
Error: processing vignette 'lm.Rmd' failed with diagnostics:
there is no package called 'parsnip'
--- failed re-building 'lm.Rmd'

--- re-building 'mars.Rmd' using rmarkdown
Quitting from lines 82-89 (mars.Rmd) 
Error: processing vignette 'mars.Rmd' failed with diagnostics:
there is no package called 'parsnip'
--- failed re-building 'mars.Rmd'

--- re-building 'non-r.Rmd' using rmarkdown
--- finished re-building 'non-r.Rmd'

--- re-building 'ranger.Rmd' using rmarkdown
Quitting from lines 11-21 (ranger.Rmd) 
Error: processing vignette 'ranger.Rmd' failed with diagnostics:
there is no package called 'parsnip'
--- failed re-building 'ranger.Rmd'

--- re-building 'regression.Rmd' using rmarkdown
--- finished re-building 'regression.Rmd'

--- re-building 'rf.Rmd' using rmarkdown
Quitting from lines 11-21 (rf.Rmd) 
Error: processing vignette 'rf.Rmd' failed with diagnostics:
there is no package called 'parsnip'
--- failed re-building 'rf.Rmd'

--- re-building 'save.Rmd' using rmarkdown
--- finished re-building 'save.Rmd'

--- re-building 'sql.Rmd' using rmarkdown
--- finished re-building 'sql.Rmd'

--- re-building 'tree.Rmd' using rmarkdown
--- finished re-building 'tree.Rmd'

--- re-building 'xgboost.Rmd' using rmarkdown
Quitting from lines 79-84 (xgboost.Rmd) 
Error: processing vignette 'xgboost.Rmd' failed with diagnostics:
there is no package called 'parsnip'
--- failed re-building 'xgboost.Rmd'

SUMMARY: processing the following files failed:
  'lm.Rmd' 'mars.Rmd' 'ranger.Rmd' 'rf.Rmd' 'xgboost.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'alphavantager', 'tidyr', 'timetk'

Packages suggested but not available for checking: 'tidyverse', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'janitor', 'tidyr'

Package suggested but not available for checking: 'redcapAPI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tidyr.Rcheck/00install.out' for details.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tidyr', 'broom'
Running examples in 'tidytext-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: reorder_within
> ### Title: Reorder an x or y axis within facets
> ### Aliases: reorder_within scale_x_reordered scale_y_reordered
> 
> ### ** Examples
> 
> 
> library(tidyr)
Error in library(tidyr) : there is no package called 'tidyr'
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggtree'
Package required but not available: 'fuzzyjoin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'modelr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'vpc'
Package suggested but not available for checking: 'tidyr'
File 'tidyxl/libs/tidyxl.so':
  Found 'abort', possibly from 'abort' (C)
    Object: 'xlex.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.
Error(s) in re-building vignettes:
  ...
--- re-building 'data-validation-rules.Rmd' using rmarkdown
Quitting from lines 34-39 (data-validation-rules.Rmd) 
Error: processing vignette 'data-validation-rules.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'data-validation-rules.Rmd'

--- re-building 'smells.Rmd' using rmarkdown
Quitting from lines 60-71 (smells.Rmd) 
Error: processing vignette 'smells.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'smells.Rmd'

--- re-building 'tidyxl.Rmd' using rmarkdown
--- finished re-building 'tidyxl.Rmd'

SUMMARY: processing the following files failed:
  'data-validation-rules.Rmd' 'smells.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'abd', 'mosaic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'alakazam', 'shazam', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
'library' or 'require' call to 'shiny' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
timeline: no visible global function definition for 'ggplot'
timeline: no visible global function definition for 'geom_segment'
timeline: no visible global function definition for 'aes_string'
timeline: no visible global function definition for 'geom_rect'
timeline: no visible global function definition for 'geom_text'
timeline: no visible global function definition for 'theme'
timeline: no visible global function definition for 'element_blank'
timeline: no visible global function definition for 'xlab'
timeline: no visible global function definition for 'ylab'
timeline: no visible global function definition for 'xlim'
timeline: no visible global function definition for
  'scale_y_continuous'
timeline: no visible global function definition for 'geom_point'
timeline: no visible global function definition for 'scale_color_grey'
timeline: no visible global function definition for 'geom_hline'
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
Package required but not available: 'mtconnectR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls in package code:
  'ggplot2' 'plyr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Matrix' 'lubridate' 'timeDate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for 'isWeekday'
plotCalendarHeatmap: no visible global function definition for 'ddply'
plotCalendarHeatmap: no visible global function definition for '.'
plotCalendarHeatmap: no visible binding for global variable 'year'
plotCalendarHeatmap: no visible binding for global variable 'month'
plotCalendarHeatmap: no visible binding for global variable 'week'
plotCalendarHeatmap: no visible global function definition for 'ggplot'
plotCalendarHeatmap: no visible global function definition for 'aes'
plotCalendarHeatmap: no visible binding for global variable 'monthweek'
plotCalendarHeatmap: no visible binding for global variable 'weekday'
plotCalendarHeatmap: no visible global function definition for
  'geom_tile'
plotCalendarHeatmap: no visible global function definition for
  'facet_grid'
plotCalendarHeatmap: no visible global function definition for
  'scale_fill_gradientn'
projectDate: no visible global function definition for 'holidayNYSE'
projectDate: no visible global function definition for
  'sparse.model.matrix'
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot_autocov: no visible global function definition for 'is.ts'
boot_autocov: no visible global function definition for 'tsboot'
boot_autocov: no visible global function definition for 'quantile'
boot_autocov: no visible global function definition for 'par'
boot_autocov: no visible global function definition for 'frequency'
boot_autocov: no visible global function definition for 'polygon'
boot_autocov: no visible global function definition for 'lines'
boot_autocov: no visible global function definition for 'abline'
boot_autocov: no visible global function definition for 'acf'
boot_spec: no visible global function definition for 'is.ts'
boot_spec: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'spec.pgram'
boot_spec: no visible global function definition for 'quantile'
boot_spec: no visible global function definition for 'polygon'
boot_spec: no visible global function definition for 'lines'
redraw: no visible global function definition for 'spec.pgram'
statistic: no visible global function definition for 'acf'
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
Packages required but not available:
  'recipes', 'rsample', 'plotly', 'tidyr'

Packages suggested but not available for checking:
  'tidyquant', 'tidymodels', 'modeltime', 'workflows', 'parsnip',
  'tune', 'tidyverse', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
author.search: no visible binding for global variable 'na.omit'
reference.list: 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.
drawGraph: no visible global function definition for 'pdf'
drawGraph: no visible global function definition for 'par'
drawGraph: no visible global function definition for 'segments'
drawGraph: no visible global function definition for 'lines'
drawGraph: no visible global function definition for 'text'
drawGraph: no visible global function definition for 'dev.off'
drugRank: no visible global function definition for 'aggregate'
floating2: no visible global function definition for 'cor'
timma: no visible global function definition for 'median'
timma: no visible global function definition for 'write.table'
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf segments text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  '_paramEst.txt'
Non-standard files/directories found at top level:
  'DESCRIPTION.orig' 'README.rst'
tipom.car: no visible global function definition for 'abline'
tipom.car: no visible global function definition for 'axis'
tipom.heat: no visible global function definition for 'image'
tipom.heat: no visible global function definition for 'gray'
tipom.lw: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis gray image
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image")
to your NAMESPACE file.
Package required but not available: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
Non-standard file/directory found at top level:
  'CONTENTS'
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'boot' 'lattice' 'splines' 'tcltk'
  Please remove these calls from your code.
Found an obsolete/platform-specific call in the following function:
  '.my.tkdev'
Found the platform-specific device:
  'X11'
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
FLXmclust.Density: no visible global function definition for 'dmvnorm'
FLXmclust.Estimate: no visible global function definition for 'flexmix'
FLXmclust.Estimate: no visible global function definition for
  'FLXmclust'
coefmclust: no visible global function definition for 'parameters'
flexmix.Density: no visible global function definition for
  'model.matrix'
flexmix.Density: no visible global function definition for
  'model.response'
flexmix.Density: no visible global function definition for
  'model.frame'
flexmix.Density: no visible global function definition for 'dnorm'
flexmix.Density: no visible global function definition for 'dpois'
flexmix.Density: no visible global function definition for 'dbinom'
flexmix.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
tleplot,TLE-data.frame: no visible global function definition for
  'legend'
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for 'dmvnorm'
EMN: no visible global function definition for 'pmvnorm'
EMT: no visible global function definition for 'GenzBretz'
EMT: no visible global function definition for 'dmvt'
EMT: no visible global function definition for 'pmvt'
MomemNT: no visible global function definition for 'pnorm'
MomemNT: no visible global function definition for 'dnorm'
MomemNT: no visible global function definition for 'pmvnorm'
MomemNT: no visible global function definition for 'dmvnorm'
TT.moment: no visible global function definition for 'GenzBretz'
TT.moment: no visible global function definition for 'pmvt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dmvt'
cdfNI: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pt'
inits: no visible global function definition for 'lm'
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
Rd file 'UTIdata.Rd':
  \examples lines wider than 100 characters:
     x = cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: 'tidyr'
extractContentDOM: no visible global function definition for
  'capture.output'
extractHTMLStrip: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
Package suggested but not available for checking: 'dexterMST'
Package required but not available: 'robCompositions'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'corpus.JSS.papers'
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Tosls.formula: no visible global function definition for 'model.matrix'
Tosls.formula: no visible global function definition for
  'model.response'
summary: no visible global function definition for 'coef'
summary: 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: 'ggmap'
Package suggested but not available for checking: 'CollessLike'
Unknown package 'CollessLike' in Rd xrefs
Package suggested but not available for checking: 'engsoccerdata'
Running examples in 'TouRnament-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: leaguetable
> ### Title: Create a league table
> ### Aliases: leaguetable
> 
> ### ** Examples
> 
> #league table for La Liga 94/95 with three point rewards (instead of two) and home and away results
> require(engsoccerdata)
Loading required package: engsoccerdata
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'engsoccerdata'
> leaguetable(dataset=engsoccerdata::spain[which(engsoccerdata::spain$Season==1994),],
+ home="home", away="visitor",score_home="hgoal", score_away="vgoal", date="Date",
+ points = c(3,1,0), rank_by = c("Pts_DC","GD_DC","GF_DC","GD","GF"), DC_display = TRUE)
Error in loadNamespace(name) : there is no package called 'engsoccerdata'
Calls: leaguetable ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Found the following files/directories:
  'test-001.png' 'test-002.png' 'test-003.png' 'test-004.png'
  'test-005.png' 'test-006.png' 'test-007.png' 'test-008.png'
  'test-009.png' 'test-010.png' 'test-011.png' 'test-012.png'
  'test-013.png' 'test-014.png' 'test-015.png' 'test-016.png'
  'test-017.png' 'test-018.png' 'test-019.png' 'test-020.png'
  'test-021.png' 'test-022.png' 'test-023.png' 'test-024.png'
  'test-025.png' 'test-026.png' 'test-027.png' 'test-028.png'
  'test-029.png' 'test-030.png' 'test-031.png' 'test-032.png'
  'test-033.png' 'test-034.png' 'test-035.png' 'test-036.png'
  'test-037.png' 'test-038.png' 'test-039.png' 'test-040.png'
  'test-041.png' 'test-042.png' 'test-043.png' 'test-044.png'
  'test-045.png' 'test-046.png' 'test-047.png' 'test-048.png'
  'test-049.png' 'test-050.png' 'test.pdf'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ConfA: no visible global function definition for 'qf'
EstM2Sn: no visible global function definition for 'nlm'
EstM2Sn: no visible global function definition for 'qnorm'
TV.model: no visible global function definition for 'dev.new'
TV.model: no visible global function definition for 'points'
betaBino: no visible global function definition for 'pbinom'
doseD: no visible global function definition for 'lm'
doseD: no visible global function definition for 'dev.new'
doseD: no visible global function definition for 'par'
doseD: no visible global function definition for 'axTicks'
doseD: no visible global function definition for 'axis'
doseD: no visible global function definition for 'lines'
doseD: no visible global function definition for 'abline'
doseD: no visible global function definition for 'legend'
setD: no visible global function definition for 'dev.new'
setD: no visible global function definition for 'par'
setD: no visible global function definition for 'pbinom'
setD: no visible global function definition for 'abline'
setD: no visible global function definition for 'axis'
setD: no visible global function definition for 'rect'
setD: no visible global function definition for 'lines'
setD: no visible global function definition for 'text'
setD: no visible global function definition for 'axTicks'
setD: no visible global function definition for 'legend'
spoD : spoD_A: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  '01_spontaneous lethality.txt' '02.sample size.txt'
  '03.dosestrategy.txt' 'doseD4.txt' 'setD.txt' 'spoDa.txt' 'spoDb.txt'
Package required but not available: 'MESS'

Package suggested but not available for checking: 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
License components which are templates and need '+ file LICENSE':
  MIT
align1d : obj: no visible global function definition for 'dist'
align2d : obj: no visible global function definition for 'dist'
align2d : pen: no visible global function definition for 'dist'
align2d: no visible global function definition for 'dist'
sumt: no visible global function definition for 'optim'
tpe1d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'cmdscale'
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
Rd file 'ci.plot.Rd':
  \usage lines wider than 90 characters:
     ci.plot(x, y, se, level = 0.95, ylim = NULL, newplot = TRUE, fun = gaussian()$linkinv, dfun = gaussian()$mu.eta, ...)

These lines will be truncated in the PDF manual.
File 'tpr/libs/tpr.so':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.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.
Package suggested but not available for checking: 'moveHMM'
Packages required but not available: 'trackeR', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following calls to attach():
File 'track/R/track.attach.R':
  attach(what = NULL, pos = pos, name = name)
See section 'Good practice' in '?attach'.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'taxidata'
Packages required but not available: 'mlrMBO', 'smoof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
microsoftTranslate: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Package required but not available: 'ggformula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
rtrapezoid: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'TreeDistData'
Package suggested but not available for checking: 'Seurat'
Error(s) in re-building vignettes:
  ...
--- re-building 'treefit.Rmd' using rmarkdown
--- finished re-building 'treefit.Rmd'

--- re-building 'working-with-seurat.Rmd' using rmarkdown
trying URL 'https://zenodo.org/record/1443566/files/real/gold/myoblast-differentiation_trapnell.rds?download=1'
Content type 'application/octet-stream' length 6299496 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Quitting from lines 104-107 (working-with-seurat.Rmd) 
Error: processing vignette 'working-with-seurat.Rmd' failed with diagnostics:
there is no package called 'Seurat'
--- failed re-building 'working-with-seurat.Rmd'

SUMMARY: processing the following file failed:
  'working-with-seurat.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Build_JTree: no visible global function definition for 'flush.console'
Run_JTree: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LikAge: no visible global function definition for 'read.table'
bd.ME.optim: no visible global function definition for 'optim'
bd.ME.optim.rho: no visible global function definition for 'optim'
bd.ME.optim.rho.all: no visible global function definition for 'optim'
bd.MEyule.optim: no visible global function definition for 'optimize'
bd.MEyule.optim: no visible global function definition for 'optim'
bd.age.optim.matlab: no visible global function definition for
  'read.table'
bd.groups.conf: no visible global function definition for 'uniroot'
bd.shifts.plot: no visible global function definition for 'lines'
bdsky.stt.optim: no visible global function definition for 'optim'
create.mat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines optim optimize read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for 'hist'
plot.treeperm: no visible global function definition for 'points'
plot.treeperm: no visible global function definition for 'text'
treeperm.formula: no visible global function definition for
  'model.frame'
treeperm.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
Package required but not available: 'adephylo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggtree'
Error(s) in re-building vignettes:
  ...
--- re-building 'structuredCoalescent.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 64-65 (structuredCoalescent.Rmd) 
Error: processing vignette 'structuredCoalescent.Rmd' failed with diagnostics:
"ggtree" %in% utils::installed.packages()[, 1] is not TRUE
--- failed re-building 'structuredCoalescent.Rmd'

SUMMARY: processing the following file failed:
  'structuredCoalescent.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'autocogs', 'tidyr'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'tidybayes'

Package suggested but not available for checking: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package vignette with placeholder title 'Vignette Title':
  'trimr-vignette.Rmd'
cinbag: no visible global function definition for 'var'
trimTrees: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'gtools' 'mgcv'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'gtools' 'mgcv' 'msm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
plot.pirls.gam: no visible global function definition for 'par'
plot.pirls.gam: no visible global function definition for 'title'
plot.pirls.gam: no visible global function definition for 'lines'
plot.pirls.gam: no visible global function definition for 'rug'
plot.pirls.gam: no visible global function definition for 'mtext'
test.trioGxE: no visible global function definition for 'write.table'
trioGxE: no visible global function definition for 'quantile'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'quantile'
trioplot: no visible global function definition for 'formula'
trioplot: no visible global function definition for 'gam'
trioplot: no visible global function definition for 'binomial'
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par qtnorm quantile rug
  title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: 'tidyr'
DrawMargin: no visible global function definition for 'qnorm'
DrawProbability: no visible global function definition for 'pnorm'
Factor: no visible global function definition for 'new'
Gaussian: no visible global function definition for 'new'
LikelihoodFactor: no visible global function definition for 'new'
Parameters: no visible global function definition for 'new'
Player: no visible global function definition for 'new'
PriorFactor: no visible global function definition for 'new'
SumFactor: no visible global function definition for 'new'
TruncateFactor: no visible global function definition for 'new'
Variable: no visible global function definition for 'new'
Vdraw: no visible global function definition for 'dnorm'
Vdraw: no visible global function definition for 'pnorm'
Vwin: no visible global function definition for 'dnorm'
Vwin: no visible global function definition for 'pnorm'
Wdraw: no visible global function definition for 'dnorm'
Wdraw: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cdens: no visible global function definition for 'head'
dplot: no visible global function definition for 'knots'
dplot: no visible global function definition for 'median'
dplot: no visible global function definition for 'par'
dplot: no visible global function definition for 'plot.stepfun'
dplot: no visible global function definition for 'abline'
edf: no visible global function definition for 'approxfun'
mctest : rdist: no visible global function definition for 'runif'
mctest : S: no visible global function definition for 'optim'
qplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approxfun head knots median optim par plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'tidygraph'

Packages suggested but not available for checking: 'ggraph', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
tfDetails: no visible global function definition for 'start'
tfDetails: no visible global function definition for 'end'
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for 'pnorm'
plrt: no visible global function definition for 'uniroot'
plrt: no visible global function definition for 'optimize'
simulatedata: no visible global function definition for 'rnorm'
tsc.test: no visible global function definition for 'shapiro.test'
tsc.test: no visible global function definition for 'p.adjust'
tsc.test: no visible global function definition for 'glm'
tsc.test : f: no visible global function definition for 'pnorm'
tsc.test: no visible global function definition for 'uniroot'
tsc.test: no visible global function definition for 'optimize'
variance: no visible global function definition for 'density'
variance: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
vintageMap: no visible global function definition for 'read.table'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'frequency'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'frequency'
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for 'cov'
FAfitStats.TSFmodel: no visible global function definition for 'cov'
FAfitStats.default: no visible global function definition for 'cor'
FAfitStats.default: no visible global function definition for
  'factanal'
FAfitStats.default: no visible global function definition for 'pchisq'
FAmodelFitStats: no visible global function definition for 'pchisq'
checkResiduals.TSFmodel: no visible global function definition for
  'cov'
distribution.factorsEstEval: no visible global function definition for
  'par'
distribution.factorsEstEval: no visible binding for global variable
  'par'
distribution.factorsEstEval: no visible global function definition for
  'density'
distribution.factorsEstEval: no visible global function definition for
  'matplot'
distribution.factorsEstEval: no visible global function definition for
  'title'
summary.TSFmodel: no visible global function definition for 'start'
summary.TSFmodel: no visible global function definition for 'end'
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'tsfeatures.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

trying URL 'https://github.com/robjhyndman/tsfeatures/raw/master/extra-data/yahoo.rda'
Content type 'application/octet-stream' length 7897660 bytes (7.5 MB)
==================================================
downloaded 7.5 MB

trying URL 'https://github.com/robjhyndman/tsfeatures/raw/master/extra-data/hwl.rda'
Content type 'application/octet-stream' length 185319 bytes (180 KB)
==================================================
downloaded 180 KB

Quitting from lines 433-448 (tsfeatures.Rmd) 
Error: processing vignette 'tsfeatures.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'tsfeatures.Rmd'

SUMMARY: processing the following file failed:
  'tsfeatures.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'tidyr'
Func.SAX: no visible global function definition for 'sd'
Func.SAX: no visible global function definition for 'qnorm'
Func.matrix: no visible global function definition for 'qnorm'
Func.motif: no visible global function definition for 'sd'
Func.motif: no visible global function definition for 'na.omit'
Func.motif: no visible global function definition for 'combn'
Func.motif.multivariate: no visible global function definition for
  'txtProgressBar'
Func.motif.multivariate: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
dLag : dlag.f: no visible global function definition for
  'complete.cases'
distmat: no visible global function definition for 'dist'
fitCity: no visible global function definition for 'glm.control'
fitCity: no visible global function definition for 'terms'
ldmvnorm: no visible global function definition for 'mahalanobis'
lspline: no visible global function definition for 'quantile'
plot.tsdecomp: no visible global function definition for 'par'
setupFormula: no visible global function definition for 'as.formula'
spatialgibbs: no visible global function definition for 'rnorm'
spatialgibbs: no visible global function definition for 'rgamma'
spatialgibbs: no visible global function definition for 'runif'
tsdecomp: no visible global function definition for 'fft'
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for 'index.search'
TransSphere : ttin: no visible global function definition for 't.test'
TransSphere: no visible global function definition for 'sd'
TransSphere: no visible global function definition for 'quantile'
TransSphere: no visible global function definition for 'pt'
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
Package required but not available: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'XMIwords.txt'
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
TT.GS : TT.GS.sp: no visible global function definition for 'qt'
TT.GS : TT.GS.sp: no visible global function definition for 'runif'
TT.GS : TT.GS.sp: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
.saveDevice: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
ttwa: no visible global function definition for 'aggregate'
ttwa: no visible global function definition for 'txtProgressBar'
ttwa: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'doBy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'CorrBin'
Packages required but not available: 'mlrMBO', 'smoof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'recipes', 'rsample', 'tidyr', 'parsnip', 'workflows'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
turf: no visible global function definition for 'read.table'
turf: no visible global function definition for 'flush.console'
turf.combos: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
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 54-62 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
TwoCop: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Found the following files/directories:
  'debug.txt'
Crm: no visible global function definition for 'integrate'
Crm : <anonymous>: no visible global function definition for
  'integrate'
Crm: no visible global function definition for 'optimize'
ail1: no visible global function definition for 'uniroot'
ail2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ail2: no visible global function definition for 'uniroot'
aip : fu : <anonymous>: no visible global function definition for
  'integrate'
aip: no visible global function definition for 'uniroot'
ait1: no visible global function definition for 'uniroot'
ait2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ait2: no visible global function definition for 'uniroot'
sim3p3: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'palette'
simCrm: no visible global function definition for 'gray'
simCrm: no visible global function definition for 'abline'
simCrm: no visible global function definition for 'lines'
ssim3p3: no visible global function definition for 'txtProgressBar'
ssim3p3: no visible global function definition for 'setTxtProgressBar'
ssimCrm: no visible global function definition for 'txtProgressBar'
ssimCrm: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  abline gray integrate lines optimize palette rbinom setTxtProgressBar
  txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package required but not available: 'PKNCA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
rmd2pdf: no visible global function definition for 'tail'
rnw2pdf: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Packages required but not available: 'ggpubr', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'TSstudio'
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ubRacing : predCandidate: no visible global function definition for
  'predict'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'pchisq'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'qt'
ubRacing : aux.friedman.edit: no visible global function definition for
  'wilcox.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  't.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  'p.adjust'
ubRacing : idFolds: no visible global function definition for
  'quantile'
ubRacing: no visible binding for global variable 'sd'
ubSmoteExs: no visible global function definition for 'runif'
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for 'quantile'
uh: no visible global function definition for 'mad'
uh.bu: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'MortalityLaws'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dudewicz.unif.test: no visible global function definition for 'runif'
frosini.unif.test: no visible global function definition for 'runif'
hegazy.unif.test: no visible global function definition for 'runif'
kolmogorov.unif.test: no visible global function definition for 'runif'
kuiper.unif.test: no visible global function definition for 'runif'
neyman.unif.test: no visible global function definition for 'runif'
quesenberry.unif.test: no visible global function definition for
  'runif'
sarkadi.unif.test: no visible global function definition for 'runif'
sherman.unif.test: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages required but not available: 'tidyverse', 'ggpubr', 'alakazam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cumcount: no visible global function definition for 'setNames'
uniqtag: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyr'
GNU make is a SystemRequirements.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'USAboundariesData'
readSEER: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'UScensus2000cdp/R/zzz.R':
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'UScensus2000tract/R/zzz.R':
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000tract\").\n")
    cat("Type help(package=\"UScensus2000tract\") to get started.\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'rgdal' 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:
  'foreign' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'MSA.Rd':
  \usage lines wider than 90 characters:
     MSA(msafips = NULL, msaname = NULL, state=NULL , statefips=FALSE, level = c("tract", "blk", "blkgrp"), proj = NULL)

Rd file 'areaPoly.Rd':
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"den00",color = list(fun = "rainbow", attr = list(4)),main="2010 US Counties \n Oregon",type="plot",border=" ... [TRUNCATED]

Rd file 'choropleth.Rd':
  \usage lines wider than 90 characters:
     choropleth(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0.6, 0 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"P0010001",color = list(fun = "rainbow", attr = list(4)),main="2010 Counties \n Oregon",type="plot",border=" ... [TRUNCATED]
     choropleth(oregon.county10,"P0010001",main="2010 Counties \n Oregon",border="transparent",type="spplot")

Rd file 'choropleth.plot.Rd':
  \usage lines wider than 90 characters:
     choropleth.plot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0 ... [TRUNCATED]

Rd file 'choropleth.spplot.Rd':
  \usage lines wider than 90 characters:
     choropleth.spplot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, ... [TRUNCATED]

Rd file 'county.Rd':
  \usage lines wider than 90 characters:
     county(fips = NULL, name = NULL, state, level = c("tract", "blk", "blkgrp"), statefips = FALSE, sp.object=NULL, proj=NULL)

These lines will be truncated in the PDF manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tidyverse', 'tidyr'
Package suggested but not available for checking: 'tidyr'
Running examples in 'usedist-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pivot_to_numeric_matrix
> ### Title: Convert a data frame in long format to a numeric matrix
> ### Aliases: pivot_to_numeric_matrix
> 
> ### ** Examples
> 
> longdata <- data.frame(
+   SampleID = paste0("Sample", c(1, 1, 1, 2, 2, 3, 3)),
+   FeatureID = paste0("Feature", c(1, 2, 3, 1, 2, 2, 3)),
+   Value = c(132, 41, 7, 56, 11, 929, 83))
> longdata
  SampleID FeatureID Value
1  Sample1  Feature1   132
2  Sample1  Feature2    41
3  Sample1  Feature3     7
4  Sample2  Feature1    56
5  Sample2  Feature2    11
6  Sample3  Feature2   929
7  Sample3  Feature3    83
> pivot_to_numeric_matrix(longdata, SampleID, FeatureID, Value)
Error: Package "tidyr" is not installed, but is needed by "usedist::pivot_to_numeric_matrix".  Please install the missing package to use this function.
Execution halted
Running 'testthat.R' [3s/3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(usedist)
  > 
  > test_check("usedist")
  -- 1. Error: Data frame in long format converted to numeric matrix (@test_long_f
  Package "tidyr" is not installed, but is needed by "usedist::pivot_to_numeric_matrix".  Please install the missing package to use this function.
  Backtrace:
   1. testthat::expect_equal(...)
   4. usedist::pivot_to_numeric_matrix(...)
   5. usedist:::check_tidyverse()
  
  -- 2. Error: Extra columns are discarded (@test_long_format.R#27)  -------------
  Package "tidyr" is not installed, but is needed by "usedist::pivot_to_numeric_matrix".  Please install the missing package to use this function.
  Backtrace:
   1. testthat::expect_equal(...)
   4. usedist::pivot_to_numeric_matrix(...)
   5. usedist:::check_tidyverse()
  
  == testthat results  ===========================================================
  [ OK: 28 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: Data frame in long format converted to numeric matrix (@test_long_format.R#18) 
  2. Error: Extra columns are discarded (@test_long_format.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'plotly', 'tidyr'
Running examples in 'USgrid-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cal_elec
> ### Title: Demand for California Independent System Operator (CISO)
> ### Aliases: Cal_elec
> ### Keywords: datasets time-series
> 
> ### ** Examples
> 
> 
> data(Cal_elec)
> 
> library(plotly)
Error in library(plotly) : there is no package called 'plotly'
Execution halted
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: 'broom'
Running examples in 'utile.visuals-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: append_table
> ### Title: Append a ggplot2 table to the bottom of a ggplot2 plot
> ### Aliases: append_table
> 
> ### ** Examples
> 
> library(survival)
> library(ggplot2)
> library(broom) # tidy() model data
Error in library(broom) : there is no package called 'broom'
Execution halted
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'
uwham.boot: no visible binding for global variable 'var'
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'PredValidationPlots.pdf' 'RepStructValidationPlots.pdf'
Package required but not available: 'broom'

Package suggested but not available for checking: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'Demo.Rmd' using rmarkdown
Quitting from lines 20-24 (Demo.Rmd) 
Error: processing vignette 'Demo.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'Demo.Rmd'

SUMMARY: processing the following file failed:
  'Demo.Rmd'

