Package required but not available: 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'plotly'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'rpart' 'withr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'lmtest' 'sandwich'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'devtools'
Namespaces in Imports field not imported from:
  'class' 'forcats' 'irr' 'lpSolve' 'purrr'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'introduction_to_prcr.Rmd' using rmarkdown
Quitting from lines 19-20 (introduction_to_prcr.Rmd) 
Error: processing vignette 'introduction_to_prcr.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'introduction_to_prcr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'covr', 'devtools', 'tidyverse'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'PRDA.Rmd' using rmarkdown
--- finished re-building 'PRDA.Rmd'

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

--- re-building 'retrospective.Rmd' using rmarkdown
Quitting from lines 21-24 (retrospective.Rmd) 
Error: processing vignette 'retrospective.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'retrospective.Rmd'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'shinycssloaders' 'shinythemes'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'usethis'

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'TH.data' 'moonBook'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'lazyeval'
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'AER', 'sampleSelection'
Packages unavailable to check Rd xrefs: 'AER', 'sampleSelection'
'LazyData' is specified without a 'data' directory
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.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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.
Namespace in Imports field not imported from: 'rpart'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'TSPred', 'tseries'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'datasets' 'dplyr' 'psycho' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package suggested but not available for checking: 'covr'
Note: found 42966 marked UTF-8 strings
Package suggested but not available for checking: 'shinytest'
Package suggested but not available for checking: 'curl'
'LazyData' is specified without a 'data' directory
Running examples in 'presser-Ex.R' failed
The error most likely occurred in:

> ### Name: httpbin_app
> ### Title: Generic web app for testing HTTP clients
> ### Aliases: httpbin_app
> 
> ### ** Examples
> 
> app <- httpbin_app()
> proc <- new_app_process(app)
> url <- proc$url("/get")
> resp <- curl::curl_fetch_memory(url)
Error in loadNamespace(x) : there is no package called 'curl'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test-tmpl-glue.R:20:3): glue templating ------------------------------
  Error: there is no package called 'curl'
  Backtrace:
      x
   1. \-base::loadNamespace(x) test-tmpl-glue.R:20:2
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 57 | WARN 0 | SKIP 0 | PASS 78 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'qpdf'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'webdriver', 'httr'

Package suggested but not available for checking: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'lintr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'rosm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'DiagrammeRsvg'
Namespaces in Imports field not imported from:
  'tidyr' 'utils'
  All declared Imports should be used.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'exactextractr'

Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'DiagrammeRsvg'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'covr'
.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.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'LaplacesDemon' 'epitools' 'rpivotTable' 'shiny' 'shinyMatrix'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'processmapR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rrtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'curl'
Package unavailable to check Rd xrefs: 'curl'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  48. no fd leak on unix (test-wait.R:50:3) - Reason: On CRAN
  
  == Failed ======================================================================
  -- 1. Error (test-poll-curl.R:5:1): (code run outside of `test_that()`) --------
  Error: there is no package called 'curl'
  Backtrace:
   1. base::loadNamespace(x) test-poll-curl.R:5:0
   2. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3. base:::withOneRestart(expr, restarts[[1L]])
   4. base:::doWithOneRestart(return(expr), restart)
  
  == DONE ========================================================================
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Package required but not available: 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gert'
Package suggested but not available for checking: 'covr'
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.
Package suggested but not available for checking: 'DiagrammeRsvg'
'LazyData' is specified without a 'data' directory
Found the following sources/headers not terminated with a newline:
  src/libprofit/include/profit/config.h
Some compilers warn on such files.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rgraphviz'
Running examples in 'proftools-Ex.R' failed
The error most likely occurred in:

> ### Name: filterProfileData
> ### Title: Filter Profile Data
> ### Aliases: filterProfileData
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> pd <- readProfileData(system.file("samples", "glmEx.out", package="proftools"))
> plotProfileCallGraph(pd)
Error in loadNamespace(x) : there is no package called 'Rgraphviz'
Calls: plotProfileCallGraph ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'proftools.Rnw' using knitr
Quitting from lines 231-232 (proftools.Rnw) 
Error: processing vignette 'proftools.Rnw' failed with diagnostics:
there is no package called 'Rgraphviz'
--- failed re-building 'proftools.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'devtools'
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.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package required but not available: 'gh'

Packages suggested but not available for checking: 'curl', 'httr', 'covr'

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

Packages suggested but not available for checking: 'rstanarm', 'brms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'vembedr'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'casestudy.Rmd' using rmarkdown
--- finished re-building 'casestudy.Rmd'

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

--- re-building 'future_promise.Rmd' using rmarkdown
Quitting from lines 48-51 (future_promise.Rmd) 
Error: processing vignette 'future_promise.Rmd' failed with diagnostics:
there is no package called 'vembedr'
--- failed re-building 'future_promise.Rmd'

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

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gert'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test-prompt-git.R:85:3): git_dirty -----------------------------------
  Error: there is no package called 'gert'
  Backtrace:
      x
   1. \-base::loadNamespace(x) test-prompt-git.R:85:2
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 5 | PASS 40 ]
  Error: Test failures
  Execution halted
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ALDEx2', 'plotly', 'SDMTools'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
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 required but not available: 'httr'

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

Package suggested but not available for checking: 'httptest'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'kableExtra', 'pkgdown'
Error(s) in re-building vignettes:
  ...
--- re-building 'PROsetta.Rmd' using rmarkdown
Quitting from lines 23-27 (PROsetta.Rmd) 
Error: processing vignette 'PROsetta.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'PROsetta.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'RColorBrewer' 'grDevices'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
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 suggested but not available for checking: 'curl'
Package suggested but not available for checking: 'covr'
Packages required but not available: 'plotly', 'curl'

Packages suggested but not available for checking:
  'covr', 'proDA', 'heatmaply', 'drc', 'httr', 'STRINGdb'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Note: found 12717 marked UTF-8 strings
Package required but not available: 'httr'

Packages suggested but not available for checking: 'rdtLite', 'rdt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rdtLite', 'rdt'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rdt', 'rdtLite'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rdt', 'rdtLite'
Namespaces in Imports field not imported from:
  'dplyr' 'readr'
  All declared Imports should be used.
Package suggested but not available for checking: 'foghorn'
Package suggested but not available for checking: 'covr'
Package required but not available: 'PogromcyDanych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Namespaces in Imports field not imported from:
  'matrixcalc' 'tidyr' 'utils'
  All declared Imports should be used.
Package suggested but not available for checking: 'car'
Package unavailable to check Rd xrefs: 'car'
Running examples in 'pscl-Ex.R' failed
The error most likely occurred in:

> ### Name: hurdletest
> ### Title: Testing for the Presence of a Zero Hurdle
> ### Aliases: hurdletest
> ### Keywords: regression
> 
> ### ** Examples
> 
> data("bioChemists", package = "pscl")
> fm <- hurdle(art ~ ., data = bioChemists, dist = "negbin", zero = "negbin")
> hurdletest(fm)
Loading required namespace: car
Failed with error:  'there is no package called 'car''
Error in hurdletest(fm) : requireNamespace("car") is not TRUE
Calls: hurdletest -> stopifnot
Execution halted
Errors in running code in vignettes:
when running code in 'countreg.Rnw'
  ...
    as.Date, as.Date.numeric


> library("MASS")

> library("car")

  When sourcing 'countreg.R':
Error: there is no package called 'car'
Execution halted

  'countreg.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'countreg.Rnw' using Sweave
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


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

--- failed re-building 'countreg.Rnw'

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

Error: Vignette re-building failed.
Execution halted
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.
Namespace in Imports field not imported from: 'raster'
  All declared Imports should be used.
Package required but not available: 'rio'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Note: found 26 marked Latin-1 strings
'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').
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'kableExtra'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'seasonal.Rmd' using rmarkdown
Loading required package: nlme
This is mgcv 1.8-36. For overview type 'help("mgcv-package")'.

Attaching package: 'dplyr'

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

    collapse

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 22-38 (seasonal.Rmd) 
Error: processing vignette 'seasonal.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'seasonal.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  Backtrace:
      x
   1. \-PSPManalysis::PSPMequi(...)
  -- Error (test.04-PNAS2002_5bsind.R:3:1): (code run outside of `test_that()`) --
  Error: 
  Executable PNAS2002_5bsind.dll not found! Computation aborted.
  
  Backtrace:
      x
   1. \-PSPManalysis::PSPMind(...) test.04-PNAS2002_5bsind.R:3:0
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking: 'covr', 'curl'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  / |   0       | winver                                                          
  / |   0       | winver                                                          
  v |   6       | winver
  
  == Results =====================================================================
  Duration: 132.3 s
  
  -- Skipped tests  --------------------------------------------------------------
  * No UNIX sockets (2)
  * On CRAN (11)
  * socat is not available (6)
  
  [ FAIL 4 | WARN 0 | SKIP 19 | PASS 228 ]
  Error: Test failures
  Execution halted
Package required but not available: 'rstan'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'GSVA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Note: found 93 marked UTF-8 strings
Package required but not available: 'curl'

Package suggested but not available for checking: 'bib2df'

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.
'library' or 'require' calls to packages already attached by Depends:
  'multilevel' 'nlme'
  Please remove these calls from your code.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'Rgraphviz'
Package required but not available: 'ez'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'lifecycle'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Note: found 93 marked UTF-8 strings
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: 'covr'
Namespace in Imports field not imported from: 'yaml'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
Packages required but not available: 'curl', 'httr'

Package suggested but not available for checking: 'KEGGREST'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'plotly'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 28898 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: 'kableExtra'

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:
  '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.
Package required but not available: 'rcrossref'

Package suggested but not available for checking: 'fulltext'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rentrez'

Package suggested but not available for checking: 'bibliometrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'GenomicFeatures'

Package suggested but not available for checking: 'TxDb.Hsapiens.UCSC.hg19.knownGene'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'data.table' 'itsadug' 'mgcv'
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'RcppProgress'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package unavailable to check Rd xrefs: 'httr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'devtools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'MazamaCoreUtils', 'MazamaSpatialUtils', 'curl', 'ggmap', 'httr'

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'ez', 'phia', 'afex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'pxweb'

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

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').
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'HURDAT'
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.
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'qdap'
Package required but not available: 'gender'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rmarkdown' 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 76102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Running 'qMRI-test.R'
Running the tests in 'tests/qMRI-test.R' failed.
Last 13 lines of output:
  +                    maskFile, TR = TR, TE = TE,
  +                    FA = FA, verbose = FALSE)
  > #
  > #  Estimate Parameters in the ESTATICS model
  > #
  > modelMPM <- estimateESTATICS(mpm, method = "NLR", verbose=FALSE)
  > #
  > #  smooth maps of ESTATICS Parameters
  > #
  > setCores(2, reprt = FALSE)
  > modelMPMsp1 <- smoothESTATICS(modelMPM,
  +                               kstar = 16,
  +                               alpha = 0.004,
  +                               patchsize=1,
  +                               verbose = FALSE)
Errors in running code in vignettes:
when running code in 'qMRI-Example.Rnw'
  ...