Error: Vignette re-building failed.
Execution halted
Package vignette with placeholder title 'Vignette Title':
  'intro-to-varbundle.Rmd'
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Mammen: no visible global function definition for 'runif'
PR2: no visible global function definition for 'ar.burg'
PR2: no visible global function definition for 'pt'
PR2: no visible global function definition for 'pf'
PR3: no visible global function definition for 'ar.burg'
PR3: no visible global function definition for 'pt'
PR3: no visible global function definition for 'pf'
VAR.FOR: no visible global function definition for 'qnorm'
VAR.ForeB: no visible global function definition for 'runif'
VAR.LRtest: no visible global function definition for 'pchisq'
VAR.LRtest: no visible global function definition for 'pf'
VAR.PI: no visible global function definition for 'quantile'
VAR.Waldtest: no visible global function definition for 'pf'
VAR.irf: no visible global function definition for 'par'
VAR.irf: no visible global function definition for 'abline'
VAR1.sim: no visible global function definition for 'rnorm'
resamp: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline ar.burg par pchisq pf pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'caret'
Error(s) in re-building vignettes:
  ...
--- re-building 'varrank.Rmd' using knitr
Quitting from lines 79-91 (varrank.Rmd) 
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
there is no package called 'caret'
--- failed re-building 'varrank.Rmd'

SUMMARY: processing the following file failed:
  'varrank.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  'Output.txt' 'Overlap.csv' 'Polar coordinates.csv'
Found the following sources/headers not terminated with a newline:
  inst/include/Algorithm.h
  inst/include/AlgorithmCategorical.h
  inst/include/AlgorithmContinuous.h
  inst/include/AlgorithmInteger.h
  inst/include/AlgorithmMixed.h
  inst/include/Data.h
  inst/include/DataCategorical.h
  inst/include/DataContinuous.h
  inst/include/DataInteger.h
  inst/include/DataMixed.h
  inst/include/Param.h
  inst/include/ParamCategorical.h
  inst/include/ParamContinuous.h
  inst/include/ParamInteger.h
  inst/include/ParamMixed.h
  inst/include/XEM.h
  inst/include/XEMCategorical.h
  inst/include/XEMContinuous.h
  inst/include/XEMInteger.h
  inst/include/XEMMixed.h
  inst/include/XEMPen.h
Some compilers warn on such files.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
black_scholes: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for 'density'
burdenPlot: no visible global function definition for 'axis'
burdenPlot: no visible global function definition for 'points'
burdenPlot: no visible global function definition for 'lines'
burdenPlot: no visible global function definition for 'abline'
burdenPlot: no visible global function definition for 'text'
burdenPlot: no visible global function definition for 'sd'
burdenPlot: no visible global function definition for 'segments'
vbdm: no visible global function definition for 'var'
vbdm: no visible global function definition for 'pchisq'
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for 'var'
vbdmR: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
compute_KL : rtnorm: no visible global function definition for 'runif'
compute_KL : rtnorm: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'qnorm'
compute_KL: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'pnorm'
compute_KL: no visible global function definition for 'var'
compute_KL: no visible global function definition for 'rbinom'
compute_KL: no visible global function definition for 'rnorm'
compute_KL: no visible global function definition for 'sd'
vbsr: no visible global function definition for 'qchisq'
vbsr: no visible global function definition for 'var'
vbsr: no visible global function definition for 'pchisq'
vbsr: no visible global function definition for 'sd'
vbsr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Package vignette with placeholder title 'Vignette Title':
  'VBTree_vignette.Rmd'
Found the following significant warnings:
  vcpen.cpp:906:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  vcpen.cpp:907:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  vcpen.cpp:959:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/vcpen.Rcheck/00install.out' for details.
Compare2FDS: no visible global function definition for 'runif'
Compare2FDS: no visible global function definition for 'lm'
Compare2FDS: no visible global function definition for 'model.matrix'
Compare2FDS: no visible global function definition for 'abline'
Compare2FDS: no visible global function definition for 'lines'
Compare2FDS: no visible global function definition for 'text'
Compare2Vdg: no visible global function definition for 'par'
Compare2Vdg: no visible global function definition for 'lines'
Compare2Vdg: no visible global function definition for 'legend'
FDSPlot: no visible global function definition for 'runif'
FDSPlot: no visible global function definition for 'lm'
FDSPlot: no visible global function definition for 'model.matrix'
FDSPlot: no visible global function definition for 'abline'
Vdgraph: no visible global function definition for 'par'
Vdgraph: no visible global function definition for 'lines'
Vdgraph: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend lines lm model.matrix par runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
calculateParameters,AffineTransformation: no visible global function
  definition for 'lm'
calculateParameters,AffineTransformation: no visible global function
  definition for 'coef'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'lm'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'coef'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'points'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'legend'
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Package required but not available: 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
DrawDensity3D: no visible global function definition for 'colorRamp'
DrawDensity3D: no visible global function definition for 'rgb'
ReadFromFile3D: no visible global function definition for 'read.table'
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package suggested but not available for checking: 'smacof'
Error(s) in re-building vignettes:
  ...
--- re-building 'VegetationClassification.Rnw' using Sweave
Loading required package: Rcpp
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-6
--- finished re-building 'VegetationClassification.Rnw'

--- re-building 'CTA.Rmd' using rmarkdown
Quitting from lines 23-27 (CTA.Rmd) 
Error: processing vignette 'CTA.Rmd' failed with diagnostics:
there is no package called 'smacof'
--- failed re-building 'CTA.Rmd'

--- re-building 'MedRegExample.Rmd' using rmarkdown
--- finished re-building 'MedRegExample.Rmd'

SUMMARY: processing the following file failed:
  'CTA.Rmd'

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to 'stats' which was already attached by Depends.
  Please remove these calls from your code.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of 'arg' to
  'args'
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
prepare_Rd: H.Rd:41-42: Dropping empty section \note
prepare_Rd: M.homog.Rd:19-21: Dropping empty section \details
prepare_Rd: M.homog.Rd:35-36: Dropping empty section \note
prepare_Rd: Rel.homog.Rd:24-25: Dropping empty section \note
prepare_Rd: bootstrap.Rd:34: Dropping empty section \note
prepare_Rd: d.Rd:35-36: Dropping empty section \note
prepare_Rd: normalize.rows.Rd:26-27: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:23-24: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:26: Dropping empty section \examples
prepare_Rd: sim.groups.Rd:27-28: Dropping empty section \note
prepare_Rd: sim.table.Rd:25-26: Dropping empty section \note
prepare_Rd: similarity.Rd:25-26: Dropping empty section \note
prepare_Rd: turnover.Rd:17-18: Dropping empty section \details
prepare_Rd: turnover.Rd:29-30: Dropping empty section \note
Package required but not available: 'taxlist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'Fig3-1_triple_labels_sub_and_superscripts.tiff'
  'Fig3-2_Euler_3set_simple_with_subscripts.tiff'
  'Pairwise_Venn_diagram.tiff' 'Quad_Venn_diagram.tiff'
  'Quintuple_Venn_diagram.tiff' 'Single_Venn_diagram.tiff'
  'Triple_Venn_diagram.tiff' 'Venn_2set_complex.tiff'
  'Venn_4set_pretty.tiff' 'Venn_5set_pretty.tiff'
Malformed Description field: should contain one or more complete sentences.
Checking should be performed on sources prepared by 'R CMD build'.
Non-standard file/directory found at top level:
  'src-java'
plot.VennDiagram : <anonymous>: no visible global function definition
  for 'hcl'
plot.VennDiagram: no visible global function definition for 'plot.new'
plot.VennDiagram: no visible global function definition for
  'plot.window'
plot.VennDiagram: no visible global function definition for 'col2rgb'
plot.VennDiagram: no visible global function definition for 'rgb'
plot.VennDiagram: no visible global function definition for 'polygon'
plot.VennDiagram: no visible global function definition for 'text'
plot.VennDiagram: no visible global function definition for 'title'
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggpubr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Unknown package 'TreeLS' in Rd xrefs
vif: no visible global function definition for 'sd'
vif: no visible global function definition for 'lm'
vif: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
Rd file 'vif.Rd':
  \usage lines wider than 90 characters:
             vif(y, x, w0 = 0.05, dw = 0.05, subsize = 200, trace = TRUE, mode = c("dense", "sparse"))
  \examples lines wider than 100 characters:
             vif.sel <- vif(housingexp$y, housingexp$x, w0 = 0.0005, dw = 0.005, subsize = 300, trace = FALSE);

These lines will be truncated in the PDF manual.
hyperpara: no visible binding for global variable 'var'
hyperpara: no visible global function definition for 'hist'
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'abalone-example.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 25-29 (abalone-example.Rmd) 
Error: processing vignette 'abalone-example.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'abalone-example.Rmd'

--- re-building 'bike-rental.Rmd' using rmarkdown
Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


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: 'scales'

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

    discard

`geom_smooth()` using formula 'y ~ x'
Quitting from lines 148-152 (bike-rental.Rmd) 
Error: processing vignette 'bike-rental.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'bike-rental.Rmd'

SUMMARY: processing the following files failed:
  'abalone-example.Rmd' 'bike-rental.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
prepare_Rd: panel.meansdplot.Rd:42-45: Dropping empty section \value
prepare_Rd: panel.meansdplot.Rd:49-51: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:40-42: Dropping empty section \details
prepare_Rd: panel.violinm.Rd:43-49: Dropping empty section \value
prepare_Rd: panel.violinm.Rd:53-55: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:50-52: Dropping empty section \author
prepare_Rd: violinmplot.Rd:34-36: Dropping empty section \details
prepare_Rd: violinmplot.Rd:48-50: Dropping empty section \note
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
viopoints.default: no visible global function definition for 'par'
viopoints.default: no visible global function definition for 'plot.new'
viopoints.default: no visible global function definition for
  'plot.window'
viopoints.default: no visible global function definition for 'axis'
viopoints.default: no visible global function definition for 'arrows'
viopoints.default: no visible global function definition for
  'getFromNamespace'
viopoints.default: no visible global function definition for 'title'
viopoints.default: no visible global function definition for 'box'
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'caret', 'NeuralNetTools', 'parsnip', 'sparklyr'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'ggraph', 'tidygraph'
Packages required but not available: 'plotly', 'highcharter'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Missing or unexported object: 'jsonlite::rbind.pages'
Package suggested but not available for checking: 'tidyr'
Decile.Plot: no visible global function definition for 'barplot'
Decile.Plot: no visible global function definition for 'axis'
Sliding.Window: no visible global function definition for 'lines'
Sliding.Window: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis barplot legend lines
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines")
to your NAMESPACE file.
Package required but not available: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'Datasets-for-Seminars.Rmd' using rmarkdown
Quitting from lines 20-35 (Datasets-for-Seminars.Rmd) 
Error: processing vignette 'Datasets-for-Seminars.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'Datasets-for-Seminars.Rmd'

--- re-building 'Introduction-to-volleystat.Rmd' using rmarkdown
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 9 rows containing non-finite values (stat_bin).
`summarise()` regrouping output by 'league_gender' (override with `.groups` argument)
`summarise()` regrouping output by 'league_gender' (override with `.groups` argument)
`summarise()` ungrouping output (override with `.groups` argument)
--- finished re-building 'Introduction-to-volleystat.Rmd'

SUMMARY: processing the following file failed:
  'Datasets-for-Seminars.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'syuzhet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyr'
Malformed Description field: should contain one or more complete sentences.
voss1d: no visible global function definition for 'approx'
voss1d: no visible global function definition for 'rnorm'
voss1g: no visible global function definition for 'dchisq'
voss1g: no visible global function definition for 'approx'
voss1g: no visible global function definition for 'rnorm'
voss2d: no visible global function definition for 'rnorm'
voss2g: no visible global function definition for 'dchisq'
voss2g: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'misc3d' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'benchmarks.Rmd' using rmarkdown
Quitting from lines 11-116 (benchmarks.Rmd) 
Error: processing vignette 'benchmarks.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'benchmarks.Rmd'

--- re-building 'vroom.Rmd' using rmarkdown
--- finished re-building 'vroom.Rmd'

SUMMARY: processing the following file failed:
  'benchmarks.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
plot.vscc: no visible global function definition for 'rainbow'
plot.vscc: no visible global function definition for 'pairs'
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Non-standard file/directory found at top level:
  'vwr-Ex.R'
Packages in Depends field not imported from:
  'lattice' 'latticeExtra' 'stringdist'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for 'detectCores'
ald: no visible global function definition for 'mclapply'
coltheart.N: no visible global function definition for 'detectCores'
coltheart.N: no visible global function definition for 'mclapply'
hamming.distance: no visible global function definition for
  'stringdist'
ldknn: no visible global function definition for 'detectCores'
ldknn: no visible global function definition for 'mclapply'
ldknn.odds: no visible global function definition for 'glm'
ldknn.odds: no visible binding for global variable 'binomial'
ldknn.odds: no visible global function definition for 'coefficients'
levenshtein.damerau.distance: no visible global function definition for
  'stringdist'
levenshtein.distance: no visible global function definition for
  'stringdist'
plot.ldknn.run: no visible global function definition for 'histogram'
plot.ldknn.run: no visible global function definition for
  'theEconomist.theme'
plot.ldknn.run: no visible global function definition for 'xyplot'
plot.ldknn.run: no visible global function definition for 'as.layer'
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
summary.whc: no visible global function definition for 'printCoefmat'
wahc.fit: no visible global function definition for 'pt'
wahc.fit: no visible global function definition for 'cor'
whc: no visible global function definition for 'model.frame'
whc: no visible global function definition for 'model.matrix'
whc: no visible global function definition for 'model.response'
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
Found the following files/directories:
  'linout.csv' 'linout.pdf' 'out.csv' 'out.pdf' 'tabel_out.csv'
Rd file 'p.storage.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

Rd file 'read.results.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]

Rd file 'wasim-package.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

These lines will be truncated in the PDF manual.
Found the following files/directories:
  'weisseritz'
Foreign function call to a different package:
  .C("comwr", ..., PACKAGE = "wavethresh")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'rPeaks'
Found the following files/directories:
  'ReconstructedData.txt' 'ReconstructedDataStDev.txt'
  'ResampledReconstructions.txt'
  'ResampledReconstructionsStandardVariation.txt'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
onesamplemeantest: no visible global function definition for 'pnorm'
twosamplemeantest: no visible global function definition for 'pnorm'
wcq: no visible global function definition for 'var'
wcq: no visible global function definition for 'pnorm'
wcq.fdrc: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyr'
Package suggested but not available for checking: 'ggmap'
Package required but not available: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rrtable', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Package vignette with placeholder title 'Vignette Title':
  'weco-vignette.Rmd'
Package required but not available: 'plotly'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Weighted.Box.test: no visible global function definition for 'acf'
Weighted.Box.test: no visible binding for global variable 'na.pass'
Weighted.Box.test: no visible global function definition for 'pgamma'
Weighted.Box.test: no visible global function definition for 'pchisq'
Weighted.LM.test: no visible global function definition for 'acf'
Weighted.LM.test: no visible binding for global variable 'na.pass'
Weighted.LM.test: no visible global function definition for 'pgamma'
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
Package suggested but not available for checking: 'misaem'
Running examples in 'WeightIt-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: method_energy
> ### Title: Entropy Balancing
> ### Aliases: method_energy
> 
> ### ** Examples
> 
> library("cobalt")
 cobalt (Version 4.2.2, Build Date: 2020-06-26 15:50:03 UTC)
> data("lalonde", package = "cobalt")
> 
> #Balancing covariates between treatment groups (binary)
> (W1 <- weightit(treat ~ age + educ + married +
+                   nodegree + re74, data = lalonde,
+                 method = "energy", estimand = "ATE"))
Error: All weights are 2143289344.
Execution halted
Package required but not available: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'broom'

Packages suggested but not available for checking: 'ggraph', 'fuzzyjoin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
Malformed Description field: should contain one or more complete sentences.
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File 'wikibooks/R/Bundesliga.Mannschaft.R':
  data(Bundesliga)
File 'wikibooks/R/Bundesliga.Tabelle.R':
  data(Bundesliga)
File 'wikibooks/R/Bundesliga.XML.R':
  data(Bundesliga)
See section 'Good practice' in '?data'.
Found the following files/directories:
  'Bundesliga.xml' 'myfile.xml'
Running 'testthat.R' [3s/14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wikifacts)
  > 
  > test_check("wikifacts")
  -- 1. Failure: wiki_randomfact() generates a valid didyouknow fact (@test-random
  `.` not equal to "Did you know".
  1/1 mismatches
  x[1]: "I got nothin"
  y[1]: "Did you know"
  
  == testthat results  ===========================================================
  [ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: wiki_randomfact() generates a valid didyouknow fact (@test-randomfact.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
wilcox.selection.split: no visible global function definition for
  'pnorm'
wilcox.test2: no visible global function definition for 'wilcox.test'
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Packages required but not available: 'plotly', 'factoextra', 'heatmaply'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'imputeTestbench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
plotTrait: no visible global function definition for 'points'
plotTrait: no visible global function definition for 'legend'
test.windex: no visible global function definition for 'hist'
test.windex: no visible global function definition for 'abline'
test.windex: no visible global function definition for 'legend'
windex: no visible global function definition for 'sd'
windex: no visible global function definition for 'var'
windex: no visible global function definition for 'dist'
windex: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline dist hist legend points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
Package suggested but not available for checking: 'rnrfa'
Error(s) in re-building vignettes:
  ...
--- re-building 'winfapReader.Rmd' using rmarkdown
Quitting from lines 145-157 (winfapReader.Rmd) 
Error: processing vignette 'winfapReader.Rmd' failed with diagnostics:
there is no package called 'rnrfa'
--- failed re-building 'winfapReader.Rmd'

SUMMARY: processing the following file failed:
  'winfapReader.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'HydeNet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dbayes: no visible global function definition for 'mahalanobis'
dbayes: no visible global function definition for 'var'
wmd: no visible global function definition for 'cor'
wmd: no visible global function definition for 'var'
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for 'lm'
plotfit,Leader: no visible global function definition for 'par'
Undefined global functions or variables:
  lm par
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidygraph', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'plyr' 'reshape2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for 'llply'
wordmatch : <anonymous>: no visible global function definition for
  'llply'
wordmatch: no visible global function definition for 'melt'
wordmatch: no visible global function definition for 'count'
Undefined global functions or variables:
  count llply melt
Package required but not available: 'parsnip'

Package suggested but not available for checking: 'recipes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'openair', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'aphiainfo.csv' 'tax.csv'
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'factoextra'
Error(s) in re-building vignettes:
  ...
--- re-building 'wrGraphVignette2.Rmd' using rmarkdown
Quitting from lines 27-33 (wrGraphVignette2.Rmd) 
Error: processing vignette 'wrGraphVignette2.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building 'wrGraphVignette2.Rmd'

SUMMARY: processing the following file failed:
  'wrGraphVignette2.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
Package suggested but not available for checking: 'tidyr'
Package suggested but not available for checking: 'tidyr'
Packages required but not available: 'caret', 'tidyr'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File
  LICENCE
is not mentioned in the DESCRIPTION file.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
simul.wsvm: no visible binding for global variable 'mixture.example'
Undefined global functions or variables:
  mixture.example
Rd file 'simul.wsvm.Rd':
  \usage lines wider than 90 characters:
         simul.wsvm(set.seeds = 123, obs.num = 1000, mu = c(0,0), cov.mat = 0.2*diag(2), X = NULL, Y = NULL)

Rd file 'wsvm.boost.Rd':
  \usage lines wider than 90 characters:
         wsvm.boost(X, Y, new.X, new.Y, c.n, B = 50, kernel.type = list(type = "rbf", par= 0.5), C = 4, eps = 1e-10, plotting = FALSE)

These lines will be truncated in the PDF manual.
Package vignette with placeholder title 'Vignette Title':
  'wTOvignette.Rmd'
Package suggested but not available for checking: 'plotly'
Package required but not available: 'simts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  'CONTENTS'
Rd file 'classroom.Rd':
  \examples lines wider than 100 characters:
     {boxplot(classroom.first8$mathgain[classroom.first8$schoolid==i] ~ classroom.first8$classid[classroom.first8$schoolid==i],ylab="Mathgai ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Packages required but not available:
  'tidyr', 'wyz.code.offensiveProgramming'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyr', 'wyz.code.offensiveProgramming'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyr', 'wyz.code.offensiveProgramming'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  'Rout.a1' 'Rout.b1' 'Rout.d10' 'Rout.d11' 'Rout.d12' 'Rout.dat'
  'Rout.ftr' 'Rout.html' 'Rout.spc' 'Rout_Profiler.txt' 'Rout_err.html'
  'Rout_log.html' 'gra_Rout'
Found the following notes/warnings:
  Non-staged installation was used
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/x13binary.Rcheck/00install.out' for details.
Found the following files/directories:
  'RP2_data_1.txt' 'RP2_data_4.txt' 'RP2_qtl_1.txt' 'RP2_qtl_4.txt'
  'hp1_effect_qtl.txt' 'hp1_freq_mrk.txt' 'hp1_freq_qtl.txt'
  'hp1_genome.txt' 'hp1_last_hp_data.txt' 'hp1_lm_mrk.txt'
  'hp1_lm_qtl.txt' 'hp1_lm_qtl_mrk.txt' 'hp1_mrk.txt' 'hp1_qtl.txt'
  'hp2_effect_qtl.txt' 'hp2_freq_mrk.txt' 'hp2_freq_qtl.txt'
  'hp2_genome.txt' 'hp2_last_hp_data.txt' 'hp2_lm_mrk.txt'
  'hp2_lm_qtl.txt' 'hp2_lm_qtl_mrk.txt' 'hp2_mrk.txt' 'hp2_qtl.txt'
  'my_RP_data_1.txt' 'my_RP_data_4.txt' 'my_RP_mrk_1.txt'
  'my_RP_mrk_4.txt'
Found a 'configure.in' file: 'configure.ac' has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
Packages required but not available: 'bupaR', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'xgb.txt'
Package suggested but not available for checking: 'DiagrammeR'
GNU make is a SystemRequirements.
Running examples in 'xgboost-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xgb.plot.multi.trees
> ### Title: Project all trees on one tree and plot it
> ### Aliases: xgb.plot.multi.trees
> 
> ### ** Examples
> 
> 
> data(agaricus.train, package='xgboost')
> 
> bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label, max_depth = 15,
+                eta = 1, nthread = 2, nrounds = 30, objective = "binary:logistic",
+                min_child_weight = 50, verbose = 0)
> 
> p <- xgb.plot.multi.trees(model = bst, features_keep = 3)
Column 2 ['No'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for  backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
Error in loadNamespace(name) : there is no package called 'DiagrammeR'
Calls: xgb.plot.multi.trees ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
File
  LICENCE
is not mentioned in the DESCRIPTION file.
quadplot: no visible global function definition for 'median'
xgobi: no visible global function definition for 'write.table'
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'sad_pkpd.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 32-42 (sad_pkpd.Rmd) 
Error: processing vignette 'sad_pkpd.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'sad_pkpd.Rmd'

--- re-building 'theoph.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

`summarise()` ungrouping output (override with `.groups` argument)
Quitting from lines 44-100 (theoph.Rmd) 
Error: processing vignette 'theoph.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'theoph.Rmd'

--- re-building 'xgxr_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

removing  points with MDV==1 & EVID==0 from dataset
--- finished re-building 'xgxr_overview.Rmd'

SUMMARY: processing the following files failed:
  'sad_pkpd.Rmd' 'theoph.Rmd'

Error: Vignette re-building failed.
Execution halted
XHWE: no visible global function definition for 'read.table'
result: no visible global function definition for 'pchisq'
result: no visible global function definition for 'rbinom'
result: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  'results.txt'
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
stampme: no visible global function definition for 'flush.console'
stampmsg: no visible global function definition for 'flush.console'
write.data.table: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LPGM: no visible global function definition for 'flush.console'
PGM: no visible global function definition for 'flush.console'
PGM.path.neighborhood: no visible global function definition for
  'runif'
PGMSim: no visible global function definition for 'rpois'
PGMSim: no visible global function definition for 'par'
WPGMSim: no visible global function definition for 'rpois'
XMRF.Sim: no visible global function definition for 'cov2cor'
XMRF.Sim: no visible global function definition for 'rbinom'
XMRF.Sim: no visible global function definition for 'rnorm'
glm.generic: no visible global function definition for 'flush.console'
mymult: no visible global function definition for 'rmultinom'
plot.GMS: no visible global function definition for 'pdf'
plot.GMS: no visible global function definition for 'dev.off'
plotNet: no visible global function definition for 'pdf'
plotNet: no visible global function definition for 'dev.off'
print.GMS: no visible global function definition for 'str'
processSeq: no visible binding for global variable 'quantile'
processSeq: no visible binding for global variable 'var'
processSeq: no visible global function definition for 'ks.test'
rmpois : <anonymous>: no visible global function definition for 'rpois'
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
Found the following files/directories:
  'ggm.fit.net.pdf'
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'descriptr', 'highcharter', 'inferr', 'plotly', 'rfm'
Packages required but not available: 'tidyr', 'vpc'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fuzzyjoin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plotly'
Package required but not available: 'tidyr'

Packages suggested but not available for checking: 'factorMerger', 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following files/directories:
  'xtable.html' 'xtable.tex'
Found the following files/directories:
  'OPT.csv' 'testTecan_defaultLiquid.csv' 'testTecan_setLiquid.csv'
Package vignette with placeholder title 'Vignette Title':
  'vignette.Rmd'
Package vignette with placeholder title 'Vignette Title':
  'xyz-vignette.Rmd'
Non-standard file/directory found at top level:
  'CONTRIBUTORS'
Malformed Title field: should not end in a period.
big.read.table: no visible global function definition for 'read.table'
big.read.table: no visible global function definition for 'object.size'
sparkline: no visible global function definition for 'is.ts'
sparkline: no visible global function definition for 'time'
sparkline: no visible global function definition for 'boxplot'
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  'CO2.csv'
Package suggested but not available for checking: 'tidyr'
Running examples in 'yardstick-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: conf_mat
> ### Title: Confusion Matrix for Categorical Data
> ### Aliases: conf_mat conf_mat.table conf_mat.default conf_mat.data.frame
> ###   tidy.conf_mat autoplot.conf_mat
> 
> ### ** 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

> data("hpc_cv")
> 
> # The confusion matrix from a single assessment set (i.e. fold)
> cm <- hpc_cv %>%
+   filter(Resample == "Fold01") %>%
+   conf_mat(obs, pred)
> cm
          Truth
Prediction  VF   F   M   L
        VF 166  33   8   1
        F   11  71  24   7
        M    0   3   5   3
        L    0   1   4  10
> 
> # Now compute the average confusion matrix across all folds in
> # terms of the proportion of the data contained in each cell.
> # First get the raw cell counts per fold using the `tidy` method
> library(purrr)
> library(tidyr)
Error in library(tidyr) : there is no package called 'tidyr'
Execution halted
Package suggested but not available for checking: 'ggtree'
Error(s) in re-building vignettes:
  ...
--- re-building 'gammaproteobacteria.Rmd' using rmarkdown
Quitting from lines 24-27 (gammaproteobacteria.Rmd) 
Error: processing vignette 'gammaproteobacteria.Rmd' failed with diagnostics:
there is no package called 'ggtree'
--- failed re-building 'gammaproteobacteria.Rmd'

SUMMARY: processing the following file failed:
  'gammaproteobacteria.Rmd'

Error: Vignette re-building failed.
Execution halted
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.
bootstrapswapcurve: no visible global function definition for 'ts'
fitted: no visible global function definition for 'ts'
forwardrates: no visible global function definition for 'ts'
residuals: no visible global function definition for 'ts'
tZC_NS: no visible global function definition for 'cmpfun'
tZC_NS_extra: no visible global function definition for 'cmpfun'
tZC_SV: no visible global function definition for 'cmpfun'
tZC_SV_extra: no visible global function definition for 'cmpfun'
ycextra: no visible global function definition for 'new'
ycinter: no visible global function definition for 'new'
ycplot: no visible global function definition for 'par'
ycplot: no visible global function definition for 'points'
ycplot: no visible global function definition for 'abline'
ycplot: no visible global function definition for 'hist'
ycplot: no visible global function definition for 'lines'
ycplot: no visible global function definition for 'density'
ycplot: no visible global function definition for 'qqnorm'
ycplot: no visible global function definition for 'qqline'
ycsummary: no visible global function definition for 'shapiro.test'
ycsummary: no visible global function definition for 'pf'
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for 'lm'
.NS.estimator: no visible global function definition for 'coef'
.NS.estimator: no visible global function definition for 'na.omit'
.NS.estimator: no visible global function definition for 'resid'
.NSS.estimator: no visible global function definition for 'lm'
.NSS.estimator: no visible global function definition for 'coef'
.NSS.estimator: no visible global function definition for 'na.omit'
.NSS.estimator: no visible global function definition for 'resid'
NSrates: no visible global function definition for 'time'
Nelson.Siegel: no visible global function definition for 'optimize'
Srates: no visible global function definition for 'time'
Svensson: no visible global function definition for 'median'
Svensson: no visible global function definition for 'optimize'
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
Rd file 'ECBYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat.ECB, ECBYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

Rd file 'FedYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat, FedYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

These lines will be truncated in the PDF manual.
kmeansN: no visible global function definition for 'kmeans'
kmeansN: no visible global function definition for 'aggregate'
kmeansN2: no visible global function definition for 'aggregate'
kmeansN2: no visible binding for global variable 'sd'
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'tidyr'
Running examples in 'ypr-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chilliwack_bt_05
> ### Title: Chilliwack Lake Bull Trout Populations Parameters (2005)
> ### Aliases: chilliwack_bt_05
> ### Keywords: datasets
> 
> ### ** Examples
> 
> chilliwack_bt_05
tmax:  20
k:     0.12
Linf:  86
t0:    0.018
k2:    0.12
Linf2: 86
L2:    1000
Wb:    2.8
Ls:    38.5
Sp:    100
es:    1
Sm:    0
fb:    1
tR:    1
BH:    1
Rk:    2.5, 4.6, 2.5, 4.6, 2.5, 4.6, 2.5, 4.6, 2.5, 4.6, 2.5, 4.6
n:     0.17
nL:    0.17
Ln:    50
Lv:    36.5
Vp:    11.7
Llo:   0, 0, 60, 60, 1000, 1000, 0, 0, 60, 60, 1000, 1000
Lup:   1000
Nc:    0.15
pi:    0.2
rho:   0
Hm:    0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2
Rmax:  250
Wa:    0.022
fa:    2.29
q:     0.1
> yield <- ypr_tabulate_yield(chilliwack_bt_05, type = "optimal")
> yield$pi <- round(yield$pi, 2)
> yield <- yield[c("Llo", "Hm", "Rk", "pi")]
> yield <- tidyr::spread(yield, Rk, pi)
Error in loadNamespace(name) : there is no package called 'tidyr'
Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'mixOmics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rnoaa', 'neonUtilities'
Missing or unexported object: 'devtools::use_data'
Found the following files/directories:
  'test.csv'
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'TSA'
Unknown package 'TSA' in Rd xrefs
Package vignette with placeholder title 'Vignette Title':
  'ZipRadius.Rmd'
Running 'testthat.R' [3s/4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(zip)
  
  Attaching package: 'zip'
  
  The following objects are masked from 'package:utils':
  
      unzip, zip
  
  > 
  > test_check("zip")
  -- 1. Error: base path with non-ASCII characters (@test-paths.R#74)  -----------
  zip error: `Cannot set permission on file `dir1/` in archive `zip1.zip`` in file `zip.c:356`
  Backtrace:
   1. zip::zip("zip1.zip", c("dir1", "dir2"), mode = "mirror")
   2. zip:::zip_internal(...)
  
  -- 2. Error: uncompressed path with non-ASCII characters (@test-paths.R#103)  --
  zip error: `Cannot set permission on file `ÃºÃ¡Ã¶<U+0151>Ã©/` in archive `zip1.zip`` in file `zip.c:356`
  Backtrace:
   1. zip::zip("zip1.zip", root, mode = "mirror")
   2. zip:::zip_internal(...)
  
  == testthat results  ===========================================================
  [ OK: 234 | SKIPPED: 3 | WARNINGS: 5 | FAILED: 2 ]
  1. Error: base path with non-ASCII characters (@test-paths.R#74) 
  2. Error: uncompressed path with non-ASCII characters (@test-paths.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'zdat'
S3 methods shown with full name in documentation object 'merge':
  'cbind.zoocat'

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 vignette with placeholder title 'Vignette Title':
  'my-vignette.Rmd'
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'SDMTools'
Package suggested but not available for checking: 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building 'ztpln.rmd' using rmarkdown
Quitting from lines 102-110 (ztpln.rmd) 
Error: processing vignette 'ztpln.rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'ztpln.rmd'

SUMMARY: processing the following file failed:
  'ztpln.rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Non-standard file/directory found at top level:
  ‘doc’
Packages in Depends field not imported from:
  ‘Rglpk’ ‘corrplot’ ‘lattice’ ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘CVrej.ps’ ‘linhc.pdf’
Package required but not available: ‘mosaic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
multiplot: no visible global function definition for ‘rainbow’
multiplot: no visible global function definition for ‘text’
multiplot: no visible global function definition for ‘lines’
multiplot: no visible global function definition for ‘par’
plot.abf2: no visible global function definition for ‘abline’
plot.abf2: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline lines par rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "text")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘geneset.txt’
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
fillCSVData: no visible global function definition for ‘read.table’
fillData: no visible global function definition for ‘edit’
plotGraphs: no visible global function definition for ‘par’
plotGraphs: no visible global function definition for ‘lines’
plotGraphs: no visible global function definition for ‘legend’
plotGraphs: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new edit legend lines par read.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "par")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
Package has no Sweave vignette sources and no VignetteBuilder field.
Malformed Description field: should contain one or more complete sentences.
print.funlinWLS: no visible global function definition for ‘pchisq’
print.linML: no visible global function definition for ‘pchisq’
print.loglinML: no visible global function definition for ‘pchisq’
print.satMarML: no visible global function definition for ‘pchisq’
print.satMcarWLS: no visible global function definition for ‘pchisq’
summary.funlinWLS: no visible global function definition for ‘pchisq’
summary.linML: no visible global function definition for ‘pchisq’
summary.loglinML: no visible global function definition for ‘pchisq’
summary.satMarML: no visible global function definition for ‘pchisq’
summary.satMcarWLS: no visible global function definition for ‘pchisq’
summary.waldTest: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
acm: no visible global function definition for ‘read.table’
clusters: no visible global function definition for ‘write.matrix’
clusters: no visible global function definition for ‘dev.new’
clusters: no visible global function definition for ‘par’
clusters: no visible global function definition for ‘hist’
clusters: no visible global function definition for ‘legend’
clusters: no visible global function definition for ‘pdf’
clusters: no visible global function definition for ‘dev.off’
erra: no visible global function definition for ‘read.table’
erra: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  dev.new dev.off hist legend par pbeta pdf read.table write.matrix
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "hist", "legend", "par")
  importFrom("stats", "pbeta")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘BABLBS_ID distribution’ ‘BABLBS_Singletons’ ‘BABLBS_clustered’
  ‘BABLBS_clustered_and_single’ ‘Genetic_Distance_1ID distribution’
  ‘Genetic_Distance_1Singletons’ ‘Genetic_Distance_1clustered’
  ‘Genetic_Distance_1clustered_and_single’ ‘acm.out.1’ ‘acm.par’
  ‘erra.out.1’ ‘erra.out.1.acm’ ‘erra.out.1_d.ite’ ‘erra.out.1_s.ite’
  ‘erra.rcm’ ‘exact_matching_ID distribution’
  ‘exact_matching_Singletons’ ‘exact_matching_clustered’
  ‘exact_matching_clustered_and_single’ ‘experiments.in’
  ‘hist_both.pdf’ ‘hist_clust.pdf’ ‘replicates.in’
Aggregate: no visible global function definition for ‘aggregate’
Aggregate: no visible binding for global variable ‘tail’
Aggregate: no visible binding for global variable ‘var’
cocktailEnsemble: no visible global function definition for ‘glm’
cocktailEnsemble: no visible global function definition for ‘binomial’
cocktailEnsemble: no visible global function definition for ‘step’
cocktailEnsemble: no visible binding for global variable ‘na.omit’
imputeMissings : <anonymous>: no visible global function definition for
  ‘median’
predict.cocktailEnsemble: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  aggregate binomial glm median na.omit predict step tail var
Consider adding
  importFrom("stats", "aggregate", "binomial", "glm", "median",
             "na.omit", "predict", "step", "var")
  importFrom("utils", "tail")
to your NAMESPACE file.
Rd file 'cocktailEnsemble.Rd':
  \examples lines wider than 100 characters:
     Credit <- data.frame(Credit[order(runif(nrow(Credit ))),])[1:100,c('V2','V3','V8','V11','V14','V15','Response')]

Rd file 'predict.cocktailEnsemble.Rd':
  \examples lines wider than 100 characters:
     Credit <- data.frame(Credit[order(runif(nrow(Credit ))),])[1:100,c('V2','V3','V8','V11','V14','V15','Response')]

These lines will be truncated in the PDF manual.
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘Example.jpeg’
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Anthropometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘SemiPar’ ‘nlme’
  Please remove these calls from your code.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘AdaptFit/R/aspm.R’:
  assign("group.vec.Handan", group.vec, pos = 1)
  assign("X.Declan", X, pos = 1)
  assign("Z.Jaida", Z, pos = 1)

Found the following calls to attach():
File ‘AdaptFit/R/asp.R’:
  attach(theta.frame)
  attach(theta.frame)
See section ‘Good practice’ in ‘?attach’.
Rd file 'asp.Rd':
  \usage lines wider than 90 characters:
                     spar.method="REML",omit.missing=NULL,niter=20,niter.var=50,tol=1e-06,returnFit=FALSE,weights=NULL,correlation=NULL,cont ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Depends: includes the non-default packages:
  'Matrix', 'coda', 'mvtnorm', 'MCMCpack', 'spatstat', 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘MCMCpack’ ‘Matrix’ ‘coda’ ‘mvtnorm’ ‘parallel’ ‘spatstat’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'getpar.Rd':
  \examples lines wider than 100 characters:
     ## Plot the conditional error function of the Lehmacher-Wassmer (1999) type that runs through (p1,p2)=(0.3,0.7)

Rd file 'parconv.Rd':
  \examples lines wider than 100 characters:
     ## Obtain the parameter c for Fisher's combination test, using the local level 0.05 for the test after the second stage

Rd file 'pathCEF.Rd':
  \examples lines wider than 100 characters:
     ## Compare the tests by Bauer and Koehne (1994), Lehmacher and Wassmer (1999) and Vandemeulebroecke (2006)

Rd file 'tsT.Rd':
  \examples lines wider than 100 characters:
     ## An example of non-uniqueness: the maximal alpha1 is returned; any smaller value would also be valid

These lines will be truncated in the PDF manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
critical.values: no visible global function definition for ‘rnorm’
critical.values: no visible global function definition for ‘quantile’
mandel.test: no visible global function definition for ‘qf’
mtukey.test : p.test: no visible global function definition for ‘qf’
mtukey.test: no visible binding for global variable ‘quantile’
mtukey.test: no visible global function definition for ‘rnorm’
tukey.test: no visible global function definition for ‘qf’
Undefined global functions or variables:
  qf quantile rnorm
Consider adding
  importFrom("stats", "qf", "quantile", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘adephylo’
Package required but not available: ‘phylobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘adephylo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘Bestmatches.csv’ ‘ID.csv’ ‘listsp.csv’ ‘mylabels.csv’
Packages required but not available: 'adephylo', 'phylobase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tidyr', 'tidyverse'
Found the following sources/headers with CR or CRLF line endings:
  inst/include/ADMMnet.h
  inst/include/ADMMnet_RcppExports.h
Some Unix compilers require LF line endings.
Packages required but not available: 'sjstats', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("aemo")
  Loading required package: aemo
  ── 1. Error: AEMO data URLs still correct (@test-aemo.R#41)  ───────────────────
  Timeout was reached: [www.aemo.com.au] Connection timed out after 10000 milliseconds
  Backtrace:
   1. testthat::expect_equal(GET(web_url)$status, 200)
   4. httr::GET(web_url)
   5. httr:::request_perform(req, hu$handle$handle)
   7. httr:::request_fetch.write_memory(req$output, req$url, handle)
   8. curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: AEMO data URLs still correct (@test-aemo.R#41) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: 'plotly', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tidyr', 'ggpubr'
Package required but not available: ‘geepack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘About.Rmd’
Packages suggested but not available for checking: 'broom', 'nullabor'
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘myplot.pdf’ ‘myplot.png’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘Starr’
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘ans_19-2.jpg’ ‘display2d_19-2.jpg’ ‘dist(3)_19-2.jpg’
  ‘dist(4)_19-2.jpg’ ‘dist(mirror)_19-2.jpg’ ‘dist(mirror2)_19-2.jpg’
Namespace with empty importFrom: ‘survival’
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘survival’
A package should be listed in only one of these fields.
backfit.cox.interaction: no visible global function definition for
  ‘coxph’
backfit.lm.interaction: no visible global function definition for ‘lm’
backfit.logistic.interaction: no visible global function definition for
  ‘glm’
backfit.logistic.main: no visible global function definition for ‘glm’
cox.interaction: no visible global function definition for ‘coxph’
cv.cox.interaction: no visible global function definition for ‘coxph’
cv.cox.main: no visible global function definition for ‘coxph’
cv.lm.interaction: no visible global function definition for ‘lm’
cv.lm.main: no visible global function definition for ‘lm’
cv.logistic.interaction: no visible global function definition for
  ‘glm’
cv.logistic.main: no visible global function definition for ‘glm’
lm.interaction: no visible global function definition for ‘lm’
logistic.interaction: no visible global function definition for ‘glm’
logistic.main: no visible global function definition for ‘glm’
Undefined global functions or variables:
  coxph glm lm
Consider adding
  importFrom("stats", "glm", "lm")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggmcmc’
Found the following files/directories:
  ‘stuve.pdf’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggraph', 'tidygraph', 'textstem', 'widyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
dke.fun.default: no visible global function definition for ‘hist’
kef: no visible global function definition for ‘dbinom’
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
plot.dke.fun: no visible global function definition for ‘hist’
plot.dke.fun: no visible global function definition for ‘lines’
plot.hcvc.fun1d: no visible global function definition for
  ‘plot.default’
plot.hcvd.fun1d: no visible global function definition for
  ‘plot.default’
plot.kern.fun1d: no visible global function definition for
  ‘plot.default’
plot.kpmfe.fun1d: no visible global function definition for
  ‘plot.default’
plot.reg.fun1d: no visible global function definition for
  ‘plot.default’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dbinom dgamma dlnorm hist lines plot.default
Consider adding
  importFrom("graphics", "hist", "lines", "plot.default")
  importFrom("stats", "approx", "dbinom", "dgamma", "dlnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
Package suggested but not available for checking: ‘tidyr’
adpbar: no visible global function definition for ‘optim’
alabama: no visible global function definition for ‘optim’
auglag: no visible global function definition for ‘modifyList’
auglag1: no visible global function definition for ‘optim’
auglag1: no visible global function definition for ‘nlminb’
auglag2: no visible global function definition for ‘optim’
auglag2: no visible global function definition for ‘nlminb’
auglag3: no visible global function definition for ‘optim’
auglag3: no visible global function definition for ‘nlminb’
augpen: no visible global function definition for ‘optim’
constrOptim.nl: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
  modifyList nlminb optim
Consider adding
  importFrom("stats", "nlminb", "optim")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘candidate_alignments.csv’ ‘open.with.excel.csv’
Malformed Description field: should contain one or more complete sentences.
allanVarSelect: no visible global function definition for ‘read.csv’
fitvbiglm: no visible global function definition for ‘read.csv’
fitvbiglm: no visible global function definition for ‘update’
getbestchunksize: no visible global function definition for ‘read.csv’
getbestchunksize: no visible global function definition for
  ‘object.size’
predictvbiglm: no visible global function definition for ‘read.csv’
predictvbiglm: no visible global function definition for ‘predict’
predictvbiglm: no visible global function definition for
  ‘weighted.mean’
readinbigdata : <anonymous>: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  object.size predict read.csv update weighted.mean
Consider adding
  importFrom("stats", "predict", "update", "weighted.mean")
  importFrom("utils", "object.size", "read.csv")
to your NAMESPACE file.
prepare_Rd: allan-package.Rd:49-51: Dropping empty section \seealso
prepare_Rd: allanVarSelect.Rd:59-60: Dropping empty section \details
prepare_Rd: allanVarSelect.Rd:66-67: Dropping empty section \references
prepare_Rd: allanVarSelect.Rd:78-79: Dropping empty section \seealso
prepare_Rd: fitvbiglm.Rd:38-39: Dropping empty section \details
prepare_Rd: fitvbiglm.Rd:49-50: Dropping empty section \note
prepare_Rd: fitvbiglm.Rd:43-44: Dropping empty section \references
prepare_Rd: fitvbiglm.Rd:53-54: Dropping empty section \seealso
prepare_Rd: getbestchunksize.Rd:35-36: Dropping empty section \details
prepare_Rd: getbestchunksize.Rd:46-47: Dropping empty section \note
prepare_Rd: getbestchunksize.Rd:40-41: Dropping empty section \references
prepare_Rd: getbestchunksize.Rd:50-51: Dropping empty section \seealso
prepare_Rd: predictvbiglm.Rd:44-45: Dropping empty section \details
prepare_Rd: predictvbiglm.Rd:56-57: Dropping empty section \note
prepare_Rd: predictvbiglm.Rd:50-51: Dropping empty section \references
prepare_Rd: predictvbiglm.Rd:60-61: Dropping empty section \seealso
prepare_Rd: readinbigdata.Rd:42-43: Dropping empty section \note
prepare_Rd: readinbigdata.Rd:45-46: Dropping empty section \seealso
File ‘allelic/libs/allelic.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.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.
Packages required but not available: 'broom', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
batch.possSpells.fnc: no visible binding for global variable ‘words’
possSpells.fnc: no visible binding for global variable ‘len.phons’
possSpells.fnc: no visible binding for global variable ‘phon1’
possSpells.fnc: no visible binding for global variable ‘len.total’
possSpells.fnc: no visible binding for global variable ‘poss.spells’
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
Found the following files/directories:
  ‘more.words.rda’ ‘more.words.txt’ ‘more.words_log.txt’
  ‘other.words.rda’ ‘other.words.txt’ ‘other.words_log.txt’
  ‘some.words.rda’ ‘some.words.txt’ ‘some.words_log.txt’
  ‘yet.more.words.rda’ ‘yet.more.words.txt’ ‘yet.more.words_log.txt’
Packages required but not available: 'dlookr', 'ggmosaic', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'timetk'

Package suggested but not available for checking: ‘tidyquant’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘tidyr’
Malformed Description field: should contain one or more complete sentences.
EXP.step: no visible global function definition for ‘rgamma’
EXP.step: no visible global function definition for ‘rnorm’
MAX.step: no visible global function definition for ‘uniroot’
Norm.GMedian: no visible binding for global variable ‘median’
RNASeq.Data.Gene: no visible binding for global variable ‘quantile’
decom.initial: no visible global function definition for ‘kmeans’
decom.initial: no visible global function definition for ‘quantile’
decom.initial: no visible global function definition for ‘var’
dispersion.nb.QL: no visible binding for global variable ‘quantile’
est.mu.nb.mle: no visible global function definition for ‘runif’
est.v.nb.QL: no visible global function definition for ‘runif’
pdf2grid: no visible global function definition for ‘dnorm’
pdf2grid: no visible global function definition for ‘dgamma’
prior.grid: no visible global function definition for ‘sd’
prior.grid: no visible global function definition for ‘dnorm’
test.AMAP: no visible global function definition for ‘rgamma’
test.AMAP: no visible global function definition for ‘rnorm’
test.AMAP: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
  importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
             "rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
Rd file 'MGN.EM.Rd':
  \usage lines wider than 90 characters:
     MGN.EM(data, nK, p0 = NULL, d0 = 0, nK0 = 0, iter.max = 10, print.steps = FALSE, MGN0 = NULL, model = NULL, nMC = 10000)

Rd file 'test.AMAP.Rd':
  \usage lines wider than 90 characters:
     test.AMAP(data, MGN, del.lim = NULL, FC = NULL, print.steps = FALSE, Integration = "MC",nMC=NULL)
  \examples lines wider than 100 characters:
     data("SimuHapMap")  # a matrix 'counts' storing simulated data with 10000 genes, two treatments, of which each has 5 replicates

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘Zelig’
Malformed Title field: should not end in a period.
amltest: no visible global function definition for ‘var’
amltest: no visible global function definition for ‘optim’
amltest: no visible global function definition for ‘lm’
cleanclust: no visible global function definition for ‘cor’
cleanclust: no visible global function definition for ‘hclust’
cleanclust: no visible global function definition for ‘as.dist’
cleanclust: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cor cutree hclust lm optim var
Consider adding
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "lm",
             "optim", "var")
to your NAMESPACE file.
AMOEBA : Classi: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘Pindoba_domicilios.dbf’ ‘Pindoba_geo.dbf’
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
Packages required but not available: 'broom', 'tidyr'

Package suggested but not available for checking: ‘moveHMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’

Package which this enhances but not available for checking: ‘SparkR’
Package suggested but not available for checking: ‘tidyr’
Analyz.loadSteps,Analyz: 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.
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
Non-standard files/directories found at top level:
  ‘AnDE.pdf’ ‘DESCRIPTION.dcf’ ‘helpme’
Packages in Depends field not imported from:
  ‘discretization’ ‘foreign’ ‘functional’ ‘stringr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aode: no visible global function definition for ‘Compose’
mdl: no visible global function definition for ‘cutPoints’
setVar: no visible global function definition for ‘Compose’
Undefined global functions or variables:
  Compose cutPoints
Malformed Description field: should contain one or more complete sentences.
andrews: no visible global function definition for ‘plot.new’
andrews: no visible global function definition for ‘plot.window’
andrews: no visible global function definition for ‘title’
andrews: no visible global function definition for ‘axis’
andrews: no visible global function definition for ‘box’
andrews: no visible global function definition for ‘lines’
andrews: no visible global function definition for ‘rainbow’
andrews: no visible global function definition for ‘hsv’
selectand: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
Package required but not available: ‘weights’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Found the following files/directories:
  ‘BM-motion-chart.html’ ‘css’ ‘images’ ‘index.html’ ‘js’
Package required but not available: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
annot : annotlist: no visible global function definition for
  ‘read.table’
annot : annotlist: no visible global function definition for
  ‘write.table’
annot: no visible global function definition for ‘flush.console’
annot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  flush.console read.table write.table
Consider adding
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘anoint’ 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 required but not available: 'timetk', 'sweep', 'tidyr'

Packages suggested but not available for checking: 'tidyverse', 'tidyquant'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘smacof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘biclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
aw_map: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'library' or 'require' call to ‘boot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
varbin: no visible global function definition for ‘boot’
Undefined global functions or variables:
  boot
Packages in Depends field not imported from:
  ‘boot’ ‘lme4’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: ‘broom’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘apaTables’
Running examples in ‘apaText-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apa.desc
> ### Title: Creates Mean (M) and Standard Deviation (SD) output with
> ###   confidence interval in APA style using Markdown.
> ### Aliases: apa.desc
> 
> ### ** Examples
> 
> #2-way ANOVA Example
> library(apaTables) #load apaTables to access goggles
Error in library(apaTables) : there is no package called ‘apaTables’
Execution halted
Package suggested but not available for checking: ‘ggtree’
Running examples in ‘aplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: insert_left
> ### Title: plot-insertion
> ### Aliases: insert_left insert_right insert_top insert_bottom
> 
> ### ** Examples
> 
> library(ggplot2)
> library(aplot)
> 
> p <- ggplot(mtcars, aes(mpg, disp)) + geom_point()
> p2 <- ggplot(mtcars, aes(mpg)) + 
+     geom_density(fill='steelblue', alpha=.5) + 
+         ggtree::theme_dendrogram()
Error in loadNamespace(name) : there is no package called ‘ggtree’
Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
TSPM: no visible global function definition for ‘glm’
TSPM: no visible binding for global variable ‘poisson’
TSPM: no visible global function definition for ‘hatvalues’
TSPM: no visible global function definition for ‘residuals’
TSPM: no visible global function definition for ‘deviance’
TSPM: no visible global function definition for ‘qchisq’
TSPM: no visible global function definition for ‘qf’
TSPM: no visible global function definition for ‘pf’
TSPM: no visible global function definition for ‘pchisq’
TSPM: no visible global function definition for ‘p.adjust’
norm.inttable: no visible global function definition for ‘median’
norm.inttable : <anonymous>: no visible global function definition for
  ‘quantile’
saint_permF: no visible global function definition for ‘read.table’
saint_permF: no visible global function definition for ‘write.table’
saint_permF: no visible global function definition for ‘write.csv2’
tspm_apms: no visible global function definition for ‘read.table’
varFilter : <anonymous>: no visible global function definition for
  ‘median’
varFilter: no visible global function definition for ‘median’
varFilter: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  deviance glm hatvalues median p.adjust pchisq pf poisson qchisq qf
  quantile read.table residuals write.csv2 write.table
Consider adding
  importFrom("stats", "deviance", "glm", "hatvalues", "median",
             "p.adjust", "pchisq", "pf", "poisson", "qchisq", "qf",
             "quantile", "residuals")
  importFrom("utils", "read.table", "write.csv2", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘1.png’ ‘2.png’ ‘output.png’
Found the following calls to attach():
File ‘apollo/R/apollo_attach.R’:
  attach(as.list(apollo_beta))
  attach(database)
  attach(draws)
  attach(randcoeff)
  attach(lcpars)
See section ‘Good practice’ in ‘?attach’.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
apple: no visible global function definition for ‘ginv’
apple: no visible global function definition for ‘runif’
deri: no visible global function definition for ‘ginv’
logit: no visible global function definition for ‘qlogis’
plot.apple: no visible global function definition for ‘matplot’
plot.apple: no visible global function definition for ‘lines’
y.app: no visible global function definition for ‘ginv’
Undefined global functions or variables:
  ginv lines matplot qlogis runif
Consider adding
  importFrom("graphics", "lines", "matplot")
  importFrom("stats", "qlogis", "runif")
to your NAMESPACE file.
prepare_Rd: plot.apple.Rd:51-53: Dropping empty section \examples
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Running examples in ‘AppliedPredictiveModeling-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: concrete
> ### Title: Compressive Strength of Concrete from Yeh (1998)
> ### Aliases: concrete mixtures
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(concrete)
> 
> library(caret)
Error in library(caret) : there is no package called ‘caret’
Execution halted
Package required but not available: ‘logistf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of ‘nline’ to
  ‘nlines’
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘apsrtable-Ex.R’
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
Package required but not available: ‘ArchaeoPhases’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggalt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qCBA’
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ardec: no visible global function definition for ‘filter’
ardec.lm: no visible global function definition for ‘ar’
ardec.lm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
Packages required but not available: 'tidyr', 'tabshiftr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Rd file 'sdafilter.Rd':
  \examples lines wider than 100 characters:
     plot(lon,lat,col="lightgrey",type="l",xlim=c(5,18), ylim=c(77.1,79.1),xlab="Longitude",ylab="Latitude")

Rd file 'vmask.Rd':
  \examples lines wider than 100 characters:
     plot(lon,lat,col="lightgrey",type="l",xlim=c(5,18), ylim=c(77.1,79.1),xlab="Longitude",ylab="Latitude")

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘MonetDBLite’
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'oligo', 'oligoClasses', 'pdInfoBuilder'
Packages unavailable to check Rd xrefs: ‘oligo’, ‘oligoClasses’
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
binarize.array: no visible binding for global variable ‘sd’
mskmeans: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans sd
Consider adding
  importFrom("stats", "kmeans", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘broom’
Running examples in ‘arsenal-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: modelsum
> ### Title: Fit models over each of a set of independent variables with a
> ###   response variable
> ### Aliases: modelsum
> 
> ### ** Examples
> 
> 
> data(mockstudy)
> 
> tab1 <- modelsum(bmi ~ sex + age, data = mockstudy)
Error in loadNamespace(name) : there is no package called ‘broom’
Calls: modelsum ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘art-contrasts.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: car
Loading required package: carData

Attaching package: 'car'

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

    recode

Quitting from lines 43-49 (art-contrasts.Rmd) 
Error: processing vignette 'art-contrasts.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘art-contrasts.Rmd’

--- re-building ‘art-effect-size.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: carData

Attaching package: 'car'

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

    Recode

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

    recode

--- finished re-building ‘art-effect-size.Rmd’

SUMMARY: processing the following file failed:
  ‘art-contrasts.Rmd’

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘ARTP’
Package suggested but not available for checking: ‘arulesViz’
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘MSToutput.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘splancs’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘shapefiles’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'calc_box.Rd':
  \examples lines wider than 100 characters:
     ## plot_box by default takes as input the result produced from the calc_box, read from the current workspace. 

Rd file 'calc_sdd.Rd':
  \examples lines wider than 100 characters:
     ## plot_sdd by default takes as input the result produced from the calc_sdd, read from the current workspace. 

Rd file 'calc_sde.Rd':
  \examples lines wider than 100 characters:
     ## plot_sde by default takes as input the result produced from the calc_sde, read from the current workspace. 

Rd file 'centre.Rd':
  \examples lines wider than 100 characters:
     ## plot_centres by default takes as input the result produced from mean_centre, median centre, CF, CF2PTS, and CMD, read from the curre ... [TRUNCATED]

Rd file 'plot_box.Rd':
  \examples lines wider than 100 characters:
     ## plot_box by default takes as input the result produced from the calc_box, read from the current workspace. 

Rd file 'plot_centres.Rd':
  \examples lines wider than 100 characters:
     ## plot_centres by default takes as input the result produced from CF, CF2PTS, and CMD, read from the current workspace. 

Rd file 'plot_sdd.Rd':
  \examples lines wider than 100 characters:
     ## plot_sdd by default takes as input the result produced from the calc_sdd, read from the current workspace. 

Rd file 'plot_sde.Rd':
  \examples lines wider than 100 characters:
     ## plot_sde by default takes as input the result produced from the calc_sde, read from the current workspace. 