> modelMPM <- estimateESTATICS(mpm, method = "NLR", 
+     verbose = FALSE)

> setCores(2, reprt = FALSE)

> modelMPMQLsp1 <- smoothESTATICS(modelMPM, mpmData = extract(mpm, 
+     "ddata"), kstar = 16, alpha = 0.004, patchsize = 1, verbose = FALSE)

... incomplete output.  Crash?

  'qMRI-Example.Rnw'... failed to complete the test
Error(s) in re-building vignettes:
  ...
--- re-building 'qMRI-Example.Rnw' using Sweave
Loading required package: awsMethods

Use the function setCores() to change the number of CPU cores.
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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'kableExtra', 'afex'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'qrmtools'
Packages required but not available: 'quantmod', 'Quandl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Packages required but not available: 'random', 'ssh'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
Package suggested but not available for checking: 'devtools'
Packages suggested but not available for checking:
  'covr', 'broman', 'devtools'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'bootstrap-cluster.Rmd' using rmarkdown
Quitting from lines 181-182 (bootstrap-cluster.Rmd) 
Error: processing vignette 'bootstrap-cluster.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'bootstrap-cluster.Rmd'

SUMMARY: processing the following file failed:
  'bootstrap-cluster.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'devtools'
Package suggested but not available for checking: 'devtools'
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'
Namespace in Imports field not imported from: 'MatrixModels'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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').
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'viridis'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
quadp: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
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.
Packages suggested but not available for checking:
  'covr', 'tigris', 'tidycensus'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'vcr', 'webmockr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 4 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
Note: found 35707 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'QuantileNPCI.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 35-38 (QuantileNPCI.Rmd) 
Error: processing vignette 'QuantileNPCI.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'QuantileNPCI.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'SparseM'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'TTR', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'usethis'
Package suggested but not available for checking: 'rsconnect'
Package suggested but not available for checking: 'covr'
Note: found 4145 marked UTF-8 strings
Packages required but not available: 'httr', 'curl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'fastshp'
Namespace in Imports field not imported from: 'psych'
  All declared Imports should be used.
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'MCMCpack' 'gridExtra' 'knitr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 12928 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
mutualCoherence : .setOneMutualP: no visible global function definition
  for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Note: found 89912 marked UTF-8 strings
Namespaces in Imports field not imported from:
  'pracma' 'zoo'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

Package suggested but not available for checking: 'ReGenesees'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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 suggested but not available for checking: 'shinytest'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'qpdf'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Note: found 34 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'gridExtra'
  All declared Imports should be used.
'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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'afex'

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

Package suggested but not available for checking: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
Packages suggested but not available for checking: 'devtools', 'covr'
Package suggested but not available for checking: 'qpdf'
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'qpdf'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'BRugs'
Package unavailable to check Rd xrefs: 'BRugs'
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 suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'magick'

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

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

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pkgdown'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'asd' 'cubature' 'data.table' 'ggplot2' 'multxpert' 'survival'
  All declared Imports should be used.
Packages suggested but not available for checking: 'batchelor', 'DESeq2'
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'comat' 'rgdal'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Note: found 4 marked UTF-8 strings
Package suggested but not available for checking: 'radsafer'
'LazyData' is specified without a 'data' directory
Package required but not available: 'radiant.data'

Package suggested but not available for checking: 'pkgdown'

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

Package suggested but not available for checking: 'pkgdown'

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

Package suggested but not available for checking: 'pkgdown'

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

Package suggested but not available for checking: 'pkgdown'

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

Package suggested but not available for checking: 'pkgdown'

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.
Package suggested but not available for checking: 'rsconnect'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    7.   \-radix:::render_website(dir, "blog")
    8.     \-rmarkdown::render_site(dir)
    9.       \-generator$render(...)
   10.         \-radix:::render_collections(input, config, collections, quiet)
   11.           \-base::lapply(...)
   12.             \-radix:::FUN(X[[i]], ...)
   13.               \-radix:::render_collection(...)
   14.                 \-base::lapply(...)
   15.                   \-radix:::FUN(X[[i]], ...)
   16.                     \-radix:::render_collection_article(...)
   17.                       \-base::file.copy(...)
  
  [ FAIL 1 | WARN 8 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted
Note: found 3 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'curl'

Package suggested but not available for checking: 'covr'

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: 'qpdf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ggtern', 'covr'
Namespace in Imports field not imported from: 'Rcompadre'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'a01_GettingStarted.Rmd' using rmarkdown
Welcome to popdemo! This is version 1.3-0
Use ?popdemo for an intro, or browseVignettes('popdemo') for vignettes
Citation for popdemo is here: doi.org/10.1111/j.2041-210X.2012.00222.x
Development and legacy versions are here: github.com/iainmstott/popdemo
--- finished re-building 'a01_GettingStarted.Rmd'

--- re-building 'a02_VitalRates.Rmd' using rmarkdown
--- finished re-building 'a02_VitalRates.Rmd'

--- re-building 'a03_LifeHistoryTraits.Rmd' using rmarkdown
--- finished re-building 'a03_LifeHistoryTraits.Rmd'

--- re-building 'a04_AgeFromStage.Rmd' using rmarkdown
--- finished re-building 'a04_AgeFromStage.Rmd'

--- re-building 'a05_TernaryPlots.Rmd' using rmarkdown
Welcome to popdemo! This is version 1.3-0
Use ?popdemo for an intro, or browseVignettes('popdemo') for vignettes
Citation for popdemo is here: doi.org/10.1111/j.2041-210X.2012.00222.x
Development and legacy versions are here: github.com/iainmstott/popdemo
Quitting from lines 30-34 (a05_TernaryPlots.Rmd) 
Error: processing vignette 'a05_TernaryPlots.Rmd' failed with diagnostics:
there is no package called 'ggtern'
--- failed re-building 'a05_TernaryPlots.Rmd'

SUMMARY: processing the following file failed:
  'a05_TernaryPlots.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Package required but not available: 'gRbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rags2ridges'

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

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

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rvest', 'robotstxt', 'curl'

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'webchem', 'MSnbase'

Package suggested but not available for checking: 'xcms'

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

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

Packages suggested but not available for checking: 'covr', 'httptest'

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

Package suggested but not available for checking: 'Heatplus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tidyverse', 'plotly'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'Intro-to-RaMS.Rmd' using rmarkdown
Quitting from lines 105-107 (Intro-to-RaMS.Rmd) 
Error: processing vignette 'Intro-to-RaMS.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'Intro-to-RaMS.Rmd'

--- re-building 'RaMS-and-friends.Rmd' using rmarkdown
--- finished re-building 'RaMS-and-friends.Rmd'

SUMMARY: processing the following file failed:
  'Intro-to-RaMS.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'httr'

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.
Package required but not available: 'exactextractr'

Package suggested but not available for checking: 'pkgdown'

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

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

Packages suggested but not available for checking:
  'biomod2', 'ecospat', 'googlesheets'

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.
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.
Packages required but not available: 'devtools', 'gistr', 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  datetime.c:724:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:725:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:763:3: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:971:6: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1115:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1116:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1199:7: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RApiDatetime/RApiDatetime.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'plumber'
Namespace in Imports field not imported from: 'jsonlite'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

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 'BSgenome.Hsapiens.UCSC.hg19' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'unix'
Package suggested but not available for checking: 'covr'
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.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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: 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building 'modify.Rmd' using rmarkdown
--- finished re-building 'modify.Rmd'

--- re-building 'sensitivity.Rmd' using rmarkdown
Quitting from lines 18-20 (sensitivity.Rmd) 
Error: processing vignette 'sensitivity.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'sensitivity.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'gurobi'
Namespace in Imports field not imported from: 'rgdal'
  All declared Imports should be used.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'devtools', 'goodpractice', 'lintr', 'usethis', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'adiv'

Package suggested but not available for checking: 'kableExtra'

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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'gert'

Packages suggested but not available for checking: 'devtools', 'rasciidoc'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'lintr', 'pkgdown'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'exactextractr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Package required but not available: 'rstan'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'arrow', 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggpubr', 'plotly'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'arulesViz', 'rggobi'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'devtools', 'magick', 'weathercan', 'tidyhydat'
Namespaces in Imports field not imported from:
  'deldir' 'lifecycle'
  All declared Imports should be used.
.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.
Packages suggested but not available for checking:
  'ChainLadder', 'devtools'
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'withr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'magick'
Running examples in 'rayimage-Ex.R' failed
The error most likely occurred in:

> ### Name: add_title
> ### Title: Add Title
> ### Aliases: add_title
> 
> ### ** Examples
> 
> #Plot the dragon
> add_title(dragon, preview = TRUE, title_text = "Dragon", title_size=20)
Error in add_title(dragon, preview = TRUE, title_text = "Dragon", title_size = 20) : 
  `magick` package required for adding title
Execution halted
Package suggested but not available for checking: 'magick'
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'magick'
Package required but not available: 'crul'

Packages suggested but not available for checking: 'vcr', 'webmockr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ggmap'
Note: found 8 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building 'Building_Benvos.Rmd' using rmarkdown

Attaching package: 'rbenvo'

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

    filter

Quitting from lines 74-75 (Building_Benvos.Rmd) 
Error: processing vignette 'Building_Benvos.Rmd' failed with diagnostics:
there is no package called 'ggmap'
--- failed re-building 'Building_Benvos.Rmd'

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

Attaching package: 'rbenvo'

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

    filter

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

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

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

Package suggested but not available for checking: 'rstanarm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'crul'

Package suggested but not available for checking: 'vcr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rhdf5'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'crul'

Packages suggested but not available for checking: 'taxize', 'vcr'

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 required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Rblpapi/Rblpapi.Rcheck/00install.out' for details.
Found the following non-empty subdirectories of 'inst' also used by R:
  inst/libs
It is recommended not to interfere with package subdirectories used by
R.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/blpapi_versioninfo.h
Some Unix compilers require LF line endings.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'plotly'

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

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.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 26334 marked UTF-8 strings
Package suggested but not available for checking: 'prettymapr'
Running examples in 'rcanvec-Ex.R' failed
The error most likely occurred in:

> ### Name: nts
> ### Title: Generate NTS References
> ### Aliases: nts
> 
> ### ** Examples
> 
> nts('21h')
[1] "021" "H"  
> nts('21h1')
[1] "021" "H"   "01" 
> nts('21h1', '21a16', '021A15')
[[1]]
[1] "021" "H"   "01" 

[[2]]
[1] "021" "A"   "16" 

[[3]]
[1] "021" "A"   "15" 

> nts(lat=45.2, lon=-64.32)
[1] "021" "H"   "01" 
> nts(lat=c(45.2, 46.2), lon=c(-64.32, -64.81))
[[1]]
[1] "021" "H"   "01" 

[[2]]
[1] "021" "I"   "02" 

> 
> library(prettymapr)
Error in library(prettymapr) : there is no package called 'prettymapr'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(rcanvec)
  Loading required package: sp
  Welcome to rcanvec!
  > 
  > test_check("rcanvec")
  == Failed tests ================================================================
  -- Error (test_nts.R:27:3): bounding boxes return correct sheets ---------------
  Error: there is no package called 'prettymapr'
  Backtrace:
      x
   1. \-base::library(prettymapr) test_nts.R:27:2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 9 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'covr'
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.
Package suggested but not available for checking: 'rgbif'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'checkpoint', 'rvest'
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'httr', 'devtools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'V8'

Packages suggested but not available for checking:
  'covr', 'googledrive', 'curl'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'factoextra', 'FactoMineR'

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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

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

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

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.
Package required but not available: 'Rcmdr'

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

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

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

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

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

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

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

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

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

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

Package suggested but not available for checking: 'car'

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

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

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

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

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

Package suggested but not available for checking: 'car'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mixlm', 'phia', 'Rcmdr', 'car'

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

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

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

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

Package suggested but not available for checking: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcmdr', 'demography', 'forecast', 'ftsa'

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

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

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

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

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

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

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

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

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

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

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

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

Packages suggested but not available for checking:
  'ROpenOffice', 'tm.plugin.factiva', 'twitteR'

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

Package suggested but not available for checking: 'car'

Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
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.
Package required but not available: 'Rcmdr'

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

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

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

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

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggtern', 'covr', 'rcrossref'
Note: found 345 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building 'a01_GettingStarted.Rmd' using rmarkdown
--- finished re-building 'a01_GettingStarted.Rmd'

--- re-building 'a02_RcompadreTidy.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

Warning: Removed 24 rows containing missing values (geom_point).
--- finished re-building 'a02_RcompadreTidy.Rmd'

--- re-building 'a03_VectorisingRcompadre.Rmd' using rmarkdown
--- finished re-building 'a03_VectorisingRcompadre.Rmd'

--- re-building 'a04_ObtainingReferences.Rmd' using rmarkdown
Quitting from lines 39-41 (a04_ObtainingReferences.Rmd) 
Error: processing vignette 'a04_ObtainingReferences.Rmd' failed with diagnostics:
there is no package called 'rcrossref'
--- failed re-building 'a04_ObtainingReferences.Rmd'

SUMMARY: processing the following file failed:
  'a04_ObtainingReferences.Rmd'

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

> ### Name: cldList
> ### Title: Compact letter display for lists of comparisons
> ### Aliases: cldList
> 
> ### ** Examples
> 
> data(PoohPiglet)
> PoohPiglet$Speaker = factor(PoohPiglet$Speaker,
+                             levels=c("Pooh", "Tigger", "Piglet"))
> library(FSA)
Error in library(FSA) : there is no package called 'FSA'
Execution halted
Packages required but not available: 'devtools', 'gert', 'gh', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Packages suggested but not available for checking: 'covr', 'httr', 'rvest'
Packages required but not available: 'crul', 'pdftools'

Packages suggested but not available for checking: 'rcrossref', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Rcplex/Rcplex.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RcppCWB/RcppCWB.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'RcppEigen'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Gauss: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Found the following non-empty subdirectories of 'inst' also used by R:
  inst/libs
It is recommended not to interfere with package subdirectories used by
R.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
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.
Packages required but not available: 'httr', 'webdriver'

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

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

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

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(rcrypt)
  > 
  > test_check("rcrypt")
  gpg: decryption failed: Bad session key
  == Failed tests ================================================================
  -- Error (test-decrypt.r:69:3): Decryption with passphrase passthrough and armor works --
  Error: cannot open the connection
  Backtrace:
      x
   1. \-base::readLines("file2-decrypt.txt") test-decrypt.r:69:2
   2.   \-base::file(con, "r")
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'SingleCellExperiment' 'mclust'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'qpdf'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages required but not available: 'curl', 'httr'

Packages suggested but not available for checking:
  'czso', 'rvest', 'devtools', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'crul'

Packages suggested but not available for checking: 'webmockr', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("devtools")
  Error in library("devtools") : there is no package called 'devtools'
  Execution halted
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggpubr'
'LazyData' is specified without a 'data' directory
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
Package required but not available: 'AER'

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

Package suggested but not available for checking: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'lintr'
'LazyData' is specified without a 'data' directory
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: 'jsonld'

Packages suggested but not available for checking: 'covr', 'httr'

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

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

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

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.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RDieHarder/RDieHarder.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'shinyMolBio', 'V8'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'curl', 'virustotal', 'aws.alexa', 'devtools'

Package suggested but not available for checking: 'lintr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Subdirectory 'src' contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
Found the following significant warnings:
  ./io/BufferedSocketWriter.hpp:102:27: warning: array subscript 4 is outside array bounds of 'long int [1]' [-Warray-bounds]
  ./io/BufferedSocketWriter.hpp:103:27: warning: array subscript 5 is outside array bounds of 'long int [1]' [-Warray-bounds]
  ./io/BufferedSocketWriter.hpp:104:27: warning: array subscript 6 is outside array bounds of 'long int [1]' [-Warray-bounds]
  ./io/BufferedSocketWriter.hpp:105:27: warning: array subscript 7 is outside array bounds of 'long int [1]' [-Warray-bounds]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/rDotNet/rDotNet.Rcheck/00install.out' for details.
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'synchronicity' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'webshot2'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'V8', 'usethis'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'rvest'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'curl'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'pdftools'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'plotly'
'LazyData' is specified without a 'data' directory
Running examples in 'rearrr-Ex.R' failed
The error most likely occurred in:

> ### Name: generate_clusters
> ### Title: Generate n-dimensional clusters
> ### Aliases: generate_clusters
> 
> ### ** Examples
> 
> # Attach packages
> library(rearrr)
> 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(ggplot2)
> library(plotly)
Error in library(plotly) : there is no package called 'plotly'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   6.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test_n_fn.R:169:3): fuzz testing create_n_fn() -----------------------
  Error: there is no package called 'covr'
  Backtrace:
      x
   1. +-testthat::skip_if(covr::in_covr()) test_n_fn.R:169:2
   2. | \-base::isTRUE(condition)
   3. \-base::loadNamespace(x)
   4.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     \-base:::withOneRestart(expr, restarts[[1L]])
   6.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 6833 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Error(s) in re-building vignettes:
--- re-building 'recexcavAAR-vignette-1.Rmd' using rmarkdown
Quitting from lines 27-33 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'recexcavAAR-vignette-1.Rmd'

--- re-building 'recexcavAAR-vignette-2.Rmd' using rmarkdown
Quitting from lines 25-29 (recexcavAAR-vignette-2.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-2.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'recexcavAAR-vignette-2.Rmd'

--- re-building 'recexcavAAR-vignette-3.Rmd' using rmarkdown
Loading required package: kriging
Transformation: 
 local centroid: 3.66666666666667 2.66666666666667 
 absolute centroid: 578172.831 6017856.63333333 
 scale: 1.08105445197455 
 rotation arc: 216.864428620413
--- finished re-building 'recexcavAAR-vignette-3.Rmd'

SUMMARY: processing the following files failed:
  'recexcavAAR-vignette-1.Rmd' 'recexcavAAR-vignette-2.Rmd'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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 suggested but not available for checking: 'covr'
Note: found 1036 marked UTF-8 strings
Package unavailable to check Rd xrefs: 'car'
Package suggested but not available for checking: 'magick'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'survminer'