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘BOX_Output.txt’ ‘CF2PTS_Output.txt’ ‘CF_Output.txt’ ‘CMD_Output.txt’
  ‘SDD_Output.txt’ ‘SDE_Output.txt’ ‘mean_centre_Output.txt’
  ‘median_centre_Output.txt’
ASP.Score: no visible global function definition for ‘pnorm’
Graphs.Bayesian: no visible global function definition for ‘dev.new’
colorhex: no visible global function definition for ‘gray’
colorhex: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  dev.new gray pnorm rgb
Consider adding
  importFrom("grDevices", "dev.new", "gray", "rgb")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘asreml’
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arulesViz', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CALPHA: no visible global function definition for ‘dbinom’
CALPHA: no visible global function definition for ‘pchisq’
CAST: no visible global function definition for ‘fisher.test’
CAST: no visible global function definition for ‘chisq.test’
CMC: no visible global function definition for ‘pf’
MULTI: no visible global function definition for ‘complete.cases’
RVT1: no visible global function definition for ‘pchisq’
RVT2: no visible global function definition for ‘pchisq’
RWAS: no visible global function definition for ‘pnorm’
SKAT: no visible global function definition for ‘dbeta’
SKAT: no visible global function definition for ‘pchisq’
TTEST: no visible global function definition for ‘complete.cases’
TTEST: no visible global function definition for ‘pf’
WST: no visible global function definition for ‘mvfft’
WST: no visible global function definition for ‘pnorm’
my_cmc_method: no visible global function definition for
  ‘complete.cases’
my_getUV: no visible global function definition for ‘complete.cases’
my_orwss_method: no visible global function definition for ‘sd’
my_rarecov_method: no visible global function definition for
  ‘chisq.test’
my_rbt_method: no visible global function definition for ‘ppois’
my_score_method: no visible global function definition for ‘pchisq’
my_ssu_method: no visible global function definition for ‘pchisq’
my_ssuw_method: no visible global function definition for ‘pchisq’
my_sum_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pmvnorm’
Undefined global functions or variables:
  chisq.test complete.cases dbeta dbinom fisher.test mvfft pchisq pf
  pmvnorm pnorm ppois sd
Consider adding
  importFrom("stats", "chisq.test", "complete.cases", "dbeta", "dbinom",
             "fisher.test", "mvfft", "pchisq", "pf", "pnorm", "ppois",
             "sd")
to your NAMESPACE file.
beamDiskOverlap: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for ‘spline’
galage: no visible global function definition for ‘integrate’
lumdist: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
VPC.graph : findQuantile: no visible global function definition for
  ‘quantile’
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for ‘quantile’
asVPC.binW: no visible global function definition for ‘median’
asVPC.binW : <anonymous>: no visible global function definition for
  ‘quantile’
asVPC.binW: no visible global function definition for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘median’
asVPC.distanceW : <anonymous>: no visible global function definition
  for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘median’
read_Simdata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package required but not available: ‘smacof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doBy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
get.est.ATT: no visible global function definition for ‘tail’
get.est.MT: no visible global function definition for ‘tail’
get.est.simple: no visible global function definition for ‘tail’
newton.r: no visible global function definition for ‘tail’
plot.ATE: no visible global function definition for ‘par’
plot.ATE: no visible global function definition for ‘axis’
plot.ATE: no visible global function definition for ‘abline’
plot.ATE: no visible global function definition for ‘lines’
plot.ATE: no visible global function definition for ‘legend’
plot.ATE: no visible global function definition for ‘points’
print.summary.ATE: no visible global function definition for
  ‘printCoefmat’
summary.ATE: no visible global function definition for ‘qnorm’
summary.ATE: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis legend lines par pnorm points printCoefmat qnorm tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
atmcmc : rmvtnorm: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘runif’
atmcmc: no visible global function definition for ‘par’
atmcmc: no visible global function definition for ‘lm’
atmcmc: no visible global function definition for ‘lines’
atmcmc: no visible global function definition for ‘var’
atmcmc: no visible global function definition for ‘cov’
atmcmc: no visible global function definition for ‘quantile’
atmcmc: no visible global function definition for ‘sd’
plotmcmc: no visible global function definition for ‘pdf’
plotmcmc: no visible global function definition for ‘par’
plotmcmc: no visible global function definition for ‘dev.new’
plotmcmc: no visible global function definition for ‘png’
plotmcmc: no visible global function definition for ‘hist’
plotmcmc: no visible global function definition for ‘dev.off’
plotmcmc: no visible global function definition for ‘lines’
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf png quantile rnorm runif sd
  var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
PlotAtm.lin : scale_image: no visible global function definition for
  ‘heat.colors’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘par’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘sd’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘approx’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘image’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘axis’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘mtext’
PlotAtm.lin: no visible global function definition for ‘arrows’
PlotAtm.lin: no visible global function definition for ‘text’
PlotAtm.lin: no visible global function definition for ‘polygon’
sky.colors: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx arrows axis heat.colors image mtext par polygon rgb sd text
Consider adding
  importFrom("grDevices", "heat.colors", "rgb")
  importFrom("graphics", "arrows", "axis", "image", "mtext", "par",
             "polygon", "text")
  importFrom("stats", "approx", "sd")
to your NAMESPACE file.
Rd file 'MakeArrivals.lin.Rd':
  \examples lines wider than 100 characters:
     MakeArrivals.lin(xs = c(100, 150), ys = c(100, 150), zs = c(100, 150), xr = 0, yr = 0, zr = 0, dt = 0.01, nt = 100, timing = c(0, 0), A ... [TRUNCATED]

Rd file 'MakeAtmList.lin.Rd':
  \usage lines wider than 90 characters:
     MakeAtmList.lin(z0 = 0, c0 = 343, gc = 0, wx0 = 0, gwx = 0, wy0 = 0, gwy = 0, rho0 = 1.2929 * exp(-z0/6800), grho = -0.0001901323 * exp ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
plot.AUC: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines
Consider adding
  importFrom("graphics", "lines")
to your NAMESPACE file.
AUCRFcv: no visible global function definition for ‘predict’
plot.AUCRF: no visible global function definition for ‘par’
plot.AUCRF: no visible global function definition for ‘dotchart’
plot.AUCRF: no visible global function definition for ‘title’
plot.AUCRF: no visible global function definition for ‘text’
Undefined global functions or variables:
  dotchart par predict text title
Consider adding
  importFrom("graphics", "dotchart", "par", "text", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘RJSONIO’ ‘hexbin’ ‘plotrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
audioHist: no visible global function definition for ‘hist’
audioHist: no visible global function definition for ‘rescale’
audioHist: no visible global function definition for ‘toJSON’
audioScatter: no visible binding for global variable ‘formula’
audioScatter: no visible global function definition for ‘hexbinplot’
audioScatter: no visible global function definition for ‘cor’
audioScatter: no visible global function definition for ‘toJSON’
audioSplom: no visible global function definition for ‘hexplom’
audioSplom: no visible binding for global variable ‘BTY’
audioSplom: no visible binding for global variable ‘panel.hexboxplot’
audioSplom: no visible global function definition for ‘combn’
audioSplom : <anonymous>: no visible global function definition for
  ‘cor’
audioSplom : <anonymous>: no visible global function definition for
  ‘toJSON’
audiolyzRcheck: no visible global function definition for
  ‘download.file’
audiolyzRcheck: no visible global function definition for ‘unzip’
matricize: no visible global function definition for ‘hexbin’
panel.audiolyzR: no visible global function definition for
  ‘panel.hexbinplot’
Undefined global functions or variables:
  BTY combn cor download.file formula hexbin hexbinplot hexplom hist
  panel.hexbinplot panel.hexboxplot rescale toJSON unzip
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "formula")
  importFrom("utils", "combn", "download.file", "unzip")
to your NAMESPACE file.
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  MIT
simulateD: no visible global function definition for ‘rgamma’
simulateT: no visible global function definition for ‘runif’
simulateT: no visible global function definition for ‘rbeta’
simulateT: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbeta rbinom rgamma runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rgamma", "runif")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’

Package which this enhances but not available for checking: ‘rPython’
Running examples in ‘aurelius-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extract_params.knn3
> ### Title: extract_params.knn3
> ### Aliases: extract_params.knn3
> 
> ### ** Examples
> 
> iris2 <- iris
> colnames(iris2) <- gsub('\\.', '_', colnames(iris2))
> model <- caret::knn3(Species ~ ., iris2)
Error in loadNamespace(name) : there is no package called ‘caret’
Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘logistf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘broom’
Error(s) in re-building vignettes:
  ...
--- re-building ‘autoimage.Rmd’ using rmarkdown
--- finished re-building ‘autoimage.Rmd’

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

--- re-building ‘ggplot2-comparison.Rmd’ using rmarkdown
Quitting from lines 185-188 (ggplot2-comparison.Rmd) 
Error: processing vignette 'ggplot2-comparison.Rmd' failed with diagnostics:
there is no package called 'broom'
--- failed re-building ‘ggplot2-comparison.Rmd’

SUMMARY: processing the following file failed:
  ‘ggplot2-comparison.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘gpclib’ ‘maptools’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'ggfortify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gLog.ep: no visible global function definition for ‘quantile’
gedestp: no visible global function definition for ‘na.omit’
gedestp: no visible global function definition for ‘optim’
gets.mean: no visible global function definition for ‘start’
gets.mean: no visible global function definition for ‘end’
gets.mean: no visible global function definition for ‘window’
gets.mean: no visible global function definition for ‘pt’
gets.mean: no visible global function definition for ‘Box.test’
gets.mean: no visible global function definition for ‘pchisq’
gets.vol: no visible global function definition for ‘start’
gets.vol: no visible global function definition for ‘end’
gets.vol: no visible global function definition for ‘window’
gets.vol: no visible global function definition for ‘pt’
gets.vol: no visible global function definition for ‘Box.test’
gets.vol: no visible global function definition for ‘pchisq’
jb.test: no visible global function definition for ‘pchisq’
skewness.test: no visible global function definition for ‘pchisq’
sm: no visible global function definition for ‘start’
sm: no visible global function definition for ‘end’
sm: no visible global function definition for ‘window’
sm: no visible global function definition for ‘pt’
sm: no visible global function definition for ‘pchisq’
sm: no visible global function definition for ‘Box.test’
Undefined global functions or variables:
  Box.test end na.omit optim pchisq pt quantile start window
Consider adding
  importFrom("stats", "Box.test", "end", "na.omit", "optim", "pchisq",
             "pt", "quantile", "start", "window")
to your NAMESPACE file.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'prophet', 'tidyr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘BiocInstaller’
Package required but not available: ‘simts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Error(s) in re-building vignettes:
  ...
--- re-building ‘full-example.Rmd’ using rmarkdown
Quitting from lines 222-243 (full-example.Rmd) 
Error: processing vignette 'full-example.Rmd' failed with diagnostics:
there is no package called 'caret'
--- failed re-building ‘full-example.Rmd’

SUMMARY: processing the following file failed:
  ‘full-example.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘tidyr’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(AzureKusto)
  
  Attaching package: 'AzureKusto'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check('AzureKusto')
  ── 1. Error: (unknown) (@test_translate.r#7)  ──────────────────────────────────
  there is no package called 'tidyr'
  Backtrace:
   1. utils::packageVersion("tidyr")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 42 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test_translate.r#7) 
  
  Error: testthat unit tests failed
  Execution halted
CRexp_set: no visible global function definition for ‘runif’
b6e6rl: no visible global function definition for ‘runif’
derand_RL: no visible global function definition for ‘runif’
derandexp_RL: no visible global function definition for ‘runif’
nahvyb_expt: no visible global function definition for ‘runif’
roulete: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.generateTransform: no visible global function definition for ‘sd’
.generateUnitHyperCube: no visible global function definition for
  ‘runif’
.makeBoundedSingleStep: no visible global function definition for
  ‘runif’
.makeBoundedStep: no visible global function definition for ‘runif’
.makeStep: no visible global function definition for ‘runif’
.staircaseSampling: no visible global function definition for ‘runif’
GaussianPrior: no visible global function definition for ‘qnorm’
LogNormalPrior: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mice’
BACprior.CV: no visible global function definition for ‘na.fail’
BACprior.CV: no visible global function definition for ‘abline’
BACprior.boot: no visible global function definition for ‘na.fail’
BACprior.boot: no visible global function definition for ‘abline’
BACprior.lm: no visible global function definition for ‘na.fail’
BACprior.lm: no visible global function definition for ‘coef’
BACprior.lm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  abline coef na.fail vcov
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
GNU make is a SystemRequirements.
Packages required but not available: 'parsnip', 'rsample', 'tidyr'

Package suggested but not available for checking: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Unexported objects imported by ':::' calls:
  ‘erah:::avoid.processing’ ‘erah:::convertMSPspectra’
  ‘erah:::convertMSPspectra.dot’ ‘erah:::getC.rq’ ‘erah:::getS.OSD’
  ‘erah:::load.file’ ‘erah:::pre.process’ ‘erah:::sparse.to.vector’
  See the note in ?`:::` about the use of this operator.
Packages suggested but not available for checking:
  'philr', 'robCompositions'
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(balance)
  > 
  > test_check("balance")
  ── 1. Error: (unknown) (@test-compute.R#3)  ────────────────────────────────────
  there is no package called 'robCompositions'
  Backtrace:
   1. utils::data(expenditures, package = "robCompositions")
   2. base::find.package(package, lib.loc, verbose = verbose)
  
  ── 2. Error: (unknown) (@test-output.R#3)  ─────────────────────────────────────
  there is no package called 'robCompositions'
  Backtrace:
   1. utils::data(expenditures, package = "robCompositions")
   2. base::find.package(package, lib.loc, verbose = verbose)
  
  ── 3. Error: (unknown) (@test-sort.R#3)  ───────────────────────────────────────
  there is no package called 'robCompositions'
  Backtrace:
   1. utils::data(expenditures, package = "robCompositions")
   2. base::find.package(package, lib.loc, verbose = verbose)
  
  ── 4. Error: (unknown) (@test-wide2long.R#3)  ──────────────────────────────────
  there is no package called 'robCompositions'
  Backtrace:
   1. utils::data(expenditures, package = "robCompositions")
   2. base::find.package(package, lib.loc, verbose = verbose)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
  1. Error: (unknown) (@test-compute.R#3) 
  2. Error: (unknown) (@test-output.R#3) 
  3. Error: (unknown) (@test-sort.R#3) 
  4. Error: (unknown) (@test-wide2long.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘balance.Rmd’ using rmarkdown
Quitting from lines 41-45 (balance.Rmd) 
Error: processing vignette 'balance.Rmd' failed with diagnostics:
there is no package called 'robCompositions'
--- failed re-building ‘balance.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘exemplary_input1.txt’ ‘exemplary_input2.txt’
Package suggested but not available for checking: ‘ffbase’
Packages required but not available: 'tidyr', 'RBMRB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
best_binomial_bandit : f: no visible global function definition for
  ‘dbeta’
best_binomial_bandit : f: no visible global function definition for
  ‘pbeta’
best_binomial_bandit: no visible global function definition for
  ‘integrate’
best_poisson_bandit : f: no visible global function definition for
  ‘dgamma’
best_poisson_bandit : f: no visible global function definition for
  ‘pgamma’
best_poisson_bandit: no visible global function definition for
  ‘integrate’
deseasonalized_trend: no visible global function definition for
  ‘predict’
distribution_estimate: no visible global function definition for
  ‘quantile’
distribution_estimate: no visible global function definition for
  ‘qbeta’
significance_analysis: no visible global function definition for
  ‘prop.test’
sim_post: no visible global function definition for ‘rbeta’
summarize_metrics: no visible global function definition for ‘median’
summarize_metrics: no visible global function definition for
  ‘prop.test’
Undefined global functions or variables:
  dbeta dgamma integrate median pbeta pgamma predict prop.test qbeta
  quantile rbeta
Consider adding
  importFrom("stats", "dbeta", "dgamma", "integrate", "median", "pbeta",
             "pgamma", "predict", "prop.test", "qbeta", "quantile",
             "rbeta")
to your NAMESPACE file.
Packages required but not available: 'rfPermute', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ArrayExpress’
extractAffybatch: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls to packages already attached by Depends:
  ‘grid’ ‘lattice’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for ‘unit’
barcode: no visible global function definition for ‘grid.newpage’
barcode: no visible global function definition for ‘grid.text’
barcode: no visible global function definition for ‘gpar’
barcode: no visible global function definition for ‘pushViewport’
barcode: no visible global function definition for ‘viewport’
barcode: no visible global function definition for ‘convertHeight’
barcode: no visible global function definition for ‘convertWidth’
barcode: no visible global function definition for ‘grid.rect’
barcode: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for ‘unit’
barcode.panel: no visible global function definition for ‘hist’
barcode.panel: no visible global function definition for ‘pushViewport’
barcode.panel: no visible global function definition for ‘viewport’
barcode.panel: no visible global function definition for ‘grid.xaxis’
barcode.panel: no visible global function definition for ‘gpar’
barcode.panel: no visible global function definition for ‘grid.text’
barcode.panel: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for
  ‘grid.segments’
barcode.panel: no visible global function definition for ‘grid.points’
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
Package required but not available: ‘janitor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Unexported objects imported by ':::' calls:
  ‘warbleR:::img_wrlbr_int’ ‘warbleR:::spectro_wrblr_int2’
  See the note in ?`:::` about the use of this operator.
Package suggested but not available for checking: ‘tidyr’
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'tidygraph', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmbb’
Running ‘testthat.R’ [10s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BAS)
  > 
  > test_check("BAS")
  ── 1. Error: poisson regression (@test-bas-glm.R#118)  ─────────────────────────
  there is no package called 'glmbb'
  Backtrace:
   1. utils::data(crabs, package = "glmbb")
   2. base::find.package(package, lib.loc, verbose = verbose)
  
  
   Marginal Posterior Summaries of Coefficients: 
  
   Using  BMA 
  
   Based on the top  16 models 
             post mean  post SD   post p(B != 0)
  Intercept  95.42308    0.67885   1.00000      
  X1          1.40116    0.35351   0.97454      
  X2          0.42326    0.38407   0.76017      
  X3         -0.03997    0.33398   0.30660      
  X4         -0.22077    0.36931   0.44354      
  
  Call:
  bas.lm(formula = Y ~ ., data = Hald, prior = "BIC", modelprior = uniform())
  
  
   Marginal Posterior Inclusion Probabilities: 
  Intercept         X1         X2         X3         X4  
     1.0000     0.9856     0.7921     0.4705     0.5220  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 160 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: poisson regression (@test-bas-glm.R#118) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘wmtsa’
Package which this enhances but not available for checking: ‘rPython’
'library' or 'require' call to ‘hwriter’ which was already attached by Depends.
  Please remove these calls from your code.
prepare_Rd: mkhtml.Rd:31-33: Dropping empty section \details
prepare_Rd: mkhtml.Rd:43-45: Dropping empty section \note
prepare_Rd: mkhtml.Rd:40-42: Dropping empty section \author
prepare_Rd: mkhtml.Rd:37-39: Dropping empty section \references
prepare_Rd: mkhtml.Rd:49-51: Dropping empty section \seealso
Found the following files/directories:
  ‘sample.html’ ‘sample.png’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Anthropometry', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
FECRT: no visible global function definition for ‘pdf’
FECRT: no visible global function definition for ‘hist’
FECRT: no visible global function definition for ‘abline’
FECRT: no visible global function definition for ‘dev.off’
FECRT.analysis: no visible global function definition for ‘pdf’
FECRT.analysis: no visible global function definition for ‘hist’
FECRT.analysis: no visible global function definition for ‘abline’
FECRT.analysis: no visible global function definition for ‘dev.off’
fecrt: no visible global function definition for ‘pdf’
fecrt: no visible global function definition for ‘hist’
fecrt: no visible global function definition for ‘abline’
fecrt: no visible global function definition for ‘dev.off’
fecrt.analysis: no visible global function definition for ‘pdf’
fecrt.analysis: no visible global function definition for ‘hist’
fecrt.analysis: no visible global function definition for ‘abline’
fecrt.analysis: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline dev.off hist pdf
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "hist")
to your NAMESPACE file.
GNU make is a SystemRequirements.
BMAnimalTrack: no visible global function definition for ‘nlm’
BMAnimalTrack: no visible global function definition for ‘qnorm’
dataSim: no visible global function definition for ‘rnorm’
rBBridge: no visible global function definition for ‘rnorm’
rBMotion: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  nlm qnorm rnorm
Consider adding
  importFrom("stats", "nlm", "qnorm", "rnorm")
to your NAMESPACE file.
Package required but not available: ‘DiagrammeR’

Package suggested but not available for checking: ‘ggmcmc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'heatmaply', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following sources/headers not terminated with a newline:
  inst/include/bayeslm.h
Some compilers warn on such files.
GNU make is a SystemRequirements.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doBy’

Package suggested but not available for checking: ‘cyjShiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
noninform_prior : a : f1: no visible global function definition for
  ‘pbeta’
noninform_prior : a : f1: no visible global function definition for
  ‘dbeta’
noninform_prior : a: no visible global function definition for
  ‘integrate’
noninform_prior: no visible global function definition for ‘rbeta’
noninform_prior: no visible global function definition for ‘optim’
postNullFun : b : f1: no visible global function definition for ‘pbeta’
postNullFun : b : f1: no visible global function definition for ‘dbeta’
postNullFun : b: no visible global function definition for ‘integrate’
prior_prob : a : f1: no visible global function definition for ‘pbeta’
prior_prob : a : f1: no visible global function definition for ‘dbeta’
prior_prob : a: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  dbeta integrate optim pbeta rbeta
Consider adding
  importFrom("stats", "dbeta", "integrate", "optim", "pbeta", "rbeta")
to your NAMESPACE file.
Packages required but not available: 'ggmcmc', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
MHratioPopPref: no visible global function definition for ‘runif’
MratioPopMult: no visible global function definition for ‘dunif’
MratioPopMult: no visible global function definition for ‘runif’
bayesPref: no visible global function definition for ‘runif’
calcP: no visible global function definition for ‘dunif’
calcP: no visible global function definition for ‘dmultinom’
calcdic: no visible global function definition for ‘median’
calcdic: no visible binding for global variable ‘median’
calcdic: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible global function definition for ‘median’
calcdicExtern: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible binding for global variable ‘median’
credibleIntervals: no visible global function definition for ‘quantile’
prefPlot: no visible global function definition for ‘postscript’
prefPlot: no visible global function definition for ‘lines’
prefPlot: no visible global function definition for ‘density’
prefPlot: no visible global function definition for ‘median’
prefPlot: no visible global function definition for ‘legend’
prefPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘gplots’ ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bayes.regress: no visible binding for global variable ‘var’
bayesregressB1S1: no visible global function definition for ‘rgamma’
bayesregressB1S2: no visible global function definition for ‘rgamma’
bayesregressB2S1: no visible global function definition for ‘rgamma’
bayesregressB2S2: no visible global function definition for ‘rgamma’
bayesregressB3S1: no visible global function definition for ‘rWishart’
bayesregressB3S1: no visible global function definition for ‘rgamma’
bayesregressB3S2: no visible global function definition for ‘rWishart’
bayesregressB3S2: no visible global function definition for ‘rgamma’
read.regress.data.ff: no visible global function definition for
  ‘chunk.ffdf’
Undefined global functions or variables:
  chunk.ffdf rWishart rgamma var
Consider adding
  importFrom("stats", "rWishart", "rgamma", "var")
to your NAMESPACE file.
Packages suggested but not available for checking: 'broom', 'tidyr'
validate: no visible binding for global variable ‘qnorm’
validate: no visible global function definition for ‘pchisq’
validate: no visible global function definition for ‘qnorm’
validate: no visible global function definition for ‘axis’
validate: no visible global function definition for ‘points’
validate: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis pchisq points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
GNU make is a SystemRequirements.
'library' or 'require' call to ‘coda’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'BPSpostSample.Rd':
  \usage lines wider than 90 characters:
     BPSpostSample(hyp, times, obs = NULL, mclen = 10, burnin = 0, thin = 1, df = 10, etastar = NULL)
  \examples lines wider than 100 characters:
     post<-BPSpostSample(hypars, times = earthquakes$ti, obs = earthquakes$ob, etastar = postmode$etastar)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘diagnostics.pdf’ ‘post.rda’
Package required but not available: ‘ArchaeoPhases’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages in Depends field not imported from:
  ‘fields’ ‘poibin’ ‘rjags’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMR.plot: no visible global function definition for ‘heat.colors’
BMR.plot: no visible global function definition for ‘image.plot’
BMR.plot: no visible global function definition for ‘title’
BMR.plot: no visible global function definition for ‘mtext’
BMR.plot: no visible global function definition for ‘par’
baysic.data: no visible global function definition for ‘layout’
baysic.data: no visible global function definition for ‘barplot’
baysic.data: no visible global function definition for ‘rainbow’
baysic.fit: no visible global function definition for ‘jags.model’
baysic.fit: no visible global function definition for ‘update’
baysic.fit: no visible global function definition for ‘coda.samples’
baysic.test: no visible global function definition for ‘ppois’
baysic.test : <anonymous>: no visible global function definition for
  ‘ppoibin’
baysic.test: no visible global function definition for ‘pbinom’
fuzzy.FDR.approx: no visible global function definition for ‘p.adjust’
fuzzy.FDR.approx: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot coda.samples heat.colors image.plot jags.model layout mtext
  p.adjust par pbinom ppoibin ppois rainbow runif title update
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "layout", "mtext", "par", "title")
  importFrom("stats", "p.adjust", "pbinom", "ppois", "runif", "update")
to your NAMESPACE file.
Rd file 'baysic.fit.Rd':
  \usage lines wider than 90 characters:
     baysic.fit(dat.out, snv.cat, covar = NULL, excl.list = NULL, burn.in = 10000,n.samp = 25000, fn.jags = "baysic.jags", prior = NULL)
  \examples lines wider than 100 characters:
     snv.cat.ex[[2]]<-unique(c(grep("TC.",colnames(ccds.19)[-c(1:2)]),grep(".CG",colnames(ccds.19)[-c(1:2)])))

Rd file 'baysic.test.Rd':
  \usage lines wider than 90 characters:
     baysic.test(dat.out, fit.out, fdr.level = 0.15, fuzzy.cnt = 10000, r = NULL,subtype = NULL, PB.approx = FALSE)
  \examples lines wider than 100 characters:
     snv.cat.ex[[2]]<-unique(c(grep("TC.",colnames(ccds.19)[-c(1:2)]),grep(".CG",colnames(ccds.19)[-c(1:2)])))

These lines will be truncated in the PDF manual.
Packages required but not available: 'ggfortify', 'tidyr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
BAYSTAR: no visible global function definition for ‘median’
BAYSTAR: no visible global function definition for ‘ar’
BAYSTAR: no visible global function definition for ‘quantile’
BAYSTAR: no visible global function definition for ‘dev.new’
BAYSTAR: no visible global function definition for ‘ts.plot’
BAYSTAR: no visible global function definition for ‘title’
BAYSTAR: no visible global function definition for ‘par’
BAYSTAR: no visible global function definition for ‘plot.ts’
BAYSTAR: no visible global function definition for ‘lines’
BAYSTAR: no visible global function definition for ‘acf’
TAR.lagd: no visible global function definition for ‘runif’
TAR.sigma: no visible global function definition for ‘rgamma’
TAR.simu: no visible global function definition for ‘rnorm’
TAR.summary: no visible global function definition for ‘quantile’
TAR.summary: no visible global function definition for ‘sd’
TAR.thres: no visible global function definition for ‘rnorm’
TAR.thres: no visible global function definition for ‘runif’
Undefined global functions or variables:
  acf ar dev.new lines median par plot.ts quantile rgamma rnorm runif
  sd title ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par", "title")
  importFrom("stats", "acf", "ar", "median", "plot.ts", "quantile",
             "rgamma", "rnorm", "runif", "sd", "ts.plot")
to your NAMESPACE file.
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.
Malformed Description field: should contain one or more complete sentences.
LaplaceMetropolis_admkr: no visible binding for global variable
  ‘median’
LaplaceMetropolis_admkr: no visible global function definition for
  ‘mad’
LaplaceMetropolis_gaussian: no visible binding for global variable
  ‘median’
LaplaceMetropolis_gaussian: no visible global function definition for
  ‘mad’
cost_admkr: no visible global function definition for ‘sd’
cov_chol: no visible global function definition for ‘qchisq’
cov_chol_admkr: no visible global function definition for ‘qchisq’
gibbs_admkr_erro: no visible global function definition for ‘rnorm’
gibbs_admkr_erro: no visible global function definition for ‘runif’
gibbs_admkr_nw: no visible global function definition for ‘qnorm’
gibbs_admkr_nw: no visible global function definition for ‘rnorm’
gibbs_admkr_nw: no visible global function definition for ‘runif’
loglikelihood_admkr: no visible global function definition for ‘sd’
margin_like_admkr: no visible global function definition for ‘sd’
np_gibbs: no visible global function definition for ‘qnorm’
np_gibbs: no visible global function definition for ‘rnorm’
np_gibbs: no visible global function definition for ‘runif’
np_gibbs: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
bbmm.contour: no visible global function definition for ‘na.omit’
bbmm.contour: no visible global function definition for ‘optimize’
bbmm.contour: no visible global function definition for ‘contour’
bbmm.contour: no visible global function definition for ‘points’
bbmm.contour: no visible global function definition for ‘lines’
brownian.bridge: no visible global function definition for ‘sd’
brownian.motion.variance: no visible global function definition for
  ‘optimize’
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
bbo: no visible global function definition for ‘runif’
bbo: no visible global function definition for ‘tail’
Undefined global functions or variables:
  runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
Package suggested but not available for checking: ‘biclust’
Running examples in ‘BcDiag-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anomedOnlybic
> ### Title: The anomedOnlybic function
> ### Aliases: anomedOnlybic
> ### Keywords: anomedOnlybic
> 
> ### ** Examples
> 
> data(breastc)
> library(biclust)
Error in library(biclust) : there is no package called ‘biclust’
Execution halted
Packages suggested but not available for checking: 'INLA', 'plotly'
Package vignette with placeholder title ‘Vignette Title’:
  ‘vignette.Rmd’
pairs.bce : panel.cor: no visible global function definition for ‘text’
pairs.bce : panel.cor: no visible global function definition for ‘cor’
pairs.bce : panel.hist: no visible global function definition for ‘par’
pairs.bce : panel.hist: no visible global function definition for
  ‘hist’
pairs.bce : panel.hist: no visible global function definition for
  ‘rect’
pairs.bce: no visible global function definition for ‘pairs’
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’
rdirichlet2: no visible global function definition for ‘rgamma’
summary.bce: no visible global function definition for ‘cov’
summary.bce: no visible binding for global variable ‘sd’
summary.bce: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  cor cov hist pairs par quantile rect rgamma sd strwidth text
Consider adding
  importFrom("graphics", "hist", "pairs", "par", "rect", "strwidth",
             "text")
  importFrom("stats", "cor", "cov", "quantile", "rgamma", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘bcmapsdata’
bcpmeta.model: no visible global function definition for ‘rbinom’
bcpmeta.model: no visible global function definition for ‘runif’
bcpmeta.parameters: no visible global function definition for ‘runif’
cp.plot: no visible global function definition for ‘postscript’
cp.plot: no visible global function definition for ‘lines’
cp.plot: no visible global function definition for ‘axis’
cp.plot: no visible global function definition for ‘box’
cp.plot: no visible global function definition for ‘points’
cp.plot: no visible global function definition for ‘dev.off’
lMarLik.EB.normAR: no visible global function definition for ‘optimize’
lMarLik.normAR: no visible global function definition for ‘integrate’
marginal.plot: no visible global function definition for ‘postscript’
marginal.plot: no visible global function definition for ‘axis’
marginal.plot: no visible global function definition for ‘box’
marginal.plot: no visible global function definition for ‘points’
marginal.plot: no visible global function definition for ‘dev.off’
simgen: no visible global function definition for ‘rnorm’
up.eta.MH.normAR: no visible global function definition for ‘runif’
up.eta.RS.normAR: no visible global function definition for ‘runif’
up.parameters.EB.normAR: no visible global function definition for
  ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘runif’
up.parameters.normAR: no visible global function definition for
  ‘rgamma’
Undefined global functions or variables:
  axis box dev.off integrate lines optimize points postscript rbinom
  rgamma rnorm runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "box", "lines", "points")
  importFrom("stats", "integrate", "optimize", "rbinom", "rgamma",
             "rnorm", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'kBET', 'lisi', 'harmony', 'dlfUtils'
plot.cvsvd: no visible binding for global variable ‘sd’
plot.cvsvd: no visible global function definition for ‘lines’
plot.cvsvd: no visible global function definition for ‘segments’
plot.cvsvd: no visible global function definition for ‘points’
print.cvsvd: no visible binding for global variable ‘sd’
summary.cvsvd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  lines points sd segments
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
mise: no visible global function definition for ‘integrate’
density,BrVitale : density.vitale : <anonymous>: no visible global
  function definition for ‘dbeta’
density,Chen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,HirukawaJLNKernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,MicroBetaChen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,Vitale : <anonymous>: no visible global function definition for
  ‘dbeta’
distribution,BernsteinPolynomials : <anonymous>: no visible global
  function definition for ‘integrate’
distribution,KernelDensity : <anonymous>: no visible global function
  definition for ‘integrate’
print,BoundedDensity: no visible global function definition for ‘str’
print,KernelDensity: no visible global function definition for ‘str’
rsample,BoundedDensity: no visible global function definition for
  ‘runif’
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for ‘integrate’
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  ‘dbeta’
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for ‘integrate’
show,BoundedDensity: no visible global function definition for ‘str’
show,KernelDensity: no visible global function definition for ‘str’
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
Found the following files/directories:
  ‘dump.txt’
Package suggested but not available for checking: ‘rinat’
Found the following files/directories:
  ‘bferrbars.eps’ ‘dataplot.eps’ ‘ppdat.eps’ ‘ppmod.eps’
Package suggested but not available for checking: ‘lumi’
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘beadarray’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
beadtypeFilter: no visible global function definition for ‘na.omit’
beadtypeFilter: no visible global function definition for ‘exprs’
beadtypeFilter: no visible global function definition for ‘se.exprs’
beadtypeFilter: no visible global function definition for ‘beadNum’
beadtypeFilter: no visible global function definition for ‘fData’
emCDF: no visible global function definition for ‘brewer.pal’
emCDF: no visible global function definition for ‘ecdf’
emCDF: no visible global function definition for ‘legend’
emCDF: no visible global function definition for ‘lines’
emCDF: no visible global function definition for ‘text’
emCDF: no visible global function definition for ‘reshape’
iccFun : <anonymous>: no visible global function definition for
  ‘quantile’
varianceplot: no visible global function definition for ‘reshape’
varianceplot: no visible global function definition for ‘points’
varianceplot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
Rd file 'iccFun.Rd':
  \examples lines wider than 100 characters:
     aaa<-na.omit(data.frame(I(rownames(exprs(exampleSummaryDataNorm))),exprs(exampleSummaryDataNorm)))[1:40,]