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: 'ggpubr'
Error(s) in re-building vignettes:
  ...
--- re-building 'RecordTest.Rmd' using rmarkdown
Quitting from lines 11-31 (RecordTest.Rmd) 
Error: processing vignette 'RecordTest.Rmd' failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building 'RecordTest.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'move'
Package unavailable to check Rd xrefs: 'move'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("recurse")
  == Skipped tests ===============================================================
  * empty test (1)
  
  == Failed tests ================================================================
  -- Error (test_recurse.R:147:6): move objects ----------------------------------
  Error: could not find function "move"
  Backtrace:
      x
   1. \-recurse:::createMoveObj(simplePts) test_recurse.R:147:24
  
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 143 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: 'igraph'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'car'
Package required but not available: 'httr'

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

Packages suggested but not available for checking: 'devtools', 'secret'

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

Packages suggested but not available for checking: 'covr', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kableExtra', 'TCGAbiolinks', 'magick'
Error(s) in re-building vignettes:
--- re-building 'Rediscover.Rmd' using rmarkdown
Loading required package: Matrix
Loading required package: speedglm
Loading required package: MASS
Loading required package: PoissonBinomial

Attaching package: 'dplyr'

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

    select

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 21-29 (Rediscover.Rmd) 
Error: processing vignette 'Rediscover.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'Rediscover.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'rmapshaper'
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'plumber'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'AER'
Running examples in 'REEMtree-Ex.R' failed
The error most likely occurred in:

> ### Name: REEMtree
> ### Title: Create a RE-EM tree
> ### Aliases: REEMtree
> ### Keywords: tree models
> 
> ### ** Examples
> 
> data(simpleREEMdata)
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID)
> 
> # Estimation allowing for autocorrelation
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID,
+ 	correlation=corAR1())
> 
> # Random parameters model for the random effects
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1+X|ID)
> 
> # Estimation with a subset
> sub <- rep(c(rep(TRUE, 10), rep(FALSE, 2)), 50)
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID,
+ 	subset=sub)
> 
> # Dataset from the R library "AER"
> data("Grunfeld", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: data -> find.package
Execution halted
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rcrossref'
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'ref-icar-vignette.Rmd' using rmarkdown
Quitting from lines 21-25 (ref-icar-vignette.Rmd) 
Error: processing vignette 'ref-icar-vignette.Rmd' failed with diagnostics:
there is no package called 'rcrossref'
--- failed re-building 'ref-icar-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'SemiPar' 'caret' 'dplyr'
  All declared Imports should be used.
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'covr'

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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'golem', 'rvest'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'knitr' 'textshaping'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'covr', 'devtools', 'eurostat'
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building 'Regional_stats.Rmd' using rmarkdown
Quitting from lines 18-20 (Regional_stats.Rmd) 
Error: processing vignette 'Regional_stats.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'Regional_stats.Rmd'

--- re-building 'mapping.Rmd' using rmarkdown
Quitting from lines 25-28 (mapping.Rmd) 
Error: processing vignette 'mapping.Rmd' failed with diagnostics:
there is no package called 'eurostat'
--- failed re-building 'mapping.Rmd'

--- re-building 'recode.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 'recode.Rmd'

--- re-building 'validation.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 'validation.Rmd'

SUMMARY: processing the following files failed:
  'Regional_stats.Rmd' 'mapping.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'ggplot2' 'gridExtra'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Package suggested but not available for checking: 'tidyverse'
Namespace in Imports field not imported from: 'Deriv'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Backtrace:
      x
   1. \-testthat::describe(...) test-08_regmedint_class_user_methods.R:12:0
   2.   \-base::eval(substitute(code), describe_environment)
   3.     \-base::eval(substitute(code), describe_environment)
   4.       \-`%>%`(...) test-08_regmedint_class_user_methods.R:16:4
  -- Error (test-09_cross_check_with_sas_macro.R:10:1): (code run outside of `test_that()`) --
  Error: there is no package called 'tidyverse'
  Backtrace:
      x
   1. \-base::library(tidyverse) test-09_cross_check_with_sas_macro.R:10:0
  
  [ FAIL 19 | WARN 0 | SKIP 0 | PASS 23 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'rtweet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("reinstallr")
  == Failed tests ================================================================
  -- Error (test_03_show_missing_packages.R:24:3): missing packages are found ----
  Error: trying to use CRAN without setting a mirror
  Backtrace:
      x
   1. \-reinstallr::show_missing_packages(path = testpath, repos = repo) test_03_show_missing_packages.R:24:2
   2.   \-reinstallr:::missing_packages(found_packages$package, ...)
   3.     \-utils::available.packages(...)
   4.       \-utils::contrib.url(repos, type)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rgraphviz'

Package which this enhances but not available for checking: 'Rcplex'
Error(s) in re-building vignettes:
--- re-building 'relations.Rnw' using Sweave
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Rgraphviz'
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Rgraphviz'
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Rgraphviz'
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Rgraphviz'
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "relations.tex" --max-iterations=20 -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/tex/latex" -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'relations.Rnw' failed with diagnostics:
running 'texi2dvi' on 'relations.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex (file ./relations-plotfig.pdf): PDF inclusion: required
 page does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!

--- failed re-building 'relations.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'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
Namespace in Imports field not imported from: 'rmarkdown'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rcmdr'
Namespace in Imports field not imported from: 'gWidgets2tcltk'
  All declared Imports should be used.
Package required but not available: 'rvest'

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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rgraphviz'
Packages suggested but not available for checking: 'curl', 'covr'
Package unavailable to check Rd xrefs: 'curl'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   \-remotes:::curl_download(url, path, quiet, headers)
  -- Error (test-script.R:5:3): install-github.R script is up to date ------------
  Error: there is no package called 'covr'
  Backtrace:
      x
   1. +-testthat::skip_if(covr::in_covr()) test-script.R:5:2
   2. | \-base::isTRUE(condition)
   3. \-base::loadNamespace(x)
   4.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     \-base:::withOneRestart(expr, restarts[[1L]])
   6.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 5 | WARN 0 | SKIP 77 | PASS 458 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking: 'texreg', 'statnet'
Package required but not available: 'plotly'

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

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'devtools'
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Error(s) in re-building vignettes:
  ...
--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 515-517 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'vignette.Rmd'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'survminer'
Package unavailable to check Rd xrefs: 'survminer'
'LazyData' is specified without a 'data' directory
Package required but not available: 'checkpoint'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'brms', 'httr', 'ivreg', 'rstanarm'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'googledrive', 'httr'
Package unavailable to check Rd xrefs: 'googledrive'
Running 'test-all.R'
Error(s) in re-building vignettes:
  ...
--- re-building 'Cache-using-postgresql.Rmd' using rmarkdown
--- finished re-building 'Cache-using-postgresql.Rmd'

--- re-building 'Intro-to-Cache.Rmd' using rmarkdown
Failed with error:  'there is no package called 'googledrive''
Quitting from lines 105-116 (Intro-to-Cache.Rmd) 
Error: processing vignette 'Intro-to-Cache.Rmd' failed with diagnostics:
googledrive is required but not yet installed. Try: install.packages('googledrive') to use google drive files
--- failed re-building 'Intro-to-Cache.Rmd'

SUMMARY: processing the following file failed:
  'Intro-to-Cache.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'plotly', 'geojsonio'
Packages unavailable to check Rd xrefs: 'geojsonio', 'plotly'
'LazyData' is specified without a 'data' directory
Note: found 25 marked UTF-8 strings
Package required but not available: 'webutils'

Packages suggested but not available for checking: 'fiery', 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'lintr'
Package suggested but not available for checking: 'covr'
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
      unlink(filesToDel, recursive = TRUE)
  })(pkgURL = dots[[1L]][[1L]], pkgTD = dots[[2L]][[1L]])
  Browse[1]> debug: untar(tarfile = tf, exdir = dirname(pkgTD))
  Browse[2]> /usr/bin/tar: C\:\\msys64\\home\\tomas\\ucrt3\\svn\\ucrt3\\r_packages\\pkgcheck\\CRAN\\Require\\tmp\\RtmpGuJmTH\\file22ad4295c1fca: Cannot open: No such file or directory
  /usr/bin/tar: Error is not recoverable: exiting now
  debug: filesToDel <- dir(pkgTD, recursive = TRUE, full.names = TRUE, 
      include.dirs = TRUE)
  Browse[2]> debug: filesToDel <- filesToDel[grep("^DESCRIPTION$", basename(filesToDel), 
      invert = TRUE)]
  Browse[2]> debug: unlink(filesToDel, recursive = TRUE)
  Browse[2]> Error from message(pkg, " dependencies not found on CRAN; perhaps incomplete description? On GitHub?") 
  Error in message(pkg, " dependencies not found on CRAN; perhaps incomplete description? On GitHub?") : 
    object 'pkg' not found
  Calls: test_pkg ... pkgDepArchive -> lapply -> FUN -> message -> .makeMessage -> lapply
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'crul'

Package suggested but not available for checking: 'vcr'

Package which this enhances but not available for checking: 'taxize'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'ssh', 'sparklyr', 'RPresto'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Running 'restfulr_unit_tests.R'
Running the tests in 'tests/restfulr_unit_tests.R' failed.
Last 13 lines of output:
    % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                   Dload  Upload   Total   Spent    Left  Speed
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  curl: (60) SSL certificate problem: unable to get local issuer certificate
  More details here: https://curl.se/docs/sslcerts.html
  
  curl failed to verify the legitimacy of the server and therefore could not
  establish a secure connection to it. To learn more about this situation and
  how to fix it, please visit the web page mentioned above.
  Error in download.file(url, dest, method = "curl", extra = "-L") : 
    'curl' call had nonzero exit status
  Calls: <Anonymous> ... maybeInstallSolr -> installSolr -> downloadSolr -> download.file
  Execution halted
Package required but not available: 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'lintr', 'curl'
Namespace in Imports field not imported from: 'Rserve'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running 'tinytest.R'
Running the tests in 'tests/tinytest.R' failed.
Last 13 lines of output:
  Running test-cl-application.R.........   49 tests [0;32mOK[0m 
  Running test-cl-application.R.........   49 tests [0;32mOK[0m 
  Running test-cl-application.R.........   49 tests [0;32mOK[0m 
  Running test-cl-application.R.........   50 tests [0;32mOK[0m 
  Running test-cl-application.R.........   50 tests [0;32mOK[0m 
  Running test-cl-application.R.........   50 tests [0;32mOK[0m 
  Running test-cl-application.R.........   51 tests [0;32mOK[0m 
  Running test-cl-application.R.........   52 tests [0;32mOK[0m 
  Running test-cl-application.R.........   52 tests [0;32mOK[0m 
  Running test-cl-application.R.........   52 tests [0;32mOK[0m 
  Running test-cl-application.R.........   52 tests [0;32mOK[0m 
  Running test-cl-application.R.........   52 tests [0;32mOK[0m 
  Running test-cl-application.R.........   52 tests [0;32mOK[0m Error in loadNamespace(x) : there is no package called 'curl'
  Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Namespace in Imports field not imported from: 'RTriangle'
  All declared Imports should be used.
Packages required but not available: 'textreadr', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'DT'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'bigrquery', 'gargle', 'golem', 'httr', 'redcapAPI', 'REDCapR'

Package suggested but not available for checking: 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

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

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.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'btergm'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rvest', 'covr'
Packages suggested but not available for checking: 'devtools', 'usethis'
Namespace in Imports field not imported from: 'pkgload'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'devtools'
Package required but not available: 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'iCluster'
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'FSA', 'covr', 'pkgdown'
Package unavailable to check Rd xrefs: 'FSA'
Running examples in 'RFishBC-Ex.R' failed
The error most likely occurred in:

> ### Name: aStandard
> ### Title: Finds standard intercept (a) for Fraser-Lee back-calculation
> ###   model for a particular species.
> ### Aliases: aStandard
> ### Keywords: manip
> 
> ### ** Examples
> 
> aStandard("Bluegill")
Error in loadNamespace(x) : there is no package called 'FSA'
Calls: aStandard ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  Error: there is no package called 'FSA'
  Backtrace:
      x
   1. +-testthat::expect_type(aStandard("Bluegill"), "integer") test_OUTPUTS.R:444:2
   2. | \-testthat::quasi_label(enquo(object), arg = "object")
   3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
   4. +-RFishBC::aStandard("Bluegill")
   5. \-base::loadNamespace(x)
   6.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     \-base:::withOneRestart(expr, restarts[[1L]])
   8.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 4 | WARN 1 | SKIP 0 | PASS 446 ]
  Error: Test failures
  Execution halted
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'sf'
  All declared Imports should be used.
Packages suggested but not available for checking: 'covr', 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'rfm-customer-level-data.Rmd' using rmarkdown
Quitting from lines 15-26 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'rfm-customer-level-data.Rmd'

--- re-building 'rfm-transaction-level-data.Rmd' using rmarkdown
Quitting from lines 15-26 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'rfm-transaction-level-data.Rmd'

SUMMARY: processing the following files failed:
  'rfm-customer-level-data.Rmd' 'rfm-transaction-level-data.Rmd'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
.testLTS: no visible binding for global variable 'stackloss'
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plotly', 'Rssa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'base'
  All declared Imports should be used.
Package required but not available: 'httr'

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: 'httr'

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

Package suggested but not available for checking: 'vcr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'magick', 'geojsonio', 'googledrive', 'googleCloudStorageR', 'httr',
  'covr'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'magick'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RefManageR'
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'httr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'leaflet' 'pals' 'raster' 'sp'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Packages required but not available: 'curl', 'httr'

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

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

Package suggested but not available for checking: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'magick', 'js', 'webshot2', 'pkgdown'
Package unavailable to check Rd xrefs: 'magick'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

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

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

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
Package suggested but not available for checking: 'quantmod'
Package suggested but not available for checking: 'covr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- Error (test-man.R:131:3): fail on bad viewer argument -----------------------
  Error: `curl` must be installed to use `download_xml()`
  Backtrace:
      x
   1. +-testthat::expect_message(...) test-man.R:131:2
   2. | \-testthat:::quasi_capture(enquo(object), label, capture_messages)
   3. |   +-testthat:::.capture(...)
   4. |   | \-base::withCallingHandlers(...)
   5. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. \-rgrassdoc::man(r.in.gdal, viewer = "wrong_viewer")
   7.   \-xml2::download_html(...)
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 5 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found a 'configure.in' file: 'configure.ac' has long been preferred.
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: '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.
Package suggested but not available for checking: 'curl'
Note: found 22 marked Latin-1 strings
  Note: found 1265 marked UTF-8 strings
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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').
Found the following significant warnings:
  RhpcMPI.c:112:28: warning: ' "' directive output may be truncated writing 2 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
  fakemaster.c:82:57: warning: embedded '\0' in format [-Wformat-contains-nul]
  fakemaster.c:123:83: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size 4046 [-Wformat-truncation=]
  fakemaster.c:109:60: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size 4069 [-Wformat-truncation=]
  fakemaster.c:97:68: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size 4061 [-Wformat-truncation=]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Rhpc/Rhpc.Rcheck/00install.out' for details.
Package required but not available: 'nonlinearTseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
Packages required but not available: 'httr', 'whoami'

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'random'

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

Packages suggested but not available for checking:
  'covr', 'mimic.demo', 'eicu.demo', 'kableExtra'

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.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ridit.raw: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'ggrepel'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

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.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'plotly', 'curl'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'curl'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  RInside.cpp:169:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 260 equals destination size [-Wstringop-truncation]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RInside/RInside.Rcheck/00install.out' for details.
Found the following sources/headers with CR or CRLF line endings:
  src/RInsideAutoloads.h
  src/RInsideEnvVars.h
Some Unix compilers require LF line endings.
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'curl'

Package suggested but not available for checking: 'arrow'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'usethis'
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'curl', 'cranlogs', 'covr', 'devtools'

Package suggested but not available for checking: 'webmockr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'portfolioBacktest'
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
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.
Note: found 14 marked UTF-8 strings
Packages required but not available: 'solrium', 'crul'

Packages suggested but not available for checking: 'webmockr', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'imputeTS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'qpdf'
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.
Package required but not available: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
  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 for x64 is not available
File 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/rJava/rJava.Rcheck/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package required but not available: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'XLConnect'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'coda'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Namespaces in Imports field not imported from:
  'Matrix' 'arules' 'pmml' 'rJava'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'genefilter', 'golubEsets'
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: 'httr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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.
Packages suggested but not available for checking: 'covr', 'pak'
Found the following significant warnings:
  internal/hash.c:142:16: warning: too many arguments for format [-Wformat-extra-args]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/rlang/rlang.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'covr'
Package required but not available: 'V8'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'Luminescence'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
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'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'geojsonio', 'geojsonlint', 'V8'

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'rsconnect'
Package suggested but not available for checking: 'tidyverse'
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rdpack' 'magrittr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'pkgdown', 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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').
Package suggested but not available for checking: 'blockcluster'
Packages required but not available: 'RMixtCompUtilities', 'plotly'

Package suggested but not available for checking: 'blockcluster'

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

Package suggested but not available for checking: 'blockcluster'

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.
Namespace in Imports field not imported from: 'e1071'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Packages required but not available: 'ecr', 'plotly'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'DESeq2', 'splineTimeR'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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', 'rmsb'
Package unavailable to check Rd xrefs: 'rmsb'
Namespace in Imports field not imported from: 'reshape2'
  All declared Imports should be used.
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.
Found the following sources/headers with CR or CRLF line endings:
  src/lib/scotch_6.0.9/include/scotch.h
  src/lib/scotch_6.0.9/include/scotchf.h
  src/lib/scotch_6.0.9/src/libscotch/scotch.h
  src/lib/scotch_6.0.9/src/libscotch/scotchf.h
Some Unix compilers require LF line endings.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
Package suggested but not available for checking: 'curl'
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Note: found 133 marked Latin-1 strings
Packages suggested but not available for checking:
  'httr', 'devtools', 'rnaturalearthhires'
Note: found 7 marked Latin-1 strings
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("rnaturalearth")
  == Skipped tests ===============================================================
  * rnaturalearthhires cannot be loaded (4)
  
  == Failed tests ================================================================
  -- Error (test-ne_file_name.r:3:1): (code run outside of `test_that()`) --------
  Error: there is no package called 'httr'
  Backtrace:
      x
   1. \-base::library(httr) test-ne_file_name.r:3:0
  
  [ FAIL 1 | WARN 2 | SKIP 4 | PASS 15 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'curl', 'httr'

Packages suggested but not available for checking: 'covr', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'qtl'
  All declared Imports should be used.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'rdflib', 'rfigshare', 'knitcitations', 'covr', 'taxadb'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
well19937.validate: 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: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Packages required but not available: 'speaq', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'crul'

Packages suggested but not available for checking:
  'taxize', 'ggmap', 'vcr', 'webmockr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'curl'

Packages suggested but not available for checking: 'covr', 'vcr'

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

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

Packages suggested but not available for checking: 'covr', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Packages suggested but not available for checking:
  'covr', 'rcrossref', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'VIM'

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 suggested but not available for checking: 'covr'
Package required but not available: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mvtnorm'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'devtools'

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

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

Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rstan', 'metaBMA'
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'rstan'
Namespace in Imports field not imported from: 'glmnet'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
RobRSVD: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'DEoptimR' 'DT' 'PerformanceAnalytics' 'ggplot2' 'graphics'
  'gridExtra' 'methods' 'shinyjs' 'utils' 'xts'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
Package suggested but not available for checking: 'devtools'
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'car'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'data.table'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xmlrpc2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'magick'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'animation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'RSelenium', 'rio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ROracle/ROracle.Rcheck/00install.out' for details.
Packages required but not available: 'crul', 'httr'