These lines will be truncated in the PDF manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Package suggested but not available for checking: ‘plotly’
Found the following files/directories:
  ‘example_Initial.parameters.Robj’ ‘example_MCMC_output1.Robj’
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘beezdemand.Rmd’ using rmarkdown
Quitting from lines 76-78 (beezdemand.Rmd) 
Error: processing vignette 'beezdemand.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘beezdemand.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
Packages required but not available: 'DiagrammeR', 'googlesheets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘tidyr’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘benthos.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 53-57 (benthos.Rmd) 
Error: processing vignette 'benthos.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘benthos.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘temp.csv’
Package which this enhances but not available for checking: ‘caret’
Package required but not available: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Non-standard file/directory found at top level:
  ‘extdata’
betafam: no visible global function definition for ‘pnorm’
betafam: no visible global function definition for ‘pchisq’
betafam: no visible global function definition for ‘lm’
betafam: no visible global function definition for ‘coefficients’
betafam: no visible global function definition for ‘glm.fit’
betafam: no visible global function definition for ‘gaussian’
betafam: no visible global function definition for ‘glmnet’
Undefined global functions or variables:
  coefficients gaussian glm.fit glmnet lm pchisq pnorm
Consider adding
  importFrom("stats", "coefficients", "gaussian", "glm.fit", "lm",
             "pchisq", "pnorm")
to your NAMESPACE file.
Rd file 'betafam.Rd':
  \usage lines wider than 90 characters:
     betafam(ped,group.threshold=-1,fix.group.index=NULL, fix.weight=NULL,mute.SMM=TRUE,trait=c("binary","qtl"),LC.test=c("LC.true","LC","si ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Checking should be performed on sources prepared by ‘R CMD build’.
Found the following files/directories:
  ‘vert.txt’ ‘vert_1.txt’ ‘vert_2.txt’
Malformed Title field: should not end in a period.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doBy’
Package required but not available: ‘janitor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'networktools', 'mice'
Error(s) in re-building vignettes:
  ...
--- re-building ‘control.Rmd’ using rmarkdown
--- finished re-building ‘control.Rmd’

--- re-building ‘hyp_3_ways.Rmd’ using rmarkdown
--- finished re-building ‘hyp_3_ways.Rmd’

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

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

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

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

--- re-building ‘netstat_custom.Rmd’ using rmarkdown
Quitting from lines 46-54 (netstat_custom.Rmd) 
Error: processing vignette 'netstat_custom.Rmd' failed with diagnostics:
there is no package called 'networktools'
--- failed re-building ‘netstat_custom.Rmd’

--- re-building ‘ppc_custom.Rmd’ using rmarkdown
Quitting from lines 72-90 (ppc_custom.Rmd) 
Error: processing vignette 'ppc_custom.Rmd' failed with diagnostics:
there is no package called 'networktools'
--- failed re-building ‘ppc_custom.Rmd’

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

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

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

SUMMARY: processing the following files failed:
  ‘netstat_custom.Rmd’ ‘ppc_custom.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘bggum.Rmd’ using rmarkdown
Quitting from lines 125-142 (bggum.Rmd) 
Error: processing vignette 'bggum.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘bggum.Rmd’

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

Error: Vignette re-building failed.
Execution halted
block.gibbs: no visible global function definition for ‘rmultinom’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
global: no visible global function definition for ‘par’
global: no visible global function definition for ‘runif’
global: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘par’
mymcmc: no visible global function definition for ‘rnorm’
mymcmc: no visible global function definition for ‘runif’
mymcmc: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘lines’
plkhci: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: ‘betareg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bias: no visible global function definition for ‘predict’
bias: no visible global function definition for ‘pnorm’
bias: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  model.matrix pnorm predict
Consider adding
  importFrom("stats", "model.matrix", "pnorm", "predict")
to your NAMESPACE file.
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘bib2df.Rmd’ using rmarkdown
Warning: `as_data_frame()` is deprecated as of tibble 2.0.0.
Please use `as_tibble()` instead.
The signature and semantics have changed, see `?as_tibble`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.

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 89-99 (bib2df.Rmd) 
Error: processing vignette 'bib2df.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘bib2df.Rmd’

SUMMARY: processing the following file failed:
  ‘bib2df.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘biclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'factoextra', 'ggraph', 'rscopus', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'biclust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘BiDimRegrOutput.txt’
Package required but not available: ‘miceadds’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ffbase’
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘test’
Packages in Depends field not imported from:
  ‘DBI’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Call with DUP:
   .Fortran("regcf", as.integer(p), as.integer(p * p/2), bigQR$D, 
       bigQR$rbar, bigQR$thetab, bigQR$tol, beta = numeric(p), nreq = as.integer(nvar), 
       ier = integer(1), DUP = FALSE)
DUP is no longer supported and will be ignored.
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults

Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
GNU make is a SystemRequirements.
Checking should be performed on sources prepared by ‘R CMD build’.
Unknown package ‘QUIC’ in Rd xrefs
Found the following files/directories:
  ‘outputs’
Packages in Depends field not imported from:
  ‘gbm’ ‘glmnet’ ‘randomForest’ ‘tree’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LDCAEst: no visible global function definition for ‘glmnet’
cv.LDCA: no visible global function definition for ‘cv.glmnet’
predict.LDCA: no visible global function definition for ‘predict’
predict.cv.LDCA: no visible global function definition for ‘predict’
predict.tsp.gbm: no visible global function definition for ‘predict’
predict.tsp.randomForest: no visible global function definition for
  ‘predict’
predict.tsp.tree: no visible global function definition for ‘predict’
tsp.gbm: no visible global function definition for ‘gbm.fit’
tsp.randomForest: no visible global function definition for
  ‘randomForest’
tsp.tree: no visible global function definition for ‘tree.control’
tsp.tree: no visible global function definition for ‘tree’
Undefined global functions or variables:
  cv.glmnet gbm.fit glmnet predict randomForest tree tree.control
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Rd file 'predict.LDCA.Rd':
  \usage lines wider than 90 characters:
     predict(object, newx, s = NULL, type = c("link", "response", "coefficients", "nonzero", "class"), exact = FALSE, offset, ...)

Rd file 'predict.tsp.randomForest.Rd':
  \usage lines wider than 90 characters:
     predict(object, newdata, type = "response", norm.votes = TRUE, predict.all = FALSE, proximity = FALSE, nodes = FALSE, cutoff, ...)

Rd file 'predict.tsp.tree.Rd':
  \usage lines wider than 90 characters:
     predict(object, newdata, type = c("vector", "tree", "class", "where"), split = FALSE, nwts, eps = 0.001, ...)

Rd file 'tsp.gbm.Rd':
  \usage lines wider than 90 characters:
     tsp.gbm(x, y, offset = NULL, misc = NULL, distribution = "bernoulli", w = NULL, var.monotone = NULL, n.trees = 100, interaction.depth = ... [TRUNCATED]

Rd file 'tsp.randomForest.Rd':
  \usage lines wider than 90 characters:
     tsp.randomForest(x, y = NULL, xtest = NULL, ytest = NULL, ntree = 500, type = "classification", mtry = if (!is.null(y) && !is.factor(y) ... [TRUNCATED]

Rd file 'tsp.tree.Rd':
  \usage lines wider than 90 characters:
     tsp.tree(X, response, control = tree.control(dim(X)[1], ...), method = "recursive.partition", split = c("deviance", "gini"), x = FALSE, ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
chisq.sim.factory : chisq.sim.func: no visible global function
  definition for ‘chisq.test’
rmultnom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  chisq.test runif
Consider adding
  importFrom("stats", "chisq.test", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
commonprob2sigma: no visible global function definition for ‘approxfun’
rmvbin: no visible global function definition for ‘qnorm’
simul.commonprob: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  approxfun qnorm
Consider adding
  importFrom("stats", "approxfun", "qnorm")
to your NAMESPACE file.
bin_ps: no visible global function definition for ‘runif’
bin_ps: no visible global function definition for ‘dbinom’
draw_i: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
IndivdRUMIndMH: no visible global function definition for
  ‘flush.console’
dRUMAuxMix: no visible global function definition for ‘flush.console’
dRUMHAM: no visible global function definition for ‘flush.console’
dRUMIndMH: no visible global function definition for ‘flush.console’
print.binomlogit: no visible global function definition for ‘is’
summary.binomlogit: no visible global function definition for ‘is’
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘lattice’ ‘polynom’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
bins.quantiles: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following files/directories:
  ‘Plots.pdf’
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
Found the following files/directories:
  ‘sum.otu.txt’
Found the following files/directories:
  ‘GRCh37_MT_ensGene.txt’
Packages required but not available: 'caret', 'tidyr'

Package suggested but not available for checking: ‘ecospat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' call to ‘MGRASTer’ 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’
biom.matrix: no visible global function definition for ‘packageVersion’
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
Packages required but not available: 'tidyr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘factoextra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggmap', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plsRcox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘bisect_vignette.Rmd’ using rmarkdown
Quitting from lines 69-101 (bisect_vignette.Rmd) 
Error: processing vignette 'bisect_vignette.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘bisect_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Seurat’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyquant’
Error(s) in re-building vignettes:
  ...
--- re-building ‘authentication.Rmd’ using rmarkdown
--- finished re-building ‘authentication.Rmd’

--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’

--- re-building ‘placing-orders.Rmd’ using rmarkdown
--- finished re-building ‘placing-orders.Rmd’

--- re-building ‘trade-data.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

Quitting from lines 20-24 (trade-data.Rmd) 
Error: processing vignette 'trade-data.Rmd' failed with diagnostics:
there is no package called 'tidyquant'
--- failed re-building ‘trade-data.Rmd’

SUMMARY: processing the following file failed:
  ‘trade-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
bivarcalcn: no visible global function definition for ‘qnorm’
bivarcalcn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
prepare_Rd: bivarcalcn.Rd:49-50: Dropping empty section \details
prepare_Rd: bivarcalcn.Rd:59-61: Dropping empty section \note
prepare_Rd: bivarcalcn.Rd:65-67: Dropping empty section \seealso
biwt.cor: no visible global function definition for ‘covMcd’
biwt.cor: no visible binding for global variable ‘mad’
biwt.est: no visible global function definition for ‘covMcd’
biwt.est: no visible global function definition for ‘mahalanobis’
chi.int: no visible global function definition for ‘pchisq’
chi.int.p: no visible global function definition for ‘dchisq’
chi.int2: no visible global function definition for ‘pchisq’
chi.int2.p: no visible global function definition for ‘dchisq’
rejpt.bw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  covMcd dchisq mad mahalanobis pchisq
Consider adding
  importFrom("stats", "dchisq", "mad", "mahalanobis", "pchisq")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2'
GNU make is a SystemRequirements.
bglmer: no visible global function definition for ‘packageVersion’
getBglmerDevianceFunctionBody: no visible global function definition
  for ‘packageVersion’
getParInfo : <anonymous>: no visible global function definition for
  ‘sd’
makeRefitDevFun: no visible global function definition for
  ‘packageVersion’
mkBglmerDevfun: no visible global function definition for
  ‘packageVersion’
namedList: no visible global function definition for ‘setNames’
refit.bmerMod: no visible global function definition for
  ‘packageVersion’
refit.bmerMod: no visible global function definition for ‘model.frame’
refit.bmerMod: no visible global function definition for ‘family’
refit.bmerMod: no visible global function definition for ‘getCall’
Undefined global functions or variables:
  family getCall model.frame packageVersion sd setNames
Consider adding
  importFrom("stats", "family", "getCall", "model.frame", "sd",
             "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
blockMessage : <anonymous>: no visible global function definition for
  ‘head’
blockMessage: no visible global function definition for ‘head’
blockMessage: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
blockmodelskmeans: no visible global function definition for ‘dist’
matrixplot: no visible global function definition for ‘image’
matrixplot: no visible global function definition for ‘hsv’
matrixplot: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis dist hsv image
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "axis", "image")
  importFrom("stats", "dist")
to your NAMESPACE file.
Found the following files/directories:
  ‘Groupa.csv’ ‘Groupa.tex’ ‘Groupb.csv’ ‘Groupb.tex’ ‘Groupc.csv’
  ‘Groupc.tex’ ‘file1.csv’ ‘file1.tex’ ‘file2.csv’ ‘file2.tex’
  ‘file3.csv’ ‘file3.tex’
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Package in Depends field not imported from: ‘drc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bmd: no visible global function definition for ‘qnorm’
bmd: no visible global function definition for ‘predict’
bmd: no visible global function definition for ‘LL.2’
bmd: no visible global function definition for ‘LN.2’
bmd: no visible global function definition for ‘W1.2’
bmd: no visible global function definition for ‘W2.2’
bmd: no visible global function definition for ‘LL.5’
bmd: no visible global function definition for ‘LN.4’
bmd: no visible global function definition for ‘W1.4’
bmd: no visible global function definition for ‘W2.4’
bmd: no visible global function definition for ‘FPL.4’
bmd: no visible global function definition for ‘maED’
bmd: no visible global function definition for ‘ED’
Undefined global functions or variables:
  ED FPL.4 LL.2 LL.5 LN.2 LN.4 W1.2 W1.4 W2.2 W2.4 maED predict qnorm
Consider adding
  importFrom("stats", "predict", "qnorm")
to your NAMESPACE file.
Rd file 'bmd.Rd':
  \examples lines wider than 100 characters:
     efsa2009p41.LL2 <- drm(number/total~dose, weights=total, data=efsa2009p41, type="binomial", fct=LL.2())
     efsa2009p41.LL3u <- drm(number/total~dose, weights=total, data=efsa2009p41, type="binomial", fct=LL.3u())
     hwang2009 <- data.frame(dose = c(0, 2.68, 10.34, 37.03), number = c(1,0,2,9), total = c(50,50,50,50))
     hwang2009.LN2 <- drm(number/total ~ dose, weights = total, data = hwang2009, type = "binomial", fct = LN.2())

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘model.txt’
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘coda’ ‘functional’ ‘plyr’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘coda’ ‘functional’ ‘plyr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HDistNoSize: no visible global function definition for ‘density’
HDistSize: no visible global function definition for ‘density’
bmkconverge: no visible global function definition for ‘Compose’
bmksensitive: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Curry’
bmksummary: no visible binding for global variable ‘quantile’
bmksummary : std.error: no visible global function definition for ‘var’
bmksummary: no visible global function definition for ‘mcmc’
bmksummary: no visible global function definition for ‘mcmc.list’
bmksummary: no visible global function definition for ‘median’
bmksummary: no visible global function definition for ‘effectiveSize’
bmksummary: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  Compose Curry density effectiveSize gelman.diag mcmc mcmc.list median
  quantile var
Consider adding
  importFrom("stats", "density", "median", "quantile", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘qgraph’
GNU make is a SystemRequirements.
Running examples in ‘bmlm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mlm_path_plot
> ### Title: Plot 'bmlm"s mediation model as a path diagram
> ### Aliases: mlm_path_plot
> 
> ### ** Examples
> 
> # Draw a template path diagram of the mediation model
> mlm_path_plot()
Error: qgraph package needed for this function. Please install it.
Execution halted
Malformed Description field: should contain one or more complete sentences.
bmmix : LL.y: no visible global function definition for ‘dmultinom’
bmmix : LL.x : <anonymous>: no visible global function definition for
  ‘dmultinom’
bmmix : LPrior.alpha: no visible global function definition for ‘dexp’
bmmix : alpha.move: no visible global function definition for ‘rnorm’
bmmix : alpha.move: no visible global function definition for ‘runif’
bmmix : phi.move: no visible global function definition for ‘rnorm’
bmmix : phi.move: no visible global function definition for ‘runif’
bmmix: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dexp dmultinom read.table rnorm runif
Consider adding
  importFrom("stats", "dexp", "dmultinom", "rnorm", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘mcmc.txt’
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_BMRSr.Rmd’ using rmarkdown
Quitting from lines 230-243 (using_BMRSr.Rmd) 
Error: processing vignette 'using_BMRSr.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘using_BMRSr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
make_topology: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
bnlr: no visible global function definition for ‘dnorm’
bnlr: no visible global function definition for ‘runif’
chainsum : <anonymous>: no visible global function definition for
  ‘quantile’
infocrit: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm quantile runif
Consider adding
  importFrom("stats", "dnorm", "quantile", "runif")
to your NAMESPACE file.
Package required but not available: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  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).
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qgraph’
BOGest: no visible global function definition for ‘read.table’
BOGstat: no visible global function definition for ‘phyper’
BOGstat: no visible global function definition for ‘wilcox.test’
BOGstat: no visible global function definition for ‘p.adjust’
gseaplot: no visible global function definition for ‘par’
gseaplot: no visible global function definition for ‘points’
gseaplot: no visible global function definition for ‘axis’
gseaplot: no visible global function definition for ‘segments’
hgplot: no visible global function definition for ‘par’
hgplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  axis barplot p.adjust par phyper points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "points", "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'janitor', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘attractors.tex’ ‘cellcycle.sbml’ ‘cellcycle.txt’ ‘pajek_export.net’
  ‘sequence.txt’ ‘testNet.bn’
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
boostBackend: no visible global function definition for ‘model.frame’
findFormulaIn: no visible global function definition for ‘as.formula’
kFoldCV: no visible binding for global variable ‘par’
predictResponseFromWeightedAverage: no visible global function
  definition for ‘weighted.mean’
print.boostr: no visible global function definition for ‘str’
Undefined global functions or variables:
  as.formula model.frame par str weighted.mean
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "model.frame", "weighted.mean")
  importFrom("utils", "str")
to your NAMESPACE file.
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'IsingFit', 'qgraph', 'tidyr', 'mgm', 'NetworkToolbox',
  'graphicalVAR', 'networktools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
specdens: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Rd file 'specdens.Rd':
  \examples lines wider than 100 characters:
                                                                                         #the first 20 values of the 
                                                                                         #time series Nile and WWWusage

These lines will be truncated in the PDF manual.
Package required but not available: ‘mixOmics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
boot.stepAIC: no visible global function definition for ‘update’
boot.stepAIC: no visible binding for global variable ‘coef’
boot.stepAIC : <anonymous>: no visible global function definition for
  ‘anova’
boot.stepAIC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  anova coef pnorm update
Consider adding
  importFrom("stats", "anova", "coef", "pnorm", "update")
to your NAMESPACE file.
bootSVD: no visible global function definition for ‘object.size’
bootSVD : <anonymous> : <anonymous>: no visible global function
  definition for ‘quantile’
bootSVD_LD: no visible global function definition for ‘txtProgressBar’
bootSVD_LD: no visible global function definition for
  ‘setTxtProgressBar’
genQ: no visible global function definition for ‘rnorm’
getHDpercentiles : <anonymous>: no visible global function definition
  for ‘quantile’
getMomentsAndMomentCI: no visible binding for global variable ‘var’
os: no visible global function definition for ‘object.size’
simEEG: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  object.size quantile rnorm setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("stats", "quantile", "rnorm", "var")
  importFrom("utils", "object.size", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
boottol: no visible global function definition for ‘setNames’
boottol : shift: no visible global function definition for ‘tail’
boottol : shift: no visible global function definition for ‘head’
boottol: no visible global function definition for ‘na.omit’
vastol: no visible global function definition for ‘setNames’
vastol: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  head na.omit setNames tail
Consider adding
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
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++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  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).
Found the following files/directories:
  ‘for_krona.txt’ ‘test.jplace’
Rd file 'beq.lin.Rd':
  \examples lines wider than 100 characters:
     plot(x,h_sol0,type="l",lty=1,main=paste("Water Surface Elevetion after",t,"days",sep=" "),xlab="x[m]",ylab="h[m]")

Rd file 'beq.song.Rd':
  \examples lines wider than 100 characters:
     plot(x,h_sol1,type="l",lty=1,main="Water Surface Elevetion (Song at's solution) ",xlab="x[m]",ylab="h[m]")

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘tidyr’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bpbounds)
  > 
  > test_check("bpbounds")
  ── 1. Error: (unknown) (@test-bpbounds.R#18)  ──────────────────────────────────
  could not find function "uncount"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test-bpbounds.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bpbounds.Rmd’ using rmarkdown
Quitting from lines 36-39 (bpbounds.Rmd) 
Error: processing vignette 'bpbounds.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘bpbounds.Rmd’

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

Error: Vignette re-building failed.
Execution halted
bPeaksAnalysis: no visible global function definition for ‘write.table’
dataReading: no visible global function definition for ‘read.table’
dataSmoothing: no visible global function definition for ‘filter’
peakDetection: no visible global function definition for ‘quantile’
peakDetection: no visible global function definition for ‘pdf’
peakDetection: no visible global function definition for ‘par’
peakDetection: no visible global function definition for ‘text’
peakDetection: no visible global function definition for ‘abline’
peakDetection: no visible global function definition for ‘points’
peakDetection: no visible global function definition for ‘dev.off’
peakDetection: no visible global function definition for ‘write.table’
peakDrawing: no visible global function definition for ‘par’
peakDrawing: no visible global function definition for ‘abline’
peakLocation: no visible global function definition for ‘read.table’
peakLocation: no visible global function definition for ‘pdf’
peakLocation: no visible global function definition for ‘barplot’
peakLocation: no visible global function definition for ‘dev.off’
peakLocation: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline barplot dev.off filter par pdf points quantile read.table text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "points", "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘bPeaks_example-chrIV.bed’ ‘bPeaks_example-chrIV_bPeaksDrawing.pdf’
  ‘bPeaks_example-chrIV_dataSummary.pdf’
  ‘bPeaks_example_bPeaks_allGenome.bed’
  ‘bPeaks_example_bPeaks_parameterSummary.txt’
  ‘bPeaks_example_chrIV.bed’ ‘bPeaks_example_chrIV_bPeaksDrawing.pdf’
  ‘bPeaks_example_chrIV_dataSummary.pdf’
  ‘bPeaks_example_peakLocation.pdf’
  ‘bPeaks_example_peakLocation_inCDS.txt’
  ‘bPeaks_example_peakLocation_inPromoters.txt’ ‘peakStats.Robject’
Package required but not available: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
apply.breaks: no visible binding for global variable ‘median’
break.clust: no visible global function definition for ‘median’
breakage.plot: no visible binding for global variable ‘median’
breakage.plot: no visible global function definition for ‘abline’
breakage.plot: no visible global function definition for ‘lm’
find.bottom: no visible global function definition for ‘filter’
fit.breakage: no visible global function definition for ‘optim’
fit.breakage: no visible global function definition for ‘points’
fit.sensitivity.plot: no visible global function definition for
  ‘contour’
fit.sensitivity.plot: no visible global function definition for
  ‘points’
fit.sensitivity.plot: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline contour filter lm median optim points text
Consider adding
  importFrom("graphics", "abline", "contour", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
Package suggested but not available for checking: ‘caret’
Error(s) in re-building vignettes:
  ...
--- re-building ‘break_caret.Rmd’ using rmarkdown
Quitting from lines 24-32 (break_caret.Rmd) 
Error: processing vignette 'break_caret.Rmd' failed with diagnostics:
there is no package called 'caret'
--- failed re-building ‘break_caret.Rmd’

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'broom', 'tidyr'

Package suggested but not available for checking: ‘breathteststan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘breathtestcore’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘brew-test-1-1.eps’ ‘brew-test-1-2.eps’ ‘brew-test-1.tex’
  ‘brew-test-2.html’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cmdstanr', 'mice'
Packages required but not available: 'broom', 'broom.mixed', 'ipmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'broom', 'tidyr'

Packages suggested but not available for checking: 'glmmADMB', 'dotwhisker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

Packages suggested but not available for checking:
  'caret', 'geepack', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Package suggested but not available for checking: ‘plotly’
Package suggested but not available for checking: ‘tidyr’
BSGS.Sample: no visible global function definition for ‘rgamma’
BSGS.Simple: no visible global function definition for ‘rgamma’
CompWiseGibbs: no visible global function definition for ‘runif’
CompWiseGibbs: no visible global function definition for ‘rnorm’
CompWiseGibbsSMP: no visible global function definition for ‘rbinom’
CompWiseGibbsSMP: no visible global function definition for ‘runif’
CompWiseGibbsSMP: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘runif’
CompWiseGibbsSimple: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘rgamma’
GroupMH: no visible global function definition for ‘runif’
GroupZ.MH: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rbinom rgamma rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
plot.bspec: no visible global function definition for ‘par’
plot.bspec: no visible global function definition for ‘matlines’
plot.bspec: no visible global function definition for ‘points’
plot.bspec: no visible global function definition for ‘axis’
plot.bspec: no visible global function definition for ‘mtext’
plot.bspec: no visible global function definition for ‘axTicks’
plot.bspec: no visible global function definition for ‘box’
plot.bspecACF: no visible global function definition for ‘abline’
plot.bspecACF: no visible global function definition for ‘matlines’
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "points")
to your NAMESPACE file.
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
Package suggested but not available for checking: ‘mice’
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
alpha.proxy: no visible global function definition for ‘filled.contour’
alpha.proxy: no visible global function definition for ‘axis’
alpha.proxy: no visible global function definition for ‘contour’
factor.model.stat: no visible global function definition for ‘quantile’
factor.model.stat: no visible global function definition for ‘lsfit’
partial.rainbow: no visible binding for global variable ‘rainbow’
var.shrink.eqcor: no visible global function definition for ‘var’
var.shrink.eqcor: no visible global function definition for ‘quantile’
var.shrink.eqcor: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  axis contour cov2cor filled.contour lsfit quantile rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "contour", "filled.contour")
  importFrom("stats", "cov2cor", "lsfit", "quantile", "var")
to your NAMESPACE file.
plot.bursts: no visible global function definition for ‘axis’
plot.bursts: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis
Consider adding
  importFrom("graphics", "arrows", "axis")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'parsnip', 'recipes', 'rsample', 'caret', 'flexsurv', 'sparklyr'
Running examples in ‘butcher-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: axe-C5.0
> ### Title: Axing a C5.0.
> ### Aliases: axe-C5.0 axe_call.C5.0 axe_ctrl.C5.0 axe_fitted.C5.0
> 
> ### ** Examples
> 
> # Load libraries
> suppressWarnings(suppressMessages(library(parsnip)))
Error in library(parsnip) : there is no package called ‘parsnip’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adding-models-to-butcher.Rmd’ using rmarkdown
--- finished re-building ‘adding-models-to-butcher.Rmd’

--- re-building ‘available-axe-methods.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 = "class"
Joining, by = "class"
Joining, by = "class"
Joining, by = "class"
--- finished re-building ‘available-axe-methods.Rmd’