Packages suggested but not available for checking:
  'rcrossref', 'handlr', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'rio', 'ufs', 'kableExtra'

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

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

Packages suggested but not available for checking: 'cartography', 'covr'

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

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

Packages suggested but not available for checking:
  'fulltext', 'phylobase', 'RNeXML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
.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.
Namespace in Imports field not imported from: 'geometry'
  All declared Imports should be used.
Packages suggested but not available for checking: 'covr', 'httr', 'magick'
Package unavailable to check Rd xrefs: 'magick'
Package required but not available: 'reqres'

Packages suggested but not available for checking: 'covr', 'fiery'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'devtools'
Package unavailable to check Rd xrefs: 'devtools'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   1. \-roxygen2:::expect_equal_strings(out1$get_value("details"), exp_details) test-rd-includermd.R:179:2
   2.   \-testthat::expect_equal(s1, s2) C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\roxygen2\roxygen2.Rcheck\tests\testthat\helper-test.R:12:2
  
  [ FAIL 1 | WARN 5 | SKIP 15 | PASS 729 ]
  Error: Test failures
  In addition: Warning messages:
  1: In for (i in seq_len(n)) { :
    closing unused connection 7 (C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\roxygen2\tmp\RtmpyAhlGi\file2af683fae169a)
  2: In for (i in seq_len(n)) { :
    closing unused connection 6 (C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\roxygen2\tmp\RtmpyAhlGi\file2af687c184748)
  3: In for (i in seq_len(n)) { :
    closing unused connection 5 (C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\roxygen2\tmp\RtmpyAhlGi\file2af68124e1e9c)
  4: In for (i in seq_len(n)) { :
    closing unused connection 4 (C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\roxygen2\tmp\RtmpyAhlGi\file2af6878e2109e)
  Execution halted
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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
Package suggested but not available for checking: 'covr'
Package unavailable to check Rd xrefs: 'rsoi'
Package required but not available: 'crul'

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Packages suggested but not available for checking: 'webmockr', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'httr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'dplyr' 'testthat'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  fe-protocol2.c:1615:2: warning: 'strncpy' specified bound 32 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1616:2: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1617:2: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1620:3: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RPostgreSQL/RPostgreSQL.Rcheck/00install.out' for details.
Found a 'configure.in' file: 'configure.ac' has long been preferred.
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'.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Rgraphviz'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'ape' 'igraph'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Packages required but not available: 'httr', 'curl'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggpubr'
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Namespace in Imports field not imported from: 'NatureSounds'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'Rraven.Rmd' using rmarkdown
Loading required package: tuneR
Loading required package: seewave
Loading required package: NatureSounds
Loading required package: knitr

NOTE: functions have been renamed (run 'print(new_function_names)' to see new names). Both old and new names are available in this version 
 Please see citation('warbleR') for use in publication
Quitting from lines 35-56 (Rraven.Rmd) 
Error: processing vignette 'Rraven.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'Rraven.Rmd'

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

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

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggtern'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'RelativePermeability.Rmd' using rmarkdown

Attaching package: 'tidyr'

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

    extract

Quitting from lines 346-379 (RelativePermeability.Rmd) 
Error: processing vignette 'RelativePermeability.Rmd' failed with diagnostics:
there is no package called 'ggtern'
--- failed re-building 'RelativePermeability.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'mvoutlier'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'car', 'kableExtra', 'pdftools', 'qpdf'
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'abind'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'editData', 'ggpubr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'plotly', 'httr', 'biomaRt'
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
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: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'dplyr' 'lubridate' 'reshape2' 'tidyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  cli.c:232:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RSclient/RSclient.Rcheck/00install.out' for details.
Package required but not available: 'rsconnect'

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

Package suggested but not available for checking: 'plumber'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'rvest'

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

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

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 required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rgraphviz'
Packages required but not available: 'httr', 'wdman', 'binman'

Packages suggested but not available for checking: 'Rcompression', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  RSserver.c:64:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Rserve/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Rserve/Rserve.Rcheck/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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 required but not available: 'usethis', 'ymlthis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'covr', 'devtools', 'usethis'
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'aire.zmvm', 'covr', 'ggmap'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RSNNS/RSNNS.Rcheck/00install.out' for details.
Packages required but not available: 'crul', 'httr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'rsolr_unit_tests.R'
Running the tests in 'tests/rsolr_unit_tests.R' failed.
Last 13 lines of output:
    % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                   Dload  Upload   Total   Spent    Left  Speed
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  curl: (60) SSL certificate problem: unable to get local issuer certificate
  More details here: https://curl.se/docs/sslcerts.html
  
  curl failed to verify the legitimacy of the server and therefore could not
  establish a secure connection to it. To learn more about this situation and
  how to fix it, please visit the web page mentioned above.
  Error in download.file(url, dest, method = "curl", extra = "-L") : 
    'curl' call had nonzero exit status
  Calls: <Anonymous> ... maybeInstallSolr -> installSolr -> downloadSolr -> download.file
  Execution halted
Errors in running code in vignettes:
when running code in 'intro.Rnw'
  ...
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: https://curl.se/docs/sslcerts.html

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.

  When sourcing 'intro.R':
Error: 'curl' call had nonzero exit status
Execution halted

  'intro.Rnw'... failed
Package required but not available: 'tigris'

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 suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gert', 'gh', 'rvest'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'covr', 'lintr', 'pkgdown'
Namespaces in Imports field not imported from:
  'RSQLite' 'knitr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'gridExtra'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'vcr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'V8'

Package suggested but not available for checking: 'shinystan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rstan', 'usethis'
Namespace in Imports field not imported from: 'RcppParallel'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'usethis'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == Failed tests ================================================================
  -- Error (test-rstan_config.R:40:1): (code run outside of `test_that()`) -------
  Error: Please install package 'usethis' to use function 'rstan_create_package'.
  Backtrace:
      x
   1. \-rstantools::rstan_create_package(...) test-rstan_config.R:40:0
  -- Error (test-rstan_create_package.R:63:5): (code run outside of `test_that()`) --
  Error: Please install package 'usethis' to use function 'rstan_create_package'.
  Backtrace:
      x
   1. \-rstantools::rstan_create_package(...) test-rstan_create_package.R:63:4
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 41 ]
  Error: Test failures
  Execution halted
Package required but not available: 'rstan'

Package suggested but not available for checking: 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

Package suggested but not available for checking: 'ggpubr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 117 marked UTF-8 strings
Package required but not available: 'httr'

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.
Namespace in Imports field not imported from: 'mc2d'
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: 'magick'
Found the following significant warnings:
  WARNING: failed to apply patch patches/CRAN/rsvg.diff
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/rsvg/rsvg.Rcheck/00install.out' for details.
Running examples in 'rsvg-Ex.R' failed
The error most likely occurred in:

> ### Name: rsvg
> ### Title: Render SVG into Bitmap
> ### Aliases: rsvg rsvg_raw rsvg_webp rsvg_png rsvg_pdf rsvg_svg rsvg_ps
> 
> ### ** Examples
> 
> # create some svg
> options(example.ask=FALSE)
> tmp <- tempfile()
> svglite::svglite(tmp, width = 10, height = 7)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = factor(cyl))
> dev.off()
pdf 
  2 
> 
> # convert directly into a bitmap format
> rsvg_pdf(tmp, "out.pdf")
> rsvg_png(tmp, "out.png")
> rsvg_svg(tmp, "out.svg")
> rsvg_ps(tmp, "out.ps")
> 
> # render into raw bitmap array
> bitmap <- rsvg(tmp, height = 1440)
> dim(bitmap) # h*w*c
[1] 1440 2057    4
> 
> # read in your package of choice
> magick::image_read(bitmap)
Error in loadNamespace(x) : there is no package called 'magick'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'svg-css.Rmd' using rmarkdown
Quitting from lines 91-92 (svg-css.Rmd) 
Error: processing vignette 'svg-css.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building 'svg-css.Rmd'

SUMMARY: processing the following file failed:
  'svg-css.Rmd'

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

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2021-06-21 r80537)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 14393)

Matrix products: default

locale:
[1] LC_COLLATE=C                          
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_4.2.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
Note: found 18627 marked UTF-8 strings
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: 'covr'
'LazyData' is specified without a 'data' directory
Running examples in 'RtD3-Ex.R' failed
The error most likely occurred in:

> ### Name: readInEpiNow2
> ### Title: Read in Results from EpiNow2
> ### Aliases: readInEpiNow2
> 
> ### ** Examples
> 
> # Read in each summary folder
> 
> base_path <- "https://raw.githubusercontent.com/epiforecasts/covid-rt-estimates/"
> rtData <- readInEpiNow2(
+   path = paste0(base_path, "master/national/cases/summary"),
+   region_var = "country")
Error in data.table::fread(paste0(path, "summary_table.csv"), integer64 = "numeric") : 
  Input URL requires https:// connection for which fread() requires 'curl' package which cannot be found. Please install 'curl' using 'install.packages('curl')'.
Calls: readInEpiNow2 -> <Anonymous>
Execution halted
Package suggested but not available for checking: 'tseries'
Running 'test-EPD.R'
  Running 'test-EUstockmarket.R'
Running the tests in 'tests/test-EUstockmarket.R' failed.
Complete output:
  > data(EuStockMarkets)
  > 
  > 
  > library(RTDE)
  Loading required package: parallel
  > library(tseries)
  Error in library(tseries) : there is no package called 'tseries'
  Execution halted
Package required but not available: 'httr'

Packages suggested but not available for checking: 'webmockr', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'FactoMineR', 'tm.plugin.factiva'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rNOMADS'
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'lifecycle'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RSQLite' 'stats'
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
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.
Package required but not available: 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'devtools'
Namespaces in Imports field not imported from:
  'DescTools' 'MASS' 'gridExtra'
  All declared Imports should be used.
Package required but not available: 'qpdf'