--- re-building ‘butcher.Rmd’ using rmarkdown
Quitting from lines 18-20 (butcher.Rmd) 
Error: processing vignette 'butcher.Rmd' failed with diagnostics:
there is no package called 'parsnip'
--- failed re-building ‘butcher.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Rd file 'bvenn.Rd':
  \examples lines wider than 100 characters:
                     bvenn(list(Set1 = sample(letters, 16), Set2 = sample(letters, 3+ 3*j), Set3 = sample(letters, 7)), add = TRUE, fontsize ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘haplo.stats’ ‘msm’
  Please remove these calls from your code.
fitBVS: no visible global function definition for ‘qnorm’
fitBVS: no visible global function definition for ‘model.matrix’
fitBVS: no visible global function definition for ‘as.formula’
fitBVS: no visible global function definition for ‘glm’
fitBVS: no visible global function definition for ‘deviance’
fitBVS: no visible global function definition for ‘pnorm’
plotBVS: no visible global function definition for ‘par’
plotBVS: no visible global function definition for ‘image’
plotBVS: no visible global function definition for ‘axis’
sampleBVS: no visible global function definition for ‘qnorm’
sampleBVS: no visible global function definition for ‘pnorm’
sampleBVS: no visible global function definition for ‘runif’
summaryBVS: no visible global function definition for ‘qnorm’
summaryBVS : inc.prob: no visible global function definition for
  ‘pnorm’
summaryBVS: no visible global function definition for ‘pnorm’
summaryBVS: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  as.formula axis deviance glm image model.matrix par pnorm qnorm runif
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "as.formula", "deviance", "glm", "model.matrix",
             "pnorm", "qnorm", "runif")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
makemim: no visible global function definition for ‘cor’
sigtestMTC: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  cor p.adjust
Consider adding
  importFrom("stats", "cor", "p.adjust")
to your NAMESPACE file.
Package required but not available: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'multichull', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cairoDevice.Rcheck/00install.out’ for details.
File ‘cairoDevice/R/zzz.R’:
  .onLoad calls:
    message("R session is headless; GTK+ not initialized.")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
File ‘cairoDevice/libs/cairoDevice.so’:
  Found non-API call to R: ‘R_CStackLimit’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Cairo/libs/Cairo.so’:
  Found non-API calls to R: ‘R_InputHandlers’, ‘addInputHandler’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘smoof’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Adapting_Algorithm_for_CAISEr.Rmd’ using rmarkdown
Quitting from lines 51-73 (Adapting_Algorithm_for_CAISEr.Rmd) 
Error: processing vignette 'Adapting_Algorithm_for_CAISEr.Rmd' failed with diagnostics:
there is no package called 'smoof'
--- failed re-building ‘Adapting_Algorithm_for_CAISEr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ReGenesees’
Package suggested but not available for checking: ‘tidyr’
Found the following files/directories:
  ‘tmp.txt’
Found the following files/directories:
  ‘MDA231_tree.pdf’
Package suggested but not available for checking: ‘tidyr’
Package suggested but not available for checking: ‘tidyr’
Package suggested but not available for checking: ‘tidyr’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
bootstrapCapwire: no visible global function definition for ‘quantile’
drawCapRatesBeta : <anonymous>: no visible global function definition
  for ‘rbeta’
drawCapRatesExp : <anonymous>: no visible global function definition
  for ‘rexp’
drawCapRatesGamma : <anonymous>: no visible global function definition
  for ‘rgamma’
drawCapRatesGeom : <anonymous>: no visible global function definition
  for ‘rgeom’
drawCapRatesUnif : <anonymous>: no visible global function definition
  for ‘runif’
partitionCountData : find.3.way.partitions: no visible global function
  definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom quantile rbeta rexp rgamma rgeom runif
Consider adding
  importFrom("stats", "dmultinom", "quantile", "rbeta", "rexp", "rgamma",
             "rgeom", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Sub.pair: no visible global function definition for ‘qnorm’
as.record: no visible global function definition for ‘capture.output’
estN: no visible global function definition for ‘sd’
estN: no visible global function definition for ‘qnorm’
estN.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  capture.output qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
abundance: no visible global function definition for ‘D’
Undefined global functions or variables:
  D
Consider adding
  importFrom("stats", "D")
to your NAMESPACE file.
barplotEQR: no visible global function definition for ‘barplot’
barplotEQR: no visible global function definition for ‘abline’
barplotEQR: no visible global function definition for ‘par’
barplotEQR: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘MASS’ ‘RSQLite’ ‘grid’ ‘sm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘foo.tab’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Vignette.Rmd’
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'janitor'

Package suggested but not available for checking: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘geepack’
Packages required but not available: 'tidyverse', 'broom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
MDR.high.forward1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for
  ‘complete.cases’
MDR.sing.mod1: no visible global function definition for ‘lm’
MDR.sing.mod1: no visible global function definition for ‘aov’
MDR.sing.mod1: no visible global function definition for ‘anova’
MDR.stage.forward1: no visible global function definition for ‘combn’
MDR.stage.forward1: no visible global function definition for
  ‘complete.cases’
MDR.stage.forward1: no visible global function definition for ‘lm’
MDR.stage.forward1: no visible global function definition for ‘resid’
MDR.stage.forward1: no visible global function definition for ‘pf’
MDR_forward1: no visible global function definition for
  ‘complete.cases’
MDR_forward1: no visible global function definition for ‘lm’
MDR_forward1: no visible global function definition for ‘aov’
low.anova: no visible global function definition for ‘complete.cases’
low.anova: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘combn’
sing.mod1: no visible global function definition for ‘complete.cases’
sing.mod1: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova aov combn complete.cases lm pf resid
Consider adding
  importFrom("stats", "anova", "aov", "complete.cases", "lm", "pf",
             "resid")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package required but not available: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'spacodiR', 'entropart', 'mice'
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Malformed Description field: should contain one or more complete sentences.
mi.inference: no visible binding for global variable ‘var’
mi.inference: no visible global function definition for ‘qt’
mi.inference: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
ctab: no visible global function definition for ‘xtabs’
mob.eqmain: no visible global function definition for ‘model.matrix’
mob.qi: no visible global function definition for ‘C’
mob.qi: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘C’
mob.rc1: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘model.matrix’
mob.symint: no visible global function definition for ‘model.matrix’
print.ctab: no visible global function definition for ‘ftable’
Undefined global functions or variables:
  C contr.treatment ftable model.matrix xtabs
Consider adding
  importFrom("stats", "C", "contr.treatment", "ftable", "model.matrix",
             "xtabs")
to your NAMESPACE file.
Rd file 'ctab.Rd':
  \usage lines wider than 90 characters:
     ctab(...,dec.places=NULL,digits=NULL,type=NULL,style=NULL,row.vars=NULL,col.vars=NULL,percentages=NULL,addmargins=NULL)

Rd file 'sqtab.Rd':
  \examples lines wider than 100 characters:
     OccFather<-gl(5,5,labels=c("Upper nonmanual","Lower nonmanual","Upper manual","Lower manual","Farm"))
     glm.q0<-glm(Freq~OccFather+OccSon+mob.qi(OccFather,OccSon,constrained=TRUE),family=poisson(),data=FHtab)
     glm.hrc1<-glm(Freq~OccFather+OccSon+mob.rc1(OccFather,OccSon,equal=TRUE),family=poisson(),data=FHtab)
     m2 <- mlogit(occupation ~ mob.qi(focc,alt)+mob.unif(focc,alt) | education+race,data=pc, reflevel = "farm")

These lines will be truncated in the PDF manual.
GNU make is a SystemRequirements.
Packages required but not available: 'DiagrammeR', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
binParamPosteriorSampling: no visible global function definition for
  ‘rbeta’
bindagMonteCarloCausalEffect: no visible global function definition for
  ‘runif’
getBinDAGModelData: no visible global function definition for ‘runif’
logitDist: no visible global function definition for ‘runif’
logitDist: no visible global function definition for ‘rnorm’
simulateWitnessModel: no visible global function definition for ‘runif’
summary.covsearch: no visible global function definition for ‘quantile’
summary.iv: no visible global function definition for ‘quantile’
summary.wpp: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile rbeta rnorm runif
Consider adding
  importFrom("stats", "quantile", "rbeta", "rnorm", "runif")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
GNU make is a SystemRequirements.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of ‘nc’ to ‘ncol’
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par points
  text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
prepare_Rd: estim.regul.Rd:24-26: Dropping empty section \details
prepare_Rd: img.estim.regul.Rd:15-17: Dropping empty section \details
prepare_Rd: img.estim.regul.Rd:24-25: Dropping empty section \examples
ccd.sequential: no visible global function definition for ‘qchisq’
dominate.random.sample: no visible global function definition for
  ‘runif’
draw.circle: no visible global function definition for ‘polygon’
juggle2: no visible global function definition for ‘rbinom’
plot.cccd: no visible global function definition for ‘gray’
plot.cccd: no visible global function definition for ‘points’
plot.cccdClassifier: no visible global function definition for ‘points’
Undefined global functions or variables:
  gray points polygon qchisq rbinom runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "points", "polygon")
  importFrom("stats", "qchisq", "rbinom", "runif")
to your NAMESPACE file.
VD: no visible binding for global variable ‘var’
stratcc : <anonymous>: no visible global function definition for
  ‘hclust’
stratcc : <anonymous>: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  cutree hclust var
Consider adding
  importFrom("stats", "cutree", "hclust", "var")
to your NAMESPACE file.
Rd file 'stratcc.Rd':
  \usage lines wider than 90 characters:
     stratcc(x, groups, alloc = "Pro", fraction = 0.1, clustering = FALSE, cluster_method = "ward")

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
p.Roy: no visible global function definition for ‘pf’
p.asym: no visible global function definition for ‘pf’
p.perm: no visible global function definition for ‘cancor’
plt.asym: no visible global function definition for ‘qf’
plt.asym: no visible global function definition for ‘df’
plt.asym: no visible global function definition for ‘abline’
plt.perm: no visible global function definition for ‘hist’
plt.perm: no visible global function definition for ‘mtext’
plt.perm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cancor df hist mtext pf qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
Rd file 'p.perm.Rd':
  \examples lines wider than 100 characters:
     ## Run permutation test using Wilks Lambda (default) as test statistic; include different numbers of canonical correlations:

Rd file 'plt.asym.Rd':
  \examples lines wider than 100 characters:
     ## Plot the F-approximation for the Hotelling-Lawley Trace, considering 3, 2, or 1 canonical correlation(s):

Rd file 'plt.perm.Rd':
  \examples lines wider than 100 characters:
     # plot the permutation distribution of an F approximation for Wilks' Lambda, considering 3 and 2 canonical correlations:
     # plot the permutation distribution of an F approximation for the Pillai-Bartlett Trace, considering 3, 2, and 1 canonical correlation( ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘hotcold.csv’
'library' or 'require' call to ‘bitops’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following files/directories:
  ‘Base.txt’
CDFt: no visible global function definition for ‘ecdf’
CDFt: no visible global function definition for ‘quantile’
CDFt: no visible global function definition for ‘approx’
KolmogorovSmirnov: no visible global function definition for ‘ecdf’
KolmogorovSmirnov: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx ecdf quantile
Consider adding
  importFrom("stats", "approx", "ecdf", "quantile")
to your NAMESPACE file.
prepare_Rd: CramerVonMisesTwoSamples.Rd:23: Dropping empty section \examples
prepare_Rd: KolmogorovSmirnov.Rd:26: Dropping empty section \examples
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'BIFIEsurvey', 'miceadds'
Packages required but not available: 'tidyr', 'broom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Packages in Depends field not imported from:
  ‘gplots’ ‘minpack.lm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
erf: no visible global function definition for ‘pnorm’
fitVolDist: no visible global function definition for ‘nls.lm’
fitVolDist: no visible global function definition for ‘nls.lm.control’
fitVolDist: no visible global function definition for ‘optim’
fitVolDist: no visible global function definition for ‘relist’
print.fitVolDist: no visible global function definition for ‘coef’
print.fitVolDist: no visible global function definition for ‘deviance’
print.fitVolDist: no visible global function definition for ‘pt’
print.fitVolDist: no visible global function definition for
  ‘printCoefmat’
resFunChiSq: no visible global function definition for ‘relist’
volEq7: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  coef deviance integrate nls.lm nls.lm.control optim pnorm
  printCoefmat pt relist
Consider adding
  importFrom("stats", "coef", "deviance", "integrate", "optim", "pnorm",
             "printCoefmat", "pt")
  importFrom("utils", "relist")
to your NAMESPACE file.
cenNID: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Malformed Description field: should contain one or more complete sentences.
MomNIT: no visible global function definition for ‘dnorm’
MomNIT: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘lm’
em.cens: no visible global function definition for ‘coefficients’
em.cens : ft: no visible global function definition for ‘dt’
em.cens : ft: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘optimize’
em.cens: no visible global function definition for ‘dnorm’
em.cens: no visible global function definition for ‘pnorm’
em.cens: no visible global function definition for ‘sd’
Undefined global functions or variables:
  coefficients dnorm dt lm optimize pnorm pt sd
Consider adding
  importFrom("stats", "coefficients", "dnorm", "dt", "lm", "optimize",
             "pnorm", "pt", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
CM: no visible global function definition for ‘sd’
Erf: no visible global function definition for ‘pnorm’
Erfc: no visible global function definition for ‘pnorm’
boot.Cenarma: no visible global function definition for ‘coef’
boot.Cenarma: no visible global function definition for ‘arima.sim’
cenarma: no visible global function definition for ‘arima’
cenarma: no visible global function definition for ‘coef’
cenarma: no visible global function definition for ‘ARMAacf’
cenarma: no visible global function definition for ‘var’
plot.cents: no visible global function definition for ‘segments’
plot.cents: no visible global function definition for ‘rgb’
plot.cents: no visible global function definition for ‘points’
rcarma: no visible global function definition for ‘arima.sim’
rcarma: no visible global function definition for ‘quantile’
scenNID: no visible global function definition for ‘sd’
se.Cenarma: no visible global function definition for ‘coef’
se.Cenarma: no visible global function definition for ‘sd’
Undefined global functions or variables:
  ARMAacf arima arima.sim coef pnorm points quantile rgb sd segments
  var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "points", "segments")
  importFrom("stats", "ARMAacf", "arima", "arima.sim", "coef", "pnorm",
             "quantile", "sd", "var")
to your NAMESPACE file.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some ‘make’ programs ignore lines not ending in LF.
select_lambda: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
cf_estimate_quantiles: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
sw.plot : <anonymous>: no visible global function definition for
  ‘median’
sw.plot : <anonymous>: no visible global function definition for ‘mad’
sw.plot : my.line: no visible global function definition for ‘lines’
sw.plot : island.line: no visible global function definition for
  ‘lines’
sw.plot: no visible global function definition for ‘rug’
sw.plot: no visible global function definition for ‘axis’
sw.plot: no visible global function definition for ‘mtext’
sw.plot: no visible global function definition for ‘abline’
sw.plot: no visible global function definition for ‘points’
sw.rob : <anonymous>: no visible global function definition for
  ‘median’
sw.rob : <anonymous>: no visible global function definition for ‘mad’
sw.threshold : <anonymous>: no visible global function definition for
  ‘median’
sw.threshold : <anonymous>: no visible global function definition for
  ‘mad’
Undefined global functions or variables:
  abline axis lines mad median mtext points rug
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "points",
             "rug")
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
Packages required but not available:
  'broom', 'ggmosaic', 'sjstats', 'tidyr'

Package suggested but not available for checking: ‘janitor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘blue.Rdata’ ‘foo.Rdata’
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Hartree2Joule: no visible binding for global variable
  ‘universalConstants’
Hertz2Joule: no visible binding for global variable
  ‘universalConstants’
Joule2Hartree: no visible binding for global variable
  ‘universalConstants’
Joule2Hertz: no visible binding for global variable
  ‘universalConstants’
Joule2Kelvin: no visible binding for global variable
  ‘universalConstants’
Joule2centimeterMinusOne: no visible binding for global variable
  ‘universalConstants’
Joule2electronVolt: no visible binding for global variable
  ‘universalConstants’
Joule2kiloCaloriePerMole: no visible binding for global variable
  ‘universalConstants’
Joule2kiloJoulePerMole: no visible binding for global variable
  ‘universalConstants’
KMC: no visible global function definition for ‘runif’
Kelvin2Joule: no visible binding for global variable
  ‘universalConstants’
LandauZener: no visible binding for global variable
  ‘universalConstants’
LandauZenerProbability: no visible binding for global variable
  ‘universalConstants’
Marcus: no visible binding for global variable ‘universalConstants’
MarcusLevichJortner: no visible binding for global variable
  ‘universalConstants’
centimeterMinusOne2Joule: no visible binding for global variable
  ‘universalConstants’
electronVolt2Joule: no visible binding for global variable
  ‘universalConstants’
kiloCaloriePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
kiloJoulePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
Undefined global functions or variables:
  runif universalConstants
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'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’ ‘bitops’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createDataset: no visible global function definition for ‘read.csv’
createInventory: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for
  ‘getURLContent’
downloadMaster: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for ‘write.csv’
getMissingScrape: no visible global function definition for ‘read.csv’
readLocalMaster: no visible global function definition for ‘read.csv’
readMonthlyCsv: no visible global function definition for ‘read.csv’
scrapeToCsv: no visible global function definition for ‘download.file’
writeData: no visible global function definition for ‘write.csv’
writeGhcn: no visible global function definition for ‘write.table’
writeInventory: no visible global function definition for ‘write.table’
writeMonthlyStations: no visible global function definition for
  ‘read.csv’
writeMonthlyStations: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  download.file getURLContent read.csv write.csv write.table
Consider adding
  importFrom("utils", "download.file", "read.csv", "write.csv",
             "write.table")
to your NAMESPACE file.
Packages suggested but not available for checking: 'tidygraph', 'ggraph'
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-cheatR.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'tidygraph''
Quitting from lines 53-54 (using-cheatR.Rmd) 
Error: processing vignette 'using-cheatR.Rmd' failed with diagnostics:
This function requares 'tidygraph' to work. Please install it.
--- failed re-building ‘using-cheatR.Rmd’

SUMMARY: processing the following file failed:
  ‘using-cheatR.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Rd file 'chebR.Rd':
  \examples lines wider than 100 characters:
     return(list(coefs=rlist$xx[1:n],resids=rlist$bb[1:m],rank=rlist$rank,iter=rlist$iter,ocode=rlist$ocode))

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘stepres00.txt’
Package suggested but not available for checking: ‘rda’
Packages suggested but not available for checking: 'mlrMBO', 'smoof'
Package required but not available: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘countreg’
Package vignette with placeholder title ‘Vignette Title’:
  ‘childhoodmortality.Rmd’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
choicemodelr : drawDelta: no visible global function definition for
  ‘rnorm’
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for ‘rnorm’
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for ‘runif’
choicemodelr : rmultireg: no visible global function definition for
  ‘rnorm’
choicemodelr : rwishart: no visible global function definition for
  ‘rchisq’
choicemodelr : rwishart: no visible global function definition for
  ‘rnorm’
choicemodelr : fsh: no visible global function definition for
  ‘flush.console’
choicemodelr: no visible global function definition for ‘matplot’
choicemodelr: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  flush.console matplot rchisq rnorm runif write.table
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "rchisq", "rnorm", "runif")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Rd file 'choicemodelr.Rd':
  \examples lines wider than 100 characters:
     estbetas = cbind(estbetas[,1:4],0-apply(estbetas[,1:4],1,sum),estbetas[,5:6],0-apply(estbetas[,5:6],1,sum))
     estbetas = cbind(estbetas[,1:4],0-apply(estbetas[,1:4],1,sum),estbetas[,5:6],0-apply(estbetas[,5:6],1,sum))

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘RBetas.csv’ ‘RLog.txt’ ‘restart.txt’
Malformed Description field: should contain one or more complete sentences.
Qh.times.dhyper: no visible global function definition for ‘var’
Qh.times.dhyper: no visible global function definition for ‘pnorm’
Qh.times.dhyper: no visible global function definition for ‘dhyper’
TDiM: no visible global function definition for ‘sd’
choplump.default: no visible global function definition for
  ‘flush.console’
choplump.formula: no visible global function definition for ‘terms’
cm.compact: no visible global function definition for ‘dhyper’
Undefined global functions or variables:
  dhyper flush.console pnorm sd terms var
Consider adding
  importFrom("stats", "dhyper", "pnorm", "sd", "terms", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Packages required but not available: 'ggmap', 'tidyr', 'tidycensus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
parse_counts: 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.
combineToSingleMatrix: no visible global function definition for
  ‘read.table’
combineToSingleMatrix: no visible global function definition for
  ‘write.table’
compareCIM: no visible global function definition for ‘sd’
correctData: no visible global function definition for ‘wd’
correctData: no visible global function definition for ‘threshold’
correctData: no visible binding for global variable ‘madmad’
correctData: no visible global function definition for ‘wr’
Undefined global functions or variables:
  madmad read.table sd threshold wd wr write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘factoextra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
cin: no visible global function definition for ‘pnorm’
gammaHRF: no visible global function definition for ‘dgamma’
intertest: no visible global function definition for ‘pnorm’
truncSum: no visible global function definition for ‘spline’
Undefined global functions or variables:
  dgamma pnorm spline
Consider adding
  importFrom("stats", "dgamma", "pnorm", "spline")
to your NAMESPACE file.
Package suggested but not available for checking: ‘userfriendlyscience’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘CISE_vignette.Rmd’
cit.assignBcmst: no visible binding for global variable ‘citbcmst’
cit.assignBcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignBcmst: no visible global function definition for ‘prcomp’
cit.assignBcmst: no visible global function definition for ‘par’
cit.assignBcmst: no visible global function definition for ‘lines’
cit.assignBcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citbcmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
cit.assignCcmst: no visible binding for global variable ‘citccmst’
cit.assignCcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignCcmst : median.na: no visible global function definition for
  ‘median’
cit.assignCcmst: no visible global function definition for ‘prcomp’
cit.assignCcmst: no visible global function definition for ‘par’
cit.assignCcmst: no visible global function definition for ‘lines’
cit.assignCcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citccmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
Packages suggested but not available for checking: 'broom', 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ciTools-binomial-vignette.Rmd’ using rmarkdown
Quitting from lines 61-65 (ciTools-binomial-vignette.Rmd) 
Error: processing vignette 'ciTools-binomial-vignette.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘ciTools-binomial-vignette.Rmd’

--- re-building ‘ciTools-demo.Rmd’ using rmarkdown
Quitting from lines 13-19 (ciTools-demo.Rmd) 
Error: processing vignette 'ciTools-demo.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘ciTools-demo.Rmd’

--- re-building ‘ciTools-glm-vignette.Rmd’ using rmarkdown
Quitting from lines 13-18 (ciTools-glm-vignette.Rmd) 
Error: processing vignette 'ciTools-glm-vignette.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘ciTools-glm-vignette.Rmd’

--- re-building ‘ciTools_survreg_vignette.Rmd’ using rmarkdown
Quitting from lines 14-19 (ciTools_survreg_vignette.Rmd) 
Error: processing vignette 'ciTools_survreg_vignette.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘ciTools_survreg_vignette.Rmd’

--- re-building ‘citools-merMod-vignette.Rmd’ using rmarkdown
Quitting from lines 13-57 (citools-merMod-vignette.Rmd) 
Error: processing vignette 'citools-merMod-vignette.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘citools-merMod-vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘ciTools-binomial-vignette.Rmd’ ‘ciTools-demo.Rmd’
  ‘ciTools-glm-vignette.Rmd’ ‘ciTools_survreg_vignette.Rmd’
  ‘citools-merMod-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
CityPlot: no visible global function definition for ‘read.table’
CityPlot: no visible global function definition for ‘tail’
CityPlot: no visible global function definition for ‘pdf’
CityPlot: no visible global function definition for ‘split.screen’
CityPlot: no visible global function definition for ‘screen’
CityPlot: no visible global function definition for ‘par’
CityPlot: no visible global function definition for ‘rect’
CityPlot: no visible global function definition for ‘text’
CityPlot: no visible global function definition for ‘lines’
CityPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off lines par pdf read.table rect screen split.screen tail text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘desciption-ciuupi.Rmd’
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rggobi’
'library' or 'require' call to ‘rggobi’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
generate_data : <anonymous>: no visible global function definition for
  ‘runif’
knnf: no visible global function definition for ‘terms’
rescaler.default: no visible global function definition for ‘sd’
rescaler.default: no visible global function definition for ‘median’
rescaler.default: no visible global function definition for ‘mad’
simvar.numeric: no visible global function definition for ‘runif’
Undefined global functions or variables:
  mad median runif sd terms
Consider adding
  importFrom("stats", "mad", "median", "runif", "sd", "terms")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Package suggested but not available for checking: ‘ggmap’
Packages required but not available: 'tidyr', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
Package suggested but not available for checking: ‘scio’
clime: no visible global function definition for ‘cov’
cv.clime: no visible global function definition for ‘cov’
cv.clime: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cov sd
Consider adding
  importFrom("stats", "cov", "sd")
to your NAMESPACE file.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gxe.cc: no visible global function definition for ‘qnorm’
gxe.coh: no visible global function definition for ‘qnorm’
utility.cc: no visible global function definition for ‘qnorm’
utility.coh: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Package required but not available: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
socp: 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').
Rd file 'socp.Rd':
  \usage lines wider than 90 characters:
     socp(A, b, c, kvec, type = rep('q',length(kvec)), use_sparse=TRUE, gamma_fac=.95, delta0 = .75, sigma0 = .25, mu0 = 0.01, zero_tol = 1e ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Packages required but not available: 'ggfortify', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘clusterhap_reports’
Package suggested but not available for checking: ‘tidyverse’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Clustering.Rmd’ using rmarkdown
Quitting from lines 13-19 (Clustering.Rmd) 
Error: processing vignette 'Clustering.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘Clustering.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
hopkins: no visible global function definition for ‘runif’
hopkins: no visible global function definition for ‘dist’
Undefined global functions or variables:
  dist runif
Consider adding
  importFrom("stats", "dist", "runif")
to your NAMESPACE file.
License components which are templates and need '+ file LICENSE':
  MIT
clustomit: no visible binding for global variable ‘weighted.mean’
sim_unif : multivariate_unif: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif weighted.mean
Consider adding
  importFrom("stats", "runif", "weighted.mean")
to your NAMESPACE file.
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Example_on_simulated_data.Rmd’ using rmarkdown
Quitting from lines 266-268 (Example_on_simulated_data.Rmd) 
Error: processing vignette 'Example_on_simulated_data.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘Example_on_simulated_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggraph', 'tidygraph'

Package suggested but not available for checking: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidygraph', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘psycho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
braycurtis: no visible global function definition for ‘as.dist’
czekanowski: no visible global function definition for ‘as.dist’
findComplementaryIndices: no visible global function definition for
  ‘na.omit’
genSimilarityProfile: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘hclust’
simprof.plot : <local> : colorizer: no visible global function
  definition for ‘is.leaf’
simprof.plot: no visible global function definition for ‘rainbow’
simprof.plot: no visible global function definition for ‘dendrapply’
simprof.plot: no visible global function definition for ‘as.dendrogram’
Undefined global functions or variables:
  as.dendrogram as.dist dendrapply dist hclust is.leaf na.omit rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.dist", "dendrapply", "dist",
             "hclust", "is.leaf", "na.omit")
to your NAMESPACE file.
cma_es: no visible global function definition for ‘rnorm’
f_rand: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package required but not available: ‘smoof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
alpha.cronbach: no visible global function definition for ‘cov’
alpha.curve: no visible global function definition for ‘text’
Undefined global functions or variables:
  cov text
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [18s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cmstatr)
  > 
  > test_check("cmstatr")
  ── 1. Error: (unknown) (@test-adk.R#4)  ────────────────────────────────────────
  there is no package called 'tidyr'
  Backtrace:
   1. base::suppressMessages(library(tidyr))
   3. base::library(tidyr)
  
  ── 2. Error: (unknown) (@test-equiv.R#4)  ──────────────────────────────────────
  there is no package called 'tidyr'
  Backtrace:
   1. base::suppressMessages(library(tidyr))
   3. base::library(tidyr)
  
  ── 3. Error: (unknown) (@test-workflow.R#4)  ───────────────────────────────────
  there is no package called 'tidyr'
  Backtrace:
   1. base::suppressMessages(library(tidyr))
   3. base::library(tidyr)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 980 | SKIPPED: 6 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: (unknown) (@test-adk.R#4) 
  2. Error: (unknown) (@test-equiv.R#4) 
  3. Error: (unknown) (@test-workflow.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adktest.Rmd’ using rmarkdown
--- finished re-building ‘adktest.Rmd’

--- re-building ‘cmstatr_Graphing.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 29-33 (cmstatr_Graphing.Rmd) 
Error: processing vignette 'cmstatr_Graphing.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘cmstatr_Graphing.Rmd’

--- re-building ‘cmstatr_Tutorial.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 31-36 (cmstatr_Tutorial.Rmd) 
Error: processing vignette 'cmstatr_Tutorial.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘cmstatr_Tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘cmstatr_Graphing.Rmd’ ‘cmstatr_Tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
copynumberBootstrap: no visible global function definition for
  ‘txtProgressBar’
copynumberBootstrap: no visible global function definition for
  ‘quantile’
copynumberBootstrap: no visible global function definition for
  ‘setTxtProgressBar’
gethits: no visible global function definition for ‘read.table’
normalizeGC: no visible global function definition for ‘median’
plotCNOGpro: no visible global function definition for ‘par’
plotCNOGpro: no visible global function definition for ‘rainbow’
plotCNOGpro: no visible global function definition for ‘density’
plotCNOGpro: no visible global function definition for ‘polygon’
plotCNOGpro: no visible global function definition for ‘lines’
plotCNOGpro: no visible global function definition for ‘legend’
plotCNOGpro: no visible global function definition for ‘boxplot’
sampleChromosome: no visible global function definition for ‘median’
sampleChromosome: no visible binding for global variable ‘var’
setupEmissionMatrix: no visible global function definition for ‘dgeom’
store: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  boxplot density dgeom legend lines median par polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
CNclusterNcenter: no visible global function definition for ‘median’
CNclusterNcenter: no visible binding for global variable ‘var’
breakIntoGaps: no visible global function definition for ‘runif’
centerprob: no visible global function definition for ‘pnorm’
getz: no visible global function definition for ‘predict’
smad: no visible global function definition for ‘mad’
smedian: no visible global function definition for ‘median’
smedian.sample: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm predict runif var
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "predict", "runif",
             "var")
to your NAMESPACE file.
Packages required but not available: 'tidyr', 'plotly'