Package suggested but not available for checking: 'Gviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'forecast', 'tidyquant', 'plotly', 'timetk', 'tidyverse'

Package suggested but not available for checking: 'Quandl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'quantmod'
Package unavailable to check Rd xrefs: 'quantmod'
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages required but not available: 'quantmod', 'alfred', 'Quandl', 'curl'

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

Package suggested but not available for checking: 'TTR'

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

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

Package suggested but not available for checking: 'vcr'

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

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

Packages suggested but not available for checking: 'magick', 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'highfrequency', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rvest'
Running examples in 'runexp-Ex.R' failed
The error most likely occurred in:

> ### Name: scrape
> ### Title: Softball Webscraper
> ### Aliases: scrape
> 
> ### ** Examples
> 
> url <-"https://wmubroncos.com/sports/softball/stats/2019"
> test <- scrape(url)
Error: Package "rvest" needed for this function to work. Please install it.
Execution halted
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'urltools'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'FactoMineR'

Package suggested but not available for checking: 'FSA'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

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

Package suggested but not available for checking: 'vcr'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
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'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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: 'httr'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 4250 marked UTF-8 strings
Running examples in 'Rwhois-Ex.R' failed
The error most likely occurred in:

> ### Name: Rwhois
> ### Title: WHOIS server querying
> ### Aliases: Rwhois Rwhois::whois_query whois_query
> ### Keywords: Rwhois whois
> 
> ### ** Examples
> 
> # Grab WHOIS data for a hostname
> whois_query("bcable.net")
socket error: A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond
Error in read.socket(conn) : Error reading data in Rsockread
Calls: whois_query -> whois_query_wrap -> whois_query_one -> read.socket
Execution halted
Package required but not available: 'marked'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RWinEdt/RWinEdt.Rcheck/00install.out' for details.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 2016 marked UTF-8 strings
Malformed Title field: should not end in a period.
Packages suggested but not available for checking: 'findR', 'foghorn'
Note: found 426306 marked UTF-8 strings
.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.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'bfast', 'vcr'

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

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

Packages suggested but not available for checking: 'covr', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'curl', 'usethis', 'rsconnect', 'devtools'
Package unavailable to check Rd xrefs: 'usethis'
Package suggested but not available for checking: 'devtools'
Packages suggested but not available for checking: 'devtools', 'unix'
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'kableExtra', 'googleAnalyticsR'

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

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

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: 'car'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  WARNING: failed to apply patch patches/CRAN/s2.diff
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/s2/s2.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'spanel'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
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.
Namespaces in Imports field not imported from:
  'R6' 'mgcv'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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 suggested but not available for checking: 'covr'
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: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Note: found 3 marked Latin-1 strings
Packages suggested but not available for checking: 'shinytest', 'plotly'
Namespace in Imports field not imported from: 'shinybusy'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Packages required but not available: 'httr', 'curl'

Package suggested but not available for checking: 'RForcecom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
Package suggested but not available for checking: 'lintr'
Package required but not available: 'systemfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Packages suggested but not available for checking:
  'GOstats', 'car', 'org.Sc.sgd.db'
Note: found 6 marked UTF-8 strings
Packages suggested but not available for checking: 'AER', 'car'
Package unavailable to check Rd xrefs: 'car'
Errors in running code in vignettes:
when running code in 'sandwich-OOP.Rnw'
  ...

> library("AER")

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

  'sandwich-CL.Rnw'... OK
  'sandwich-OOP.Rnw'... failed
  'sandwich.Rnw'... OK
Error(s) in re-building vignettes:
--- re-building 'sandwich-CL.Rnw' using Sweave
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'pcse'

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

    vcovPC

Classes and Methods for R developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University
Simon Jackman
hurdle and zeroinfl functions by Achim Zeileis
--- finished re-building 'sandwich-CL.Rnw'

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

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

--- failed 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-OOP.Rnw'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'gridExtra'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'smacof'
Packages required but not available: 'AzureRMR', 'AzureStor', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tidyverse', 'covr'
Package suggested but not available for checking: 'covr'
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.
Namespace in Imports field not imported from: 'stringi'
  All declared Imports should be used.
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.
Package suggested but not available for checking: 'curl'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'maptools'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
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: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'forecast'

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.
Namespace in Imports field not imported from: 'network'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
Package required but not available: 'httr'

Package suggested but not available for checking: 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'pvclust'
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'kableExtra'

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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'R6' 'cowplot' 'ggplot2' 'ggridges' 'ggstance' 'jmvcore'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rgraphviz'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'rvest'

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.
Package suggested but not available for checking: 'ez'
Package unavailable to check Rd xrefs: 'ez'
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'dplyr' 'ggplot2' 'stringi' 'stringr' 'tibble' 'tidyr' 'tidytext'
  All declared Imports should be used.
Note: found 464 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Seurat', 'GSVA', 'gprofiler2', 'ADAPTS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   6.           \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.             \-value[[3L]](cond)
  -- Error (test-list_result_files.R:31:3): list_result_files fails works with remote index? --
  Error: Could not find index file: https://raw.githubusercontent.com/rethomics/scopr/master/inst/extdata/ethoscope_results/index.txt
  Backtrace:
      x
   1. \-scopr:::list_result_files(dir, index_file = "index.txt") test-list_result_files.R:31:2
   2.   \-base::tryCatch(...)
   3.     \-base:::tryCatchList(expr, classes, parentenv, handlers)
   4.       \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5.         \-value[[3L]](cond)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pkgdown'
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.
'LazyData' is specified without a 'data' directory
CreatePssm: no visible binding for global variable 'training'
Undefined global functions or variables:
  training
Packages suggested but not available for checking: 'plotly', 'covr'
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'pracma'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Packages required but not available: 'car', 'forecast'

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pkgdown'
'LazyData' is specified without a 'data' directory
Package required but not available: 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 1 marked UTF-8 string
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 required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'oligoClasses'
Packages suggested but not available for checking: 'lintr', 'devtools'
Package required but not available: 'RCy3'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'crul', 'curl'

Package suggested but not available for checking: 'rgbif'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  'methods' 'pbapply' 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package which this enhances but not available for checking: 'glmGamPoi'
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'spatstat'
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'devtools'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Packages required but not available: 'car', 'VIM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'lpSolveAPI'
  All declared Imports should be used.
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.
Package required but not available: 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'PostcodesioR'
Package unavailable to check Rd xrefs: 'PostcodesioR'
Running examples in 'sdglinkage-Ex.R' failed
The error most likely occurred in:

> ### Name: get_address
> ### Title: Get an address.
> ### Aliases: get_address
> 
> ### ** Examples
> 
> get_address()
Error in loadNamespace(x) : there is no package called 'PostcodesioR'
Calls: get_address ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'ggsn', 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'biomod2', 'ggpubr', 'tidyverse'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'gbm'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'RCurl'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'covr', 'kableExtra', 'pkgdown'
'LazyData' is specified without a 'data' directory
Package required but not available: 'covr'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'rgdal' 'rgeos' 'tidyr'
  All declared Imports should be used.
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 required but not available: 'googleAuthR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
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 required but not available: 'TTR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Note: found 3 marked UTF-8 strings
Package required but not available: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'waterData'
Errors in running code in vignettes:
when running code in 'vignette.Rnw'
  ...

> options(width = 65)

> library(waterData)

  When sourcing 'vignette.R':
Error: there is no package called 'waterData'
Execution halted

  'vignette.Rnw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'vignette.Rnw' using Sweave

Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 1 
Error in library(waterData) : there is no package called 'waterData'

--- failed re-building 'vignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
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.
'LazyData' is specified without a 'data' directory
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: 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'testthat'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package required but not available: 'phylobase'

Package which this enhances but not available for checking: 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'lintr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'fansi'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'drc', 'car'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'brms', 'httr', 'rstanarm'
Packages required but not available: 'forecast', 'forecTheta', 'tsfeatures'

Packages suggested but not available for checking:
  'covr', 'repmis', 'Mcomp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'moveHMM', 'move', 'devtools'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: 'flowClust', 'flowMerge'
Package suggested but not available for checking: 'covr'
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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: 'factoextra', 'rvest'

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.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/selac/selac.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package required but not available: 'Cascade'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'FD'
  All declared Imports should be used.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'RSauceLabs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
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.
Packages suggested but not available for checking: 'lintr', 'covr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("semantic.dashboard")
  [1] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/semantic.dashboard/semantic.dashboard.Rcheck/tests/testthat"
  == Failed tests ================================================================
  -- Error (test-lintr.R:5:3): lintr ---------------------------------------------
  Error: there is no package called 'lintr'
  Backtrace:
      x
   1. \-base::loadNamespace(x) test-lintr.R:5:2
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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.
Namespaces in Imports field not imported from:
  'dplyr' 'lavaan' 'psych' 'semPlot' 'semTools' 'shinyAce'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'DiagrammeRsvg'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  file.info(fname)$size is not strictly more than 0. Difference: NA
  -- Failure (test-plot-save-plot.R:39:7): Saving a plot works -------------------
  file.exists(fname) not equal to TRUE.
  1 element mismatch
  -- Failure (test-plot-save-plot.R:40:7): Saving a plot works -------------------
  file.info(fname)$size is not strictly more than 0. Difference: NA
  -- Failure (test-plot-save-plot.R:39:7): Saving a plot works -------------------
  file.exists(fname) not equal to TRUE.
  1 element mismatch
  -- Failure (test-plot-save-plot.R:40:7): Saving a plot works -------------------
  file.info(fname)$size is not strictly more than 0. Difference: NA
  
  [ FAIL 8 | WARN 0 | SKIP 0 | PASS 202 ]
  Error: Test failures
  Execution halted
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.
Package required but not available: 'urlshorteneR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Package required but not available: 'car'

Package suggested but not available for checking: 'animation'