Package suggested but not available for checking: ‘heatmaply’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
coalescentMCMC: no visible global function definition for
  ‘packageVersion’
coalescentMCMC : getparams: no visible global function definition for
  ‘nlminb’
sim.coalescent: no visible global function definition for ‘segments’
sim.coalescent: no visible global function definition for ‘points’
Undefined global functions or variables:
  nlminb packageVersion points segments
Consider adding
  importFrom("graphics", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mice', 'MatchThem'
Running examples in ‘cobalt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bal.tab.mimids
> ### Title: Balance Statistics for MatchThem Objects
> ### Aliases: bal.tab.mimids bal.tab.wimids
> ### Keywords: tables
> 
> ### ** Examples
> 
> library(mice)
Error in library(mice) : there is no package called ‘mice’
Execution halted
'library' or 'require' calls in package code:
  ‘lars’ ‘randomForest’ ‘ridge’ ‘snowfall’ ‘tree’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
COBRA : COBRA.lars: no visible global function definition for ‘lars’
COBRA : COBRA.lars: no visible global function definition for
  ‘predict.lars’
COBRA : COBRA.tree: no visible global function definition for ‘tree’
COBRA : COBRA.tree: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.tree: no visible global function definition for ‘predict’
COBRA : COBRA.ridge: no visible global function definition for
  ‘linearRidge’
COBRA : COBRA.ridge: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.ridge: no visible global function definition for
  ‘predict’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘randomForest’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘predict’
COBRA: no visible global function definition for ‘sfInit’
COBRA: no visible global function definition for ‘sfLibrary’
COBRA: no visible global function definition for ‘sfExportAll’
COBRA: no visible global function definition for ‘sfSapply’
COBRA: no visible global function definition for ‘sfStop’
COBRA: no visible global function definition for ‘write.table’
COBRA: no visible global function definition for ‘pdf’
COBRA: no visible global function definition for ‘points’
COBRA: no visible global function definition for ‘legend’
COBRA: no visible global function definition for ‘abline’
COBRA: no visible global function definition for ‘lines’
COBRA: no visible global function definition for ‘dev.off’
COBRA: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline as.formula dev.new dev.off lars legend linearRidge lines pdf
  points predict predict.lars randomForest sfExportAll sfInit sfLibrary
  sfSapply sfStop tree write.table
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "abline", "legend", "lines", "points")
  importFrom("stats", "as.formula", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Package in Depends field not imported from: ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available: 'tidyr', 'skimr'

Package suggested but not available for checking: ‘userfriendlyscience’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Found the following files/directories:
  ‘fda7wnr6u.c’ ‘fda7wnr6u.o’ ‘fda7wnr6u.so’ ‘symbols.rds’
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘REDCapR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Rd file 'fast.flexsim.Rd':
  \usage lines wider than 90 characters:
     fast.flexsim(scale = 2, island,dispersalscale = 51, allee = 1, T = 1000, initp,parcombination, spnum = 2, sourcetype = "constant", type ... [TRUNCATED]

Rd file 'flexsim.Rd':
  \usage lines wider than 90 characters:
     flexsim(scale = 2, dispersalscale = 51, allee = 1, T = 1000, prange, initp,spnum = 2, island=10, sourcetype = "constant", type, path =  ... [TRUNCATED]

Rd file 'make.heatmap.Rd':
  \usage lines wider than 90 characters:
     make.heatmap(mat, type = "gray", xname = "x", yname = "y", xlab = NULL, ylab = NULL, title = NULL)

Rd file 'sim.coarse.Rd':
  \usage lines wider than 90 characters:
     sim.coarse(island=10,scale = 2, dispersalscale = 51, allee = 1, T = 1000, prange, type, initp, path = NULL)

These lines will be truncated in the PDF manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
BMDE: no visible global function definition for ‘quantile’
BMDU: no visible global function definition for ‘runif’
BMDU: no visible global function definition for ‘quantile’
FS: no visible global function definition for ‘qnorm’
GM: no visible global function definition for ‘qchisq’
QH: no visible global function definition for ‘qchisq’
SG : sgp: no visible global function definition for ‘ppois’
SG : sgp: no visible global function definition for ‘dpois’
WALD: no visible global function definition for ‘qchisq’
WALDCC: no visible global function definition for ‘qchisq’
WS: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  dpois ppois qchisq qnorm quantile runif
Consider adding
  importFrom("stats", "dpois", "ppois", "qchisq", "qnorm", "quantile",
             "runif")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘collectArgs_and_iterateWithArgs.Rmd’
Packages required but not available: 'evaluator', 'ggpubr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Error(s) in re-building vignettes:
  ...
--- re-building ‘colorDF.Rmd’ using rmarkdown
Quitting from lines 41-44 (colorDF.Rmd) 
Error: processing vignette 'colorDF.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘colorDF.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
cICA: no visible global function definition for ‘mvfft’
cICA: no visible global function definition for ‘ar.yw’
cICA: no visible global function definition for ‘rnorm’
scICA: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  ar.yw mvfft rnorm
Consider adding
  importFrom("stats", "ar.yw", "mvfft", "rnorm")
to your NAMESPACE file.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.text’
plotVenn2d: no visible global function definition for ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.text’
plotVenn3d: no visible global function definition for ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.polygon’
plotVenn4d : getCommonEllipse: no visible global function definition
  for ‘aggregate’
plotVenn4d : region.polygon: no visible global function definition for
  ‘head’
plotVenn4d : region.polygon: no visible global function definition for
  ‘grid.polygon’
plotVenn4d : region.polygon: no visible global function definition for
  ‘gpar’
plotVenn4d: no visible global function definition for ‘grid.text’
plotVenn4d: no visible global function definition for ‘gpar’
plotVenn4d: no visible global function definition for ‘pushViewport’
plotVenn4d: no visible global function definition for ‘viewport’
plotVenn4d: no visible global function definition for ‘grid.polygon’
plotVenn4d: no visible global function definition for ‘upViewport’
resizeCircles: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  aggregate gpar grid.polygon grid.text head pushViewport uniroot
  upViewport viewport
Consider adding
  importFrom("stats", "aggregate", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
generateMonochromaticColors: no visible global function definition for
  ‘col2rgb’
generateMonochromaticColors: no visible global function definition for
  ‘rgb’
generateMonochromaticColors: no visible global function definition for
  ‘tail’
hsv2rgb: no visible global function definition for ‘rgb’
rotational_dispersion: no visible global function definition for
  ‘col2rgb’
rotational_dispersion: no visible global function definition for
  ‘rgb2hsv’
tetradicColors: no visible global function definition for ‘head’
triadicColors: no visible global function definition for ‘head’
Undefined global functions or variables:
  col2rgb head rgb rgb2hsv tail
Consider adding
  importFrom("grDevices", "col2rgb", "rgb", "rgb2hsv")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Package suggested but not available for checking: ‘plotly’
Malformed Description field: should contain one or more complete sentences.
primary.colors: no visible global function definition for ‘rgb’
rgb.tables: no visible global function definition for ‘rgb’
ygobb: no visible global function definition for ‘approx’
ygobb: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
Found the following files/directories:
  ‘random.txt’
Malformed Description field: should contain one or more complete sentences.
Package vignette with placeholder title ‘Vignette Title’:
  ‘colr.Rmd’
Malformed Description field: should contain one or more complete sentences.
competitive.test: no visible global function definition for ‘runif’
selfcontained.test : fun2: no visible global function definition for
  ‘qchisq’
selfcontained.test: no visible global function definition for ‘cov’
selfcontained.test: no visible global function definition for ‘qchisq’
selfcontained.test: no visible global function definition for ‘cor’
selfcontained.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor cov pchisq qchisq runif
Consider adding
  importFrom("stats", "cor", "cov", "pchisq", "qchisq", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘lattice’ ‘rgl’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'TMC.Rd':
  \usage lines wider than 90 characters:
     TMC(num.Iter = 50, data.Size = 100, make.Data = gen.Data, make.Params = gen.Params, model.List, weight.Vector = rep(1, times = length(m ... [TRUNCATED]
  \examples lines wider than 100 characters:
     result <- TMC(num.Iter = 3, model.List = make.Model.List.Reg(vars), msc.List = list(BIC, AIC, PRESS), var.Frame = vars)

Rd file 'make.Model.List.Reg.Rd':
  \usage lines wider than 90 characters:
     make.Model.List.Reg(fram, max.Size = min(8, dim(fram)[2]), no.Intercepts = FALSE, GLM = FALSE)

Rd file 'sarima.Sim.Rd':
  \usage lines wider than 90 characters:
     sarima.Sim(n = 20, period = 12, model, seasonal, rand.Gen.Fun = rnorm, rand.Gen.Seas = rnorm)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
Package required but not available: ‘adespatial’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
CommT.anova: no visible global function definition for ‘aov’
CommT.legendpos: no visible global function definition for ‘quantile’
CommT.plotcolors: no visible global function definition for ‘hcl’
Undefined global functions or variables:
  aov hcl quantile
Consider adding
  importFrom("grDevices", "hcl")
  importFrom("stats", "aov", "quantile")
to your NAMESPACE file.
addxaxis: no visible global function definition for ‘par’
addxaxis: no visible global function definition for ‘axis’
addxaxis: no visible global function definition for ‘mtext’
eplot: no visible global function definition for ‘par’
eplot: no visible global function definition for ‘axis’
eplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext par
Consider adding
  importFrom("graphics", "axis", "mtext", "par")
to your NAMESPACE file.
Packages suggested but not available for checking: 'CAM', 'flare'
compareC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘HardyWeinberg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘XML’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
compareODM: no visible global function definition for ‘xmlRoot’
compareODM: no visible global function definition for ‘xmlTreeParse’
compareODM: no visible global function definition for ‘xmlChildren’
compareODM: no visible global function definition for ‘xmlAttrs’
compareODM: no visible global function definition for ‘xmlValue’
Undefined global functions or variables:
  xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
Package required but not available: ‘GEOquery’

Packages suggested but not available for checking:
  'inSilicoDb', 'GEOmetadb'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘comperes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dcomplnorm: no visible global function definition for ‘grad’
dcomplnorm : f1: no visible global function definition for ‘dlnorm’
dcomplnorm : F1: no visible global function definition for ‘plnorm’
dcomplnorm : f1L: no visible global function definition for ‘dlnorm’
dcomplnorm : F1L: no visible global function definition for ‘plnorm’
pcomplnorm: no visible global function definition for ‘grad’
pcomplnorm : f1: no visible global function definition for ‘dlnorm’
pcomplnorm : F1: no visible global function definition for ‘plnorm’
pcomplnorm : F1L: no visible global function definition for ‘plnorm’
qcomplnorm: no visible global function definition for ‘grad’
qcomplnorm : f1: no visible global function definition for ‘dlnorm’
qcomplnorm : F1q: no visible global function definition for ‘qlnorm’
qcomplnorm : F1: no visible global function definition for ‘plnorm’
rcomplnorm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dlnorm grad plnorm qlnorm runif
Consider adding
  importFrom("stats", "dlnorm", "plnorm", "qlnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘hypergeo’ which was already attached by Depends.
  Please remove these calls from your code.
momentCompound: no visible global function definition for ‘integrate’
pgfIhypergeometric: no visible global function definition for ‘uniroot’
pgfIhyperpoisson: no visible global function definition for ‘uniroot’
pgfIkattitypeh1: no visible global function definition for ‘uniroot’
pgfIkattitypeh2: no visible global function definition for ‘uniroot’
pgfIneymantypeb: no visible global function definition for ‘uniroot’
pgfIneymantypec: no visible global function definition for ‘uniroot’
pgfIpoissonlindley: no visible global function definition for ‘uniroot’
pgfIthomas: no visible global function definition for ‘uniroot’
pgfIwaring: no visible global function definition for ‘uniroot’
pgfIyule: no visible global function definition for ‘uniroot’
rCompound: no visible global function definition for ‘runif’
Undefined global functions or variables:
  integrate runif uniroot
Consider adding
  importFrom("stats", "integrate", "runif", "uniroot")
to your NAMESPACE file.
Packages required but not available: 'janitor', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dgamma dlnorm
Consider adding
  importFrom("stats", "approx", "dgamma", "dlnorm")
to your NAMESPACE file.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/ConConPiWiFun.h
  inst/include/convex_function_manip.hpp
  inst/include/convex_functions_tools.hpp
  inst/include/cplfunction.hpp
  inst/include/cplfunctionvec.hpp
  inst/include/cpqfunction.hpp
  inst/include/cpqfunctionvec.hpp
Some Unix compilers require LF line endings.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
prepare_Rd: concor.Rd:4: Dropping empty section \keyword
prepare_Rd: concor.Rd:5: Dropping empty section \keyword
prepare_Rd: concorcano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorcano.Rd:5: Dropping empty section \keyword
prepare_Rd: concoreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concoreg.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgm.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgm.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgmcano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgmcano.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgmreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgmreg.Rd:5: Dropping empty section \keyword
prepare_Rd: concors.Rd:4: Dropping empty section \keyword
prepare_Rd: concors.Rd:5: Dropping empty section \keyword
prepare_Rd: concorscano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorscano.Rd:5: Dropping empty section \keyword
prepare_Rd: concorsreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concorsreg.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbip.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbip.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbip2.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbip2.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbips.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbips.Rd:5: Dropping empty section \keyword
prepare_Rd: svdcp.Rd:4: Dropping empty section \keyword
prepare_Rd: svdcp.Rd:5: Dropping empty section \keyword
Packages required but not available: 'survminer', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
K1.norm: no visible global function definition for ‘dnorm’
K1.norm: no visible global function definition for ‘pnorm’
K1.t3: no visible global function definition for ‘pt’
K2.norm: no visible global function definition for ‘dnorm’
K2.norm: no visible global function definition for ‘pnorm’
K2.t3: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dnorm pnorm pt
Consider adding
  importFrom("stats", "dnorm", "pnorm", "pt")
to your NAMESPACE file.
Package required but not available: ‘rminer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
ml_solver: no visible global function definition for ‘approx’
select_kmax: no visible global function definition for ‘median’
Undefined global functions or variables:
  approx median
Consider adding
  importFrom("stats", "approx", "median")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
conicPlot: no visible global function definition for ‘palette’
conicPlotAsymptotes: no visible global function definition for
  ‘palette’
conicPlotAsymptotes: no visible global function definition for ‘abline’
conicPlotAxes: no visible global function definition for ‘palette’
conicPlotAxes: no visible global function definition for ‘abline’
plotDegenerateConic: no visible global function definition for ‘points’
plotDegenerateConic: no visible global function definition for ‘abline’
plotEllipsis: no visible global function definition for ‘lines’
plotEllipsis: no visible global function definition for ‘points’
plotHyperbola: no visible global function definition for ‘lines’
plotHyperbola: no visible global function definition for ‘points’
plotParabola: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline lines palette points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "points")
to your NAMESPACE file.
Package required but not available: ‘miceadds’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘parallel’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Rmpi’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
ConjointChecks: no visible global function definition for ‘makeCluster’
ConjointChecks: no visible global function definition for
  ‘clusterSetRNGStream’
ConjointChecks: no visible global function definition for
  ‘clusterApply’
ConjointChecks: no visible global function definition for ‘stopCluster’
omni.check: no visible global function definition for ‘runif’
omni.check: no visible global function definition for ‘quantile’
plot.checks: no visible global function definition for ‘mtext’
plot.checks: no visible global function definition for ‘text’
Undefined global functions or variables:
  clusterApply clusterSetRNGStream makeCluster mtext quantile runif
  stopCluster text
Consider adding
  importFrom("graphics", "mtext", "text")
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
Packages required but not available: 'broom', 'ggfortify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tidyr', 'geepack'
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(contrast)
  > 
  > test_check("contrast")
  ── 1. Error: (unknown) (@test-geese.R#5)  ──────────────────────────────────────
  there is no package called 'geepack'
  Backtrace:
   1. base::library(geepack)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-geese.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘contrast.Rmd’ using rmarkdown
Quitting from lines 12-26 (contrast.Rmd) 
Error: processing vignette 'contrast.Rmd' failed with diagnostics:
there is no package called 'geepack'
--- failed re-building ‘contrast.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'eurostat', 'tidyr', 'broom', 'ggpubr'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘cooccurNetwork’ ‘memory.limits’
maCooperative: no visible global function definition for ‘points’
maCooperative: no visible global function definition for ‘legend’
maPessimistic: no visible global function definition for ‘combn’
maRules: no visible global function definition for ‘capture.output’
mstCooperative: no visible global function definition for ‘points’
mstCooperative: no visible global function definition for ‘legend’
mstOptimistic: no visible global function definition for ‘combn’
mstPessimistic: no visible global function definition for ‘combn’
mstRules: no visible global function definition for ‘capture.output’
plotCoreSet: no visible global function definition for ‘points’
plotCoreSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘par’
plotImputationSet: no visible global function definition for ‘box’
plotImputationSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘text’
shapleyValue: no visible global function definition for ‘combn’
Undefined global functions or variables:
  box capture.output combn legend par points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "points", "polygon",
             "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
Package required but not available: ‘smacof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'flexsurv', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cec2005benchmark’
advanceRNG: no visible global function definition for ‘runif’
randomEventMoves: no visible global function definition for ‘runif’
randomRescaledEventMoves: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
coreTDT_geneset: no visible global function definition for
  ‘write.table’
pvalue_calculator: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom write.table
Consider adding
  importFrom("stats", "dbinom")
  importFrom("utils", "write.table")
to your NAMESPACE file.
compute.llh: no visible global function definition for ‘dnorm’
compute.u.hat.simple: no visible global function definition for ‘dnorm’
fit.CLM.1u.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start.NA: no visible global function definition for
  ‘kmeans’
Undefined global functions or variables:
  dnorm kmeans
Consider adding
  importFrom("stats", "dnorm", "kmeans")
to your NAMESPACE file.
Package suggested but not available for checking: ‘plotly’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geepack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'recipes', 'plotly', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
Package suggested but not available for checking: ‘sparklyr’
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
corr.Qmatrix: no visible global function definition for ‘cor’
corr.Qmatrix: no visible global function definition for ‘cor.test’
summarise.Fst: no visible global function definition for ‘cor’
summarise.Fst: no visible global function definition for ‘sd’
summarise.lnPD: no visible global function definition for ‘sd’
Undefined global functions or variables:
  cor cor.test sd
Consider adding
  importFrom("stats", "cor", "cor.test", "sd")
to your NAMESPACE file.
Rd file 'corr.Qmatrix.Rd':
  \usage lines wider than 90 characters:
     corr.Qmatrix(filepath = "./", instruct = FALSE, rowncol = TRUE, avmax = TRUE, pvalue = FALSE, raw = TRUE, r = 0.99, p = 0.05)

Rd file 'rowncolMatrix-method.Rd':
  \examples lines wider than 100 characters:
     test <- rowncolMatrix(K = 3, filtermatrix = table(matrix(c("Y","Y","Y",NA,"Y","Y",NA,NA,"Y"),ncol = 3, byrow = TRUE)))

These lines will be truncated in the PDF manual.
dist: no visible global function definition for ‘quantile’
edgecount: no visible global function definition for ‘reshape’
edgecutoff: no visible global function definition for ‘boxplot’
edgecutoff: no visible global function definition for ‘sd’
edgecutoff: no visible global function definition for ‘median’
edgecutoff: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR boxplot median quantile reshape sd
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "IQR", "median", "quantile", "reshape", "sd")
to your NAMESPACE file.
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
GA_search : subset_score: no visible global function definition for
  ‘combn’
choose_lambda : subset_score: no visible global function definition for
  ‘combn’
cond.fyx: no visible global function definition for ‘var’
cond.fyx: no visible global function definition for ‘cor’
diff_gen_PPI: no visible global function definition for ‘cov’
diff_gen_PPI: no visible global function definition for ‘sd’
f.test: no visible binding for global variable ‘var’
get_quantiles : node_edge: no visible global function definition for
  ‘combn’
score_scaling: no visible global function definition for ‘hist’
score_scaling: no visible global function definition for ‘sd’
Undefined global functions or variables:
  combn cor cov hist sd var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "cov", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
cosinor.lm: no visible binding for global variable ‘na.omit’
cosinor.lm: no visible global function definition for ‘terms’
cosinor.lm: no visible global function definition for ‘as.formula’
cosinor.lm: no visible global function definition for ‘lm’
cosinor_analyzer: no visible binding for global variable ‘vitamind’
cosinor_analyzer : <anonymous>: no visible global function definition
  for ‘as.formula’
ggplot.cosinor.lm: no visible global function definition for ‘predict’
predict.cosinor.lm: no visible global function definition for ‘fitted’
predict.cosinor.lm: no visible global function definition for ‘predict’
simulate_cosinor: no visible global function definition for ‘runif’
simulate_cosinor: no visible global function definition for ‘rbinom’
simulate_cosinor: no visible global function definition for ‘rnorm’
summary.cosinor.lm: no visible global function definition for ‘vcov’
summary.cosinor.lm: no visible global function definition for ‘qnorm’
summary.cosinor.lm: no visible global function definition for ‘pnorm’
test_cosinor: no visible global function definition for ‘pchisq’
test_cosinor: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm
  runif terms vcov vitamind
Consider adding
  importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif",
             "terms", "vcov")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
D.M: no visible global function definition for ‘integrate’
lookbackTime: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Rd file 'mass.CO.Rd':
  \usage lines wider than 90 characters:
     mass.CO(intInt, z, alpha = 0.8, f.rest = 115.27, omega.m = 0.27, omega.lambda = 0.73, H.0 = 71)

These lines will be truncated in the PDF manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rglpk’ ‘glmnet’ ‘parallel’ ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: ‘colordistance’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘hurricaneexposure’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘choroplethr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘countytimezones.Rmd’ using rmarkdown
Quitting from lines 111-123 (countytimezones.Rmd) 
Error: processing vignette 'countytimezones.Rmd' failed with diagnostics:
there is no package called 'choroplethr'
--- failed re-building ‘countytimezones.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggmap', 'rnoaa', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qgraph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘CovCombR.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 66-68 (CovCombR.rmd) 
Error: processing vignette 'CovCombR.rmd' failed with diagnostics:
there is no package called 'qgraph'
--- failed re-building ‘CovCombR.rmd’

SUMMARY: processing the following file failed:
  ‘CovCombR.rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘covfefe_inauguration.txt’
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'janitor', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'wbstats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘mlogit’ ‘poLCA’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Matrix’ ‘mlogit’ ‘poLCA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
covLCA: no visible global function definition for ‘model.response’
covLCA: no visible global function definition for ‘model.frame’
covLCA: no visible global function definition for ‘model.matrix’
covLCA: no visible global function definition for ‘rnorm’
covLCA: no visible global function definition for ‘flush.console’
covLCA: no visible global function definition for ‘ginv’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘as.formula’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘mlogit.data’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘mlogit’
covLCA.initialBeta: no visible global function definition for
  ‘as.formula’
covLCA.initialBeta: no visible global function definition for ‘poLCA’
covLCA.initialBeta: no visible global function definition for
  ‘mlogit.data’
covLCA.initialBeta: no visible global function definition for ‘mlogit’
covLCA.paramVariance: no visible global function definition for ‘ginv’
covLCA.varianceFirst: no visible global function definition for ‘bdiag’
Undefined global functions or variables:
  as.formula bdiag flush.console ginv mlogit mlogit.data model.frame
  model.matrix model.response poLCA rnorm
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response", "rnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
covreg.mcmc: no visible global function definition for ‘model.frame’
covreg.mcmc: no visible global function definition for ‘model.matrix’
covreg.mcmc: no visible global function definition for ‘model.response’
covreg.mcmc: no visible global function definition for ‘lm’
covreg.mcmc: no visible global function definition for ‘rnorm’
covreg.mcmc: no visible global function definition for ‘cov’
rmn: no visible global function definition for ‘rnorm’
rwish: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cov lm model.frame model.matrix model.response rnorm
Consider adding
  importFrom("stats", "cov", "lm", "model.frame", "model.matrix",
             "model.response", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘tidyr’
Running examples in ‘cowplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: axis_canvas
> ### Title: Generates a canvas onto which one can draw axis-like objects.
> ### Aliases: axis_canvas
> 
> ### ** Examples
> 
> # annotate line graphs with labels on the right
> 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(tidyr)
Error in library(tidyr) : there is no package called ‘tidyr’
Execution halted
Package suggested but not available for checking: ‘multicolor’
Error(s) in re-building vignettes:
  ...
--- re-building ‘cowsay_tutorial.Rmd’ using rmarkdown
Quitting from lines 111-113 (cowsay_tutorial.Rmd) 
Error: processing vignette 'cowsay_tutorial.Rmd' failed with diagnostics:
there is no package called 'multicolor'
--- failed re-building ‘cowsay_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘changeLog’
'library' or 'require' calls in package code:
  ‘parallel’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘prodlim’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CoxBoost: no visible global function definition for ‘Matrix’
CoxBoost: no visible binding for global variable ‘sd’
CoxBoost: no visible global function definition for ‘predict’
cv.CoxBoost : eval.fold: no visible global function definition for
  ‘predict’
cv.CoxBoost: no visible global function definition for ‘mclapply’
cv.CoxBoost: no visible binding for global variable ‘sd’
estimPVal: no visible global function definition for ‘mclapply’
iCoxBoost: no visible global function definition for ‘terms’
iCoxBoost: no visible global function definition for ‘model.response’
iCoxBoost: no visible global function definition for ‘model.frame’
iCoxBoost: no visible global function definition for ‘model.matrix’
iCoxBoost: no visible global function definition for ‘Matrix’
plot.CoxBoost: no visible global function definition for ‘lines’
plot.CoxBoost: no visible global function definition for ‘text’
predict.iCoxBoost: no visible global function definition for
  ‘model.response’
predict.iCoxBoost: no visible global function definition for
  ‘model.frame’
predict.iCoxBoost: no visible global function definition for
  ‘model.matrix’
Undefined global functions or variables:
  Matrix lines mclapply model.frame model.matrix model.response predict
  sd terms text
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "predict", "sd", "terms")
to your NAMESPACE file.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
GNU make is a SystemRequirements.
comp.graph: no visible global function definition for ‘qnorm’
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 polygon qnorm terms
Consider adding
  importFrom("graphics", "lines", "polygon")
  importFrom("stats", "hat", "model.extract", "model.matrix", "qnorm",
             "terms")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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 ‘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 pnorm
  points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
Package required but not available: ‘MESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Found the following files/directories:
  ‘rs1234.pdf’
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘geepack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘geepack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
distance.comoving: no visible global function definition for
  ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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.
Packages suggested but not available for checking: 'tidyr', 'broom'
Malformed Description field: should contain one or more complete sentences.
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.
Package suggested but not available for checking: ‘clusterProfiler’
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Package suggested but not available for checking: ‘ggmcmc’
Package vignette with placeholder title ‘Vignette Title’:
  ‘guidelines.Rmd’
'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.
Rd file 'downloadCRN.Rd':
  \usage lines wider than 90 characters:
     downloadCRN(url = CRN.DAILY.URL, directory = DAILY_DIR, years = seq(from = 2000, to = 2011, by = 1))

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
get.plan: no visible global function definition for ‘menu’
Undefined global functions or variables:
  menu
Consider adding
  importFrom("utils", "menu")
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.
crossmatchtest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Rd file 'crossmatch-package.Rd':
  \examples lines wider than 100 characters:
                  c(0.03,0.11,0.16,-0.1,-0.05,0.16,0.12,0.4,0.04,0.71,0.01,0.21,-0.18,-0.08             ,-0.35,0.26,-0.6,-1.0))

Rd file 'crossmatchtest.Rd':
  \examples lines wider than 100 characters:
                  c(0.03,0.11,0.16,-0.1,-0.05,0.16,0.12,0.4,0.04,0.71,0.01,0.21,-0.18,-0.08             ,-0.35,0.26,-0.6,-1.0))

These lines will be truncated in the PDF manual.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘vignettecrossrun.Rmd’
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.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘adabag’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survminer', 'miceadds'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tidyr', 'plotly'
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 ‘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 quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
Found the following files/directories:
  ‘Example File.pdf’
Malformed Title field: should not end in a period.
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.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘Hello.csv’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘caret’
Error(s) in re-building vignettes:
  ...
--- re-building ‘cubist.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 12-20 (cubist.Rmd) 
Error: processing vignette 'cubist.Rmd' failed with diagnostics:
there is no package called 'caret'
--- 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.
Malformed Title field: should not end in a period.
License components which are templates and need '+ file LICENSE':
  MIT
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 ‘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 ‘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 ‘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 ‘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 quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Package required but not available: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
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.
Malformed Description field: should contain one or more complete sentences.
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.
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘how_to_test_CVs.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 171-182 (how_to_test_CVs.Rmd) 
Error: processing vignette 'how_to_test_CVs.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- 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
Package suggested but not available for checking: ‘geepack’
Running examples in ‘cvGEE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv_gee
> ### Title: Proper Scoring Rules for Generalized Estimating Equations
> ### Aliases: cv_gee
> 
> ### ** Examples
> 
> library("geepack")
Error in library("geepack") : there is no package called ‘geepack’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Scoring_Rules_GEE.Rmd’ using rmarkdown
Quitting from lines 15-23 (Scoring_Rules_GEE.Rmd) 
Error: processing vignette 'Scoring_Rules_GEE.Rmd' failed with diagnostics:
there is no package called 'geepack'
--- failed re-building ‘Scoring_Rules_GEE.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'broom', 'recipes', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some ‘make’ programs ignore lines not ending in LF.
Packages suggested but not available for checking: 'gurobi', 'rcbc'
Found the following files/directories:
  ‘tex.table.tex’
.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.
Malformed Description field: should contain one or more complete sentences.
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 suggested but not available for checking: ‘tidyr’
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.
Malformed Description field: should contain one or more complete sentences.
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.
Rd file 'cytoDiv.Rd':
  \usage lines wider than 90 characters:
     cytoDiv(df, x.var="fsc_small", y.var="chl_small", Ncat = 16, Nbit = 16, do.plot=FALSE, ...)
  \examples lines wider than 100 characters:
     rainbow.cols <- colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow","#FF7F00", "red", "#7F0000"))
     plot(cleaned.df[,2], cleaned.df[,3], col= densCols(cleaned.df[,2], cleaned.df[,3], colramp = rainbow.cols))

These lines will be truncated in the PDF manual.
Packages required but not available: 'caret', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘GRCh38_browser’ ‘GRCh38_map’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘d3r’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
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.
Rd file 'intPlot.Rd':
  \usage lines wider than 90 characters:
      intPlot(y, fac1 = NULL, fac2 = NULL, xlab = NULL, xlab2 = NULL, ylab = NULL, data.order=TRUE, exlim=0.1, jitter=0.02, conf.level=0.95, ... [TRUNCATED]
      intPlot(y, data, xlab = NULL, xlab2 = NULL, ylab = NULL, data.order = TRUE, exlim=0.1, jitter=0.02, conf.level=0.95, interval.type="tu ... [TRUNCATED]

These lines will be truncated in the PDF manual.
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 ‘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 points
  rbinom rnorm text
Consider adding
  importFrom("graphics", "arrows", "identify", "locator", "points",
             "text")
  importFrom("stats", "na.omit", "rbinom", "rnorm")
  importFrom("utils", "combn", "installed.packages")
to your NAMESPACE file.
Package required but not available: ‘ggmcmc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘janitor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'xesreadR', 'bupaR', 'edeaR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
drawAimSpot: no visible global function definition for ‘points’
drawBoard: no visible global function definition for ‘par’
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 points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "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.
Packages suggested but not available for checking: 'dash', 'plotly'
Package suggested but not available for checking: ‘dash’
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dash’
Package suggested but not available for checking: ‘ProjectionBasedClustering’
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’
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 read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Package has no Sweave vignette sources and no VignetteBuilder field.
Package vignette with placeholder title ‘Vignette Title’:
  ‘datadigest.Rmd’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following assignments to the global environment:
File ‘DataEntry/R/Export.R’:
  assign(svalue(edObnm), d, envir = .GlobalEnv)
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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’.
Found the following files/directories:
  ‘my new data set.rds’
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  MIT
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.
Package suggested but not available for checking: ‘doBy’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘DiagrammeR’
Running examples in ‘data.tree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.Node
> ### Title: Plot a graph, or get a graphviz dot representation of the tree
> ### Aliases: plot.Node ToDiagrammeRGraph SetNodeStyle SetEdgeStyle
> ###   SetGraphStyle GetDefaultTooltip
> 
> ### ** Examples
> 
> data(acme)
> SetGraphStyle(acme, rankdir = "TB")
> SetEdgeStyle(acme, arrowhead = "vee", color = "blue", penwidth = 2)
> #per default, Node style attributes will be inherited:
> SetNodeStyle(acme, style = "filled,rounded", shape = "box", fillcolor = "GreenYellow", 
+              fontname = "helvetica", tooltip = GetDefaultTooltip)
> SetNodeStyle(acme$IT, fillcolor = "LightBlue", penwidth = "5px")
> #inheritance can be avoided:
> SetNodeStyle(acme$Accounting, inherit = FALSE, fillcolor = "Thistle", 
+              fontcolor = "Firebrick", tooltip = "This is the accounting department")
> SetEdgeStyle(acme$Research$`New Labs`, 
+              color = "red", 
+              label = "Focus!", 
+              penwidth = 3, 
+              fontcolor = "red")
> #use Do to set style on specific nodes:
> Do(acme$leaves, function(node) SetNodeStyle(node, shape = "egg"))
> plot(acme)
Error in plot.Node(acme) : 
  Package "DiagrammeR" is required to plot a `data.tree::Node`object. Please install it.
Calls: plot -> plot.Node
Execution halted
Packages suggested but not available for checking:
  'ggmap', 'choroplethr', 'plotly'
Running examples in ‘DataVisualizations-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Classplot
> ### Title: Classplot
> ### Aliases: Classplot
> ### Keywords: Classplot dotplot
> 
> ### ** Examples
> 
> data(Lsun3D)
> Classplot(Lsun3D$Data[,1],Lsun3D$Data[,2],Lsun3D$Cls)
Error in loadNamespace(name) : there is no package called ‘plotly’
Calls: Classplot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
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.
Malformed Description field: should contain one or more complete sentences.
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.
Malformed Title field: should not end in a period.
'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.
Rd file 'distable.Rd':
  \examples lines wider than 100 characters:
     ##before using "b1.txt" data, we need to find "b1.txt" in the data file and  put it in the work space of R

Rd file 'functionall.Rd':
  \examples lines wider than 100 characters:
     ##before running this funtion, we need to find out "b1.txt" data file, and put it into the R workspace.
     functionall(system.file("data","b1.txt",package="DBGSA"),10,avelinkdis,"euclidean","distance",afExp,2000,10,"rand.txt","pvalue.txt")

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘tidyr’
Packages required but not available: 'skimr', 'visdat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘LFC.d.jpeg’ ‘LFC.s.jpeg’ ‘TF_bridged_DCL.pdf’
  ‘TF_bridged_DCL_int.pdf’
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.
Package suggested but not available for checking: ‘INLA’
Packages required but not available: 'janitor', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  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).
test.LM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
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++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  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).
Packages required but not available: 'ggalt', 'MEGENA'

Package suggested but not available for checking: ‘ggfortify’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GEOquery’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ifft: no visible global function definition for ‘fft’
lines.deamer: no visible global function definition for ‘lines’
rlaplace: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fft lines runif
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
Packages required but not available: 'tidyr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 ‘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 pnorm qchisq sd vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
Packages required but not available: 'tidyr', 'DiagrammeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘broom’
Running ‘testthat.R’ [62s/92s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DeclareDesign)
  Loading required package: randomizr
  Loading required package: fabricatr
  Loading required package: estimatr
  > 
  > test_check("DeclareDesign")
  ── 1. Error: (unknown) (@test-model.R#199)  ────────────────────────────────────
  there is no package called 'broom'
  Backtrace:
   1. base::library(broom)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 485 | SKIPPED: 5 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-model.R#199) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘decoder.Rmd’ using rmarkdown
--- finished re-building ‘decoder.Rmd’

--- re-building ‘sjukhus.Rmd’ using rmarkdown
Quitting from lines 78-90 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘sjukhus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package vignette with placeholder title ‘Vignette Title’:
  ‘decomposedPSF-vignette.Rmd’
Package suggested but not available for checking: ‘tidyverse’
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.
Depends: includes the non-default packages:
  'Deducer', 'psych', 'GPArotation', 'mvnormtest', 'irr', 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'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').
Depends: includes the non-default packages:
  'JavaGD', 'Deducer', 'sp', 'maptools', 'OpenStreetMap', 'scales',
  'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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.
Rd file 'loadCensusData.Rd':
  \usage lines wider than 90 characters:
                     year=c("2010","2000"), verbose=TRUE, osmTransform=TRUE, envir = .GlobalEnv)

Rd file 'spatialTextPlot.Rd':
  \examples lines wider than 100 characters:
     plot.window(c(-1.3160249151515616E7,-1.3155204307648793E7),c(3992993.9205893227,3996691.5618326175), xaxs = 'i', yaxs = 'i')
     plot(openmap(c(33.760525217369974,-118.22052955627441),c(33.73290566922855,-118.17521095275879),14,'bing'),add=TRUE)

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
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.
Malformed Description field: should contain one or more complete sentences.
.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').
Package suggested but not available for checking: ‘caret’
Package required but not available: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Malformed Description field: should contain one or more complete sentences.
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.
Package suggested but not available for checking: ‘DiagrammeR’
Package required but not available: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
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 ‘lines’
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 points polygon rnorm runif var
Consider adding
  importFrom("graphics", "lines", "points", "polygon")
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘smd_table.docx’
Packages suggested but not available for checking: 'heatmaply', 'd3heatmap'
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
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.
Package suggested but not available for checking: ‘gapmap’
Package suggested but not available for checking: ‘missMDA’
Packages required but not available: 'broom', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
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 ‘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 polygon runif
  wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "legend", "lines", "matlines", "matplot", "par",
             "polygon")
  importFrom("stats", "runif", "wilcox.test")
to your NAMESPACE file.
Skipping vignette re-building
Package suggested but not available for checking: ‘tidyr’

VignetteBuilder package required for checking but not installed: ‘tidyr’
Errors in running code in vignettes:
when running code in ‘derivmkts-vignette.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘tidyr’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘derivmkts-vignette.Rmd’ using ‘UTF-8’... failed to complete the test
Packages required but not available: 'tidyr', 'broom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘x.R’ ‘x.sps’ ‘x.txt’
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.
Rd file 'ds.Rd':
  \usage lines wider than 90 characters:
     ds(z, Fm = 6, Fs = 6, type = c("daily", "monthly"), searchQ=TRUE, lag.max=20, ic=c("BIC","AIC"), standardizeQ=TRUE)

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
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 ‘text’
plotAllScores: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘myDesignGGSAplot.png’ ‘myDesignGG_arrayDesign.csv’
  ‘myDesignGG_conditionDesign.csv’
Package which this enhances but not available for checking: ‘gurobi’
Malformed Description field: should contain one or more complete sentences.
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 ‘points’
plot.FIT: no visible global function definition for ‘abline’
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 points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "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').
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’
Rd file 'EPS.value.Rd':
  \examples lines wider than 100 characters:
     co021.subset<-co021.subset[,-c(28,30,31)] ## to remove the following series "645232","646107" and "646118"

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘data’
Package suggested but not available for checking: ‘tidyr’
GNU make is a SystemRequirements.
Packages required but not available: 'dexter', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dexter', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MVN’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
makeAdjMatrix: no visible global function definition for ‘combn’
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 ‘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 ‘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 points runif text title
Consider adding
  importFrom("graphics", "legend", "lines", "points", "text", "title")
  importFrom("stats", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: ‘MEGENA’
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++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  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).
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.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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').
Found the following files/directories:
  ‘module_list.txt’ ‘res.txt’
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.
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ShinyItemAnalysis’
Running examples in ‘difNLR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: difORD
> ### Title: DIF detection among ordinal data.
> ### Aliases: difORD
> ### Keywords: DIF
> 
> ### ** Examples
> 
> # Loading data
> data(dataMedicalgraded, package = "ShinyItemAnalysis")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘ShinyItemAnalysis’
Calls: data -> find.package
Execution halted
Package required but not available: ‘TestDataImputation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
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.
Package suggested but not available for checking: ‘bibliometrix’
Package suggested but not available for checking: ‘tidyr’
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))
2020-08-11 20:05:45: Isomap START
2020-08-11 20:05:45: constructing knn graph
2020-08-11 20:05:45: calculating geodesic distances
2020-08-11 20:05:45: 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 chckpkg("tidyr") : 
  require 'tidyr' package, install it using install.packages('tidyr')
Calls: plot_R_NX -> chckpkg
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 ‘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 runif title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "title")
  importFrom("stats", "approx", "complete.cases", "ecdf", "runif")
to your NAMESPACE file.
Output for data("exHartigan", package = "diptest"):
  'exHartigan' data is identical to 'statfaculty' and hence deprecated.
   Use the 'statfaculty' instead
Package suggested but not available for checking: ‘tidyr’
Malformed Title field: should not end in a period.
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.
Package suggested but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
rdisclap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘factoextra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Malformed Title field: should not end in a period.
value: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘parsnip’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Running examples in ‘discSurv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aucUno
> ### Title: Area under the Curve Estimation
> ### Aliases: aucUno
> ### Keywords: survival
> 
> ### ** Examples
> 
> #####################################################
> # Example with cross validation and unemployment data 
> 
> library(Ecdat)
Loading required package: Ecfun

Attaching package: ‘Ecfun’

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

    sign


Attaching package: ‘Ecdat’

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

    Orange

> library(caret)
Error in library(caret) : there is no package called ‘caret’
Execution halted
Package which this enhances but not available for checking: ‘INLA’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘broom’
Running examples in ‘disk.frame-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dfglm
> ### Title: Fit generalized linear models (glm) with disk.frame
> ### Aliases: dfglm
> 
> ### ** Examples
> 
> cars.df = as.disk.frame(cars)
> m = dfglm(dist ~ speed, data = cars.df)
Loading required namespace: biglm
> 
> # can use normal R functions
> # Only works in version > R 3.6
> majorv = as.integer(version$major)
> minorv = as.integer(strsplit(version$minor, ".", fixed=TRUE)[[1]][1])
> if(((majorv == 3) & (minorv >= 6)) | (majorv > 3)) {
+   summary(m)
+   predict(m, get_chunk(cars.df, 1))
+   predict(m, collect(cars.df))
+   # can use broom to tidy up the returned info
+   broom::tidy(m)
+ }
Error in loadNamespace(name) : there is no package called ‘broom’
Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Rd file 'dualFlashlight.fn.Rd':
  \usage lines wider than 90 characters:
     dualFlashlight.fn(result.df, wellName = "WELL_USAGE", x.name = "mean", y.name = "ssmd", sampleName = "Sample", sampleColor = "black", c ... [TRUNCATED]

Rd file 'imageDesign.fn.Rd':
  \usage lines wider than 90 characters:
     imageDesign.fn(dataOnePlate.df, wellName = NA, rowName, colName, wells = NULL, colors = NULL, title = " ")

Rd file 'imageIntensity.fn.Rd':
  \usage lines wider than 90 characters:
     imageIntensity.fn(data.df, intensityName = NA, plateName = "BARCODE", wellName = "WELL_USAGE", rowName, colName, sampleName = "Sample", ... [TRUNCATED]

Rd file 'plateWellSeries.fn.Rd':
  \usage lines wider than 90 characters:
     plateWellSeries.fn(data.df, intensityName = NA, plateName = "BARCODE", wellName = "WELL_USAGE", rowName, colName, show.wellTypes = NULL ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package suggested but not available for checking: ‘DiagrammeR’
Packages required but not available: 'tidyr', 'factoextra', 'broom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Running ‘testthat.R’ [219s/305s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(distr6)
  
  -----------------------------
  	distr6 v 1.4.2
  
  Get started:	?distr6
  Changelog:	distr6News()
  -----------------------------
  
  
  Attaching package: 'distr6'
  
  The following object is masked from 'package:stats':
  
      qqplot
  
  The following object is masked from 'package:grDevices':
  
      pdf
  
  The following objects are masked from 'package:base':
  
      mode, truncate
  
  > 
  > test_check("distr6")
  ── 1. Error: multivariate (@test-plot.R#84)  ───────────────────────────────────
  there is no package called 'plotly'
  Backtrace:
    1. testthat::expect_silent(plot(dist, fun = "pdf", npoints = 10))
   10. distr6:::plot.Distribution(dist, fun = "pdf", npoints = 10)
   11. distr6:::.plot_multivariate(x, fun, npoints)
   12. plotly::add_surface
   13. base::getExportedValue(pkg, name)
   14. base::asNamespace(ns)
   15. base::getNamespace(ns)
   16. base::loadNamespace(name)
   17. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   18. base:::withOneRestart(expr, restarts[[1L]])
   19. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3938 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: multivariate (@test-plot.R#84) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggdist’
Package suggested but not available for checking: ‘tidyverse’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘csim’ ‘xyz’ ‘xyz.sav’ ‘xyz.sav.comment’
Found the following files/directories:
  ‘csim.mean’ ‘csim.mean.comment’
Malformed Title field: should not end in a period.
prepare_Rd: extract.val.Rd:25-26: Dropping empty section \note
prepare_Rd: extract.val.Rd:27: Dropping empty section \seealso
Package suggested but not available for checking: ‘entropart’
Package required but not available: ‘qgraph’

Package suggested but not available for checking: ‘HWxtest’

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.
Found the following files/directories:
  ‘new_model.rda’
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.
Rd file 'dlcross.Rd':
  \usage lines wider than 90 characters:
     dlcross(format = c("rqtl", "dlmap", "other"), genobj, pheobj, mapobj, idname="ID", genfile, phefile, mapfile, type, step=0, fixpos=0, e ... [TRUNCATED]

Rd file 'dlmap-internal.Rd':
  \usage lines wider than 90 characters:
     dlcross.dlmap(genobj, pheobj, mapobj, idname, genfile, mapfile, phefile, type, step, fixpos, estmap, ...)
     calc.genoprob2(cross, pos, error.prob=1e-04, map.function=c("haldane", "kosambi", "c-f", "morgan"))

Rd file 'dlmap.Rd':
  \usage lines wider than 90 characters:
     plot(x, chr, max.dist, qcol="light blue", mcol="red", pcol="purple", marker.names=FALSE, ...)

These lines will be truncated in the PDF manual.
Packages suggested but not available for checking: 'broom', 'tidyr'
Package suggested but not available for checking: ‘geepack’
Packages required but not available: 'mice', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘dlstats.Rmd’ using rmarkdown
Quitting from lines 31-34 (dlstats.Rmd) 
Error: processing vignette 'dlstats.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘dlstats.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rPython’
Package required but not available: ‘tidyr’

Packages suggested but not available for checking:
  'DiagrammeR', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
GNU make is a SystemRequirements.
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.
Package suggested but not available for checking: ‘OutliersO3’
Error(s) in re-building vignettes:
  ...
--- re-building ‘dobin.Rmd’ using rmarkdown
Quitting from lines 22-34 (dobin.Rmd) 
Error: processing vignette 'dobin.Rmd' failed with diagnostics:
Package OutliersO3 is needed for the vignette. Please install it.
--- failed re-building ‘dobin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘broom’

Package suggested but not available for checking: ‘geepack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'textstem', 'textclean'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘documenter.Rmd’
Found the following files/directories:
  ‘annotation_file.yml’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidygraph’
GNU make is a SystemRequirements.
Running examples in ‘dodgr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dodgr_to_tidygraph
> ### Title: dodgr_to_tidygraph
> ### Aliases: dodgr_to_tidygraph
> 
> ### ** Examples
> 
> graph <- weight_streetnet (hampi)
> grapht <- dodgr_to_tidygraph (graph)
Loading required namespace: tidygraph
Failed with error:  ‘there is no package called ‘tidygraph’’
Error in loadNamespace(name) : there is no package called ‘tidygraph’
Calls: dodgr_to_tidygraph ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package which this enhances but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘caret’
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘caret’
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').
Package vignette with placeholder title ‘Vignette Title’:
  ‘dotdot.Rmd’
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Package required but not available: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Rd file 'dpa.generate.lag.Rd':
  \usage lines wider than 90 characters:
     dpa.generate.lag(dataframe = NULL, tickColumn = NULL, sourceColumn = NULL, minLag=1,maxLag=1)

Rd file 'dpa.relations.addRelations.Rd':
  \usage lines wider than 90 characters:
     dpa.relations.addRelations(From_column = NULL, To_column = NULL, Lag_in = NULL, minLag = NULL, maxLag = NULL, Direction = NULL)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘ansic_gram.c’
Packages required but not available: 'tidyverse', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘broom’
Packages required but not available: 'tidyr', 'broom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggraph’
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
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').
Found the following files/directories:
  ‘output_sample.uni.sample.undir.weight.type.50.1e-04.0.7.base’
  ‘output_sample.uni.sample.undir.weight.type.50.1e-04.1.1.0.7.sample.setlist.stats’
Package suggested but not available for checking: ‘DiagrammeR’
GNU make is a SystemRequirements.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SmartML.Rmd’ using rmarkdown
Quitting from lines 20-26 (SmartML.Rmd) 
Error: processing vignette 'SmartML.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘SmartML.Rmd’

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

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.
Package required but not available: ‘MESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
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.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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').
Package required but not available: ‘frailtypack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
create_frame: no visible global function definition for ‘as.integer64’
Undefined global functions or variables:
  as.integer64
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 ‘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 predict rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "lines", "par")
  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 ‘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 ‘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 predict pt var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "cor", "glm", "median", "na.omit", "p.adjust",
             "pchisq", "predict", "pt", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘tidyr’
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘vignette.Rmd’
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 points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
DTMC: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
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.
Rd file 'dummy.Rd':
  \usage lines wider than 90 characters:
     dummy.data.frame(data, names = NULL, omit.constants=TRUE, dummy.classes = getOption("dummy.classes"), all = TRUE, ...)

These lines will be truncated in the PDF manual.
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.
Malformed Description field: should contain one or more complete sentences.
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.
Packages suggested but not available for checking: 'destiny', 'smacof'
Running ‘testthat.R’ [22s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dyndimred)
  > library(dynutils)
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  > 
  > test_check("dyndimred")
  ── 1. Error: Perform dimred mds_smacof  ────────────────────────────────────────
  Please install the following packages: 
    "smacof"
  Backtrace:
   1. dyndimred:::method_fun(expr)
   2. dynutils::install_packages("smacof", "dyndimred")
  
  ── 2. Error: Perform dimred dm_destiny  ────────────────────────────────────────
  Please install the following packages: 
    "destiny"
  Backtrace:
   1. dyndimred:::method_fun(expr)
   2. dynutils::install_packages("destiny")
  
  ── 3. Error: Perform dimred mds_smacof  ────────────────────────────────────────
  Please install the following packages: 
    "smacof"
  Backtrace:
   1. dyndimred:::method_fun(small_expr)
   2. dynutils::install_packages("smacof", "dyndimred")
  
  ── 4. Error: Perform dimred dm_destiny  ────────────────────────────────────────
  Please install the following packages: 
    "destiny"
  Backtrace:
   1. dyndimred:::method_fun(small_expr)
   2. dynutils::install_packages("destiny")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 177 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 4 ]
  1. Error: Perform dimred mds_smacof 
  2. Error: Perform dimred dm_destiny 
  3. Error: Perform dimred mds_smacof 
  4. Error: Perform dimred dm_destiny 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package suggested but not available for checking: ‘TSA’
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dynparam', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyr', 'ggalluvial', 'recipes', 'caret'

Package suggested but not available for checking: ‘parcats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
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.
Malformed Title field: should not end in a period.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ebSNP: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
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++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  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).
Packages required but not available: 'd3r', 'broom'

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘ggspatial’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘factoextra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package suggested but not available for checking: ‘ggraph’
Package suggested but not available for checking: ‘ggraph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
   [[ suppressing 785 column names '0011', '0012', '0013' ... ]]
   [[ suppressing 785 column names '0011', '0012', '0013' ... ]]

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

computing product projection...
--------------------------------------------------
0 threshold...
0.05 threshold...
0.1 threshold...
0.15 threshold...
0.2 threshold...
0.25 threshold...
0.3 threshold...
0.35 threshold...
0.4 threshold...
0.45 threshold achieves the avg number of connections
computing product projection...
--------------------------------------------------
0 threshold...
0.05 threshold...
0.1 threshold...
0.15 threshold...
0.2 threshold...
0.25 threshold...
0.3 threshold...
0.35 threshold...
0.4 threshold...
0.45 threshold...
0.5 threshold...
0.55 threshold achieves the avg number of connections
Quitting from lines 122-144 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building ‘basic-usage.Rmd’

SUMMARY: processing the following file failed:
  ‘basic-usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘ecosim_example_plot1.pdf’ ‘ecosim_example_plot2.pdf’
  ‘ecosim_example_plot3.pdf’
GNU make is a SystemRequirements.
Package required but not available: ‘biomod2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
plot.ETdiagnosis: no visible global function definition for ‘par’
plot.ETdiagnosis: no visible global function definition for ‘lines’
plot.ETdiagnosis: no visible global function definition for ‘legend’
plot.ETmain: no visible global function definition for ‘par’
plot.ETmain: no visible global function definition for ‘polygon’
plot.ETmain: no visible global function definition for ‘axis’
plot.ETmain: no visible global function definition for ‘legend’
plot.ETmain: no visible global function definition for ‘lines’
plot.Transpose: no visible global function definition for ‘par’
plot.Transpose: no visible global function definition for ‘polygon’
plot.Transpose: no visible global function definition for ‘axis’
plot.Transpose: no visible global function definition for ‘legend’
plot.smooth: no visible global function definition for ‘lines’
plot_ETdiagnosis_isopleth: no visible global function definition for
  ‘par’
plot_ETdiagnosis_isopleth: no visible global function definition for
  ‘rainbow’
plot_ETdiagnosis_isopleth: no visible global function definition for
  ‘filled.contour’
regPB: no visible global function definition for ‘coef’
regPB: no visible global function definition for ‘lm’
regPB.ac: no visible global function definition for ‘coef’
regPB.ac: no visible global function definition for ‘lm’
regPB.ctsa: no visible global function definition for ‘coef’
regPB.ctsa: no visible global function definition for ‘lm’
Undefined global functions or variables:
  axis coef filled.contour legend lines lm par polygon rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "filled.contour", "legend", "lines",
             "par", "polygon")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Package required but not available: ‘smoof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Rd file 'ecoCusum.Rd':
  \examples lines wider than 100 characters:
     ## global optimization to h, H and n, when lambda = 0.01, "Nelder-Mead" optimization algorithm doesn't work

Rd file 'ecoEwma.Rd':
  \examples lines wider than 100 characters:
     #yy = ecoEwma(h = seq(.7,1,by=.01), w = seq(0.8,1,by=.01),k = seq(2.9,3.3, by = 0.01), n = 4:5, P0 = 110, P1 = 10, Cf = 50, contour.plo ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Packages required but not available: 'bupaR', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘tmplp.dat’
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').
Package required but not available: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'tidyr'

Packages suggested but not available for checking: 'broom', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Packages suggested but not available for checking: 'cdom', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘custom-import-function.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 53-92 (custom-import-function.Rmd) 
Error: processing vignette 'custom-import-function.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘custom-import-function.Rmd’

--- 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 14-21 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘custom-import-function.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘tidyr’
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

Quitting from lines 14-19 (eesim.Rmd) 
Error: processing vignette 'eesim.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘eesim.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
Malformed Title field: should not end in a period.
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Packages required but not available:
  'qgraph', 'semPlot', 'NetworkToolbox', 'plotly'

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘eggCountsExtra’
GNU make is a SystemRequirements.
Packages required but not available: 'tidygraph', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘logistf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyr’
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.
Malformed Description field: should contain one or more complete sentences.
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').
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggiraphExtra', 'tidyr'

Package suggested but not available for checking: ‘lightgbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’ ‘combined.csv’
Packages required but not available: 'tidyr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Rd file 'KM.audit.Rd':
  \usage lines wider than 90 characters:
     KM.audit(data, U, Z, alpha = 0.25, plot = FALSE, debug = FALSE, return.Ps = FALSE, truncate.Ps = TRUE)

Rd file 'make.audit.Rd':
  \usage lines wider than 90 characters:
     make.audit(Z = NULL, method = c("tweak", "opt.bad", "opt.bad.WPM", "opt.bad.packed", "opt.bad.packed.WPM", "ok", "no error"), p_d = 0.2 ... [TRUNCATED]

Rd file 'make.opt.packed.bad.Rd':
  \usage lines wider than 90 characters:
     make.opt.packed.bad(Z, max.taint = 1, max.taint.good = max.taint, WPM = FALSE, add.good = 0, add.random = FALSE)

Rd file 'simulateIt.Rd':
  \usage lines wider than 90 characters:
     simulateIt(data, M = 50, alpha = 0.25, plot = FALSE, debug = FALSE, return.Ps = FALSE, truncate.Ps = TRUE)

These lines will be truncated in the PDF manual.
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
Malformed Description field: should contain one or more complete sentences.
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').
Package suggested but not available for checking: ‘lumi’
Package required but not available: ‘sjstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'recipes', 'tidyr', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
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.
License components which are templates and need '+ file LICENSE':
  MIT
Package vignette with placeholder title ‘Vignette Title’:
  ‘example.Rmd’
Package suggested but not available for checking: ‘eixport’
Found the following files/directories:
  ‘EmiStatR_output’ ‘Temporal aggregation of precipitation P1 (res =
  120 min).pdf’
Package suggested but not available for checking: ‘rdflib’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown
Quitting from lines 129-130 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'rdflib'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building 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.
Malformed Description field: should contain one or more complete sentences.
'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
Rd file 'emme2.Rd':
  \usage lines wider than 90 characters:
          write.mf(data, numname, bank, file0, mcent, mmat, mat.dir, newname=NULL, newdesc=NULL)
  \examples lines wider than 100 characters:
          x <- matrix(rnorm(mf2), nrow(mf2), ncol(mf2)) #Random generate length(mf) numbers to write dummy data to bank
          write.mf(x, 2, "emme2/emme2ban", file0, file1$global["mcent"], file1$global["mmat"], mat.dir, newname="test", newdesc="test matrix ... [TRUNCATED]
          link.data <- read.link.data("emme2/emme2ban", 1, file0, file1$global["mscen"], file1$global["mlink"], file1$global["mnode"])
          nodes <- read.nodes("emme2/emme2ban", 1, file0, file1$global["mscen"], file1$global["mlink"], file1$global["mnode"])

These lines will be truncated in the PDF manual.
Packages which this enhances but not available for checking:
  'geepack', 'mice'
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 ‘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 predict rnorm
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines")
  importFrom("stats", "loess", "predict", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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.
Rd file 'EMT-internal.Rd':
  \usage lines wider than 90 characters:
     MonteCarloMultinomialTestChisquare(observed, prob, size, groups, numEvents, ntrial, atOnce)

Rd file 'multinomial.test.Rd':
  \usage lines wider than 90 characters:
     multinomial.test(observed, prob, useChisq = FALSE, MonteCarlo = FALSE, ntrial = 100000, atOnce = 1000000)
  \examples lines wider than 100 characters:
     observed <- c(5,2,1)            # observed data: 5 items in category one, 2 items in category two, 1 item in category three
     prob <- c(0.25, 0.5, 0.25)      # model: hypothetical probability that an item falls into category one, two, or three
     ## Test the hypothesis that all sides of a dice pop up with the same probability (a 6-dimesional problem):
     prob <- c(pdice, pdice, pdice, pdice, pdice, pdice)     # the model, determined by the hypothetical probabilities
     observed <- c(4, 5, 2, 7, 0, 1)                         # the observation consisting of 19 throws ( = sample size)

These lines will be truncated in the PDF manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

Packages suggested but not available for checking: 'ecospat', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘somefile’
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qwraps2’
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package suggested but not available for checking: ‘plotly’
Found the following files/directories:
  ‘Environmental variables.csv’ ‘Inf.txt’ ‘List of species.csv’ ‘Mean
  overlap among taxa.csv’ ‘Overlap among taxa.csv’ ‘Pointsize.dat’
  ‘Polar coordinates.csv’