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

> ### Name: modelMatrices
> ### Title: Extract SEM model matrices
> ### Aliases: modelMatrices
> 
> ### ** Examples
> 
> ## Mplus user guide SEM example:
> outfile <- tempfile(fileext=".out")
> download.file("http://www.statmodel.com/usersguide/chap5/ex5.11.out",outfile)
trying URL 'http://www.statmodel.com/usersguide/chap5/ex5.11.out'
Content length 8916 bytes
==================================================
downloaded 8916 bytes

> 
> # Plot model:
> semPaths(outfile, intercepts = FALSE)
Loading required namespace: MplusAutomation
Failed with error:  'there is no package called 'MplusAutomation''
Error in semPlotModel.mplus.model(object, ...) : 
  'MplusAutomation' package must be installed to read Mplus output.
Calls: semPaths ... <Anonymous> -> semPlotModel.default -> semPlotModel.mplus.model
Execution halted
'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'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'blavaan'
Package unavailable to check Rd xrefs: 'blavaan'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'geojsonio', 'httr'

Packages suggested but not available for checking:
  'geojsonlint', 'httptest'

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

Package suggested but not available for checking: 'covr'

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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 suggested but not available for checking: 'covr'
Package required but not available: 'FactoMineR'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'sva', 'cate'

Packages suggested but not available for checking:
  'covr', 'DESeq2', 'airway'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'FactoMineR', 'GDAtools'
Error(s) in re-building vignettes:
--- re-building 'Tutoriel.Rmd' using rmarkdown

TraMineR stable version 2.2-2 (Built: 2021-06-21)
Website: http://traminer.unige.ch
Please type 'citation("TraMineR")' for citation information.

TraMineRextras stable version 0.6.1 (Built: 2021-06-21)
Functions provided by this package are still in test
    and subject to changes in future releases.
This is WeightedCluster stable version 1.4-1 (Built: 2021-06-21)

To get the manuals, please run:
   vignette("WeightedCluster") ## Complete manual in English
   vignette("WeightedClusterFR") ## Complete manual in French
   vignette("WeightedClusterPreview") ## Short preview in English

To cite WeightedCluster in publications please use:
Studer, Matthias (2013). WeightedCluster Library Manual: A practical
   guide to creating typologies of trajectories in the social sciences
   with R. LIVES Working Papers, 24. doi:
   10.12682/lives.2296-1658.2013.24
Quitting from lines 43-56 (Tutoriel.Rmd) 
Error: processing vignette 'Tutoriel.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building 'Tutoriel.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'RcppProgress'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Packages suggested but not available for checking: 'stevedore', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
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.
Package required but not available: 'do'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'plotly'
Packages required but not available: 'httr', 'plotly'

Packages suggested but not available for checking:
  'MAST', 'DESeq2', 'monocle', 'enrichR'

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.
'LazyData' is specified without a 'data' directory
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: 'arrow'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'kableExtra'

Packages suggested but not available for checking: 'pkgdown', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'geometries'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tidyverse'
Package suggested but not available for checking: 'plotly'
Error(s) in re-building vignettes:
--- re-building 'v1_intro.Rmd' using rmarkdown
--- finished re-building 'v1_intro.Rmd'

--- re-building 'v3_analyzing_landing.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 30-37 (v3_analyzing_landing.Rmd) 
Error: processing vignette 'v3_analyzing_landing.Rmd' failed with diagnostics:
there is no package called 'plotly'
--- failed re-building 'v3_analyzing_landing.Rmd'

SUMMARY: processing the following file failed:
  'v3_analyzing_landing.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Error(s) in re-building vignettes:
--- re-building 'sftrack1_overview.Rmd' using rmarkdown
--- finished re-building 'sftrack1_overview.Rmd'

--- re-building 'sftrack2_reading.Rmd' using rmarkdown
Loading required package: sp
Loading required package: ade4
Loading required package: adehabitatMA
Loading required package: CircStats
Loading required package: MASS
Loading required package: boot
--- finished re-building 'sftrack2_reading.Rmd'

--- re-building 'sftrack3_workingwith.Rmd' using rmarkdown
--- finished re-building 'sftrack3_workingwith.Rmd'

--- re-building 'sftrack4_groups.Rmd' using rmarkdown
--- finished re-building 'sftrack4_groups.Rmd'

--- re-building 'sftrack5_spatial.Rmd' using rmarkdown
Quitting from lines 143-152 (sftrack5_spatial.Rmd) 
Error: processing vignette 'sftrack5_spatial.Rmd' failed with diagnostics:
no applicable method for 'group_labels' applied to an object of class "NULL"
--- failed re-building 'sftrack5_spatial.Rmd'

SUMMARY: processing the following file failed:
  'sftrack5_spatial.Rmd'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SGP'
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.
Package suggested but not available for checking: 'covr'
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.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyDataCompression' is specified without 'LazyData'
Package required but not available: 'ggpubr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'qpdf'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'quantmod', 'TTR'
Error(s) in re-building vignettes:
  ...
--- re-building 'AsymptoticMarkowitz.Rnw' using knitr
Quitting from lines 54-109 (AsymptoticMarkowitz.Rnw) 
Error: processing vignette 'AsymptoticMarkowitz.Rnw' failed with diagnostics:
there is no package called 'quantmod'
--- failed re-building 'AsymptoticMarkowitz.Rnw'

--- re-building 'SharpeR.Rnw' using knitr
Quitting from lines 27-72 (SharpeR.Rnw) 
Error: processing vignette 'SharpeR.Rnw' failed with diagnostics:
there is no package called 'quantmod'
--- failed re-building 'SharpeR.Rnw'

--- re-building 'SharpeRatio.Rnw' using knitr
Quitting from lines 34-89 (SharpeRatio.Rnw) 
Error: processing vignette 'SharpeRatio.Rnw' failed with diagnostics:
there is no package called 'quantmod'
--- failed re-building 'SharpeRatio.Rnw'

SUMMARY: processing the following files failed:
  'AsymptoticMarkowitz.Rnw' 'SharpeR.Rnw' 'SharpeRatio.Rnw'

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

Packages suggested but not available for checking:
  'rvest', 'httr', 'hydromad', 'daymetr', 'elevatr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'shazam-Ex.R' failed
The error most likely occurred in:

> ### Name: plotMutability
> ### Title: Plot mutability probabilities
> ### Aliases: plotMutability
> 
> ### ** Examples
> 
> # Plot one nucleotide in circular style
> plotMutability(HH_S5F, "C")
Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
> 
> # Plot two nucleotides in barchart style
> plotMutability(HH_S5F, c("G", "T"), style="bar")
Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
Error in `[[<-.data.frame`(`*tmp*`, i, value = c(`WRC/GYW` = "#e41a1c",  : 
  replacement has 3 rows, data has 5
Calls: plotMutability ... lapply -> FUN -> modify_list -> [[<- -> [[<-.data.frame
Execution halted
Packages required but not available: 'ggpubr', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'AER'
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test_se.R:53:5): Homoscedastic and EHW standard errors on ADH data ---
  Error: there is no package called 'AER'
  Backtrace:
      x
   1. \-base::loadNamespace(x) test_se.R:53:4
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 44 ]
  Error: Test failures
  Execution halted
Package required but not available: 'plotly'

Packages suggested but not available for checking: 'covr', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'brms', 'rstan'

Packages suggested but not available for checking:
  'shinystan', 'rstanarm', 'shinytest'

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 suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'lifecycle'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'reactable'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'heatmaply', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'markdown'
  All declared Imports should be used.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'googleLanguageR', 'covr'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'lintr', 'covr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("shiny.info")
  == Failed tests ================================================================
  -- Error (test-lintr.R:1:1): (code run outside of `test_that()`) ---------------
  Error: there is no package called 'lintr'
  Backtrace:
      x
   1. \-base::loadNamespace(x) test-lintr.R:1:0
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 24 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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'
'LazyData' is specified without a 'data' directory
Running examples in 'shinyjqui-Ex.R' failed
The error most likely occurred in:

> ### Name: Interactions
> ### Title: Mouse interactions
> ### Aliases: Interactions 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
Namespace in Imports field not imported from: 'htmltools'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'KGode' 'XML' 'ggplot2' 'gridExtra' 'mvtnorm' 'reshape2' 'shinyjs'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cranlogs'
Packages required but not available: 'plotly', 'sparklyr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'purrr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'shiny' 'shinyjs'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'htmltools'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'lintr', 'covr', 'plotly'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("shiny.semantic")
  [1] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/shiny.semantic/shiny.semantic.Rcheck/tests/testthat"
  == Failed tests ================================================================
  -- Error (test_style.R:5:3): lintr ---------------------------------------------
  Error: there is no package called 'lintr'
  Backtrace:
      x
   1. \-base::loadNamespace(x) test_style.R:5:2
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 264 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rsconnect', 'rstan'

Package suggested but not available for checking: 'rstanarm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'webdriver'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'R6' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'MplusAutomation'
Package unavailable to check Rd xrefs: 'MplusAutomation'
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'
Package unavailable to check Rd xrefs: 'mvoutlier'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'curl'
Running examples in 'showtextdb-Ex.R' failed
The error most likely occurred in:

> ### Name: google_fonts
> ### Title: Meta-information for the Google Fonts
> ### Aliases: google_fonts
> 
> ### ** Examples
> 
> opensans = google_fonts("Open Sans")
Error in loadNamespace(x) : there is no package called 'curl'
Calls: google_fonts ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: 'curl'
Found the following sources/headers with CR or CRLF line endings:
  src/include/freetype/ftautoh.h
  src/include/freetype/ftcffdrv.h
  src/include/freetype/ftttdrv.h
  src/include/freetype/internal/ftdriver.h
  src/include/freetype/internal/ftpic.h
  src/include/freetype/ttunpat.h
  src/include/zconf.h
  src/include/zlib.h
Some Unix compilers require LF line endings.
Error(s) in re-building vignettes:
  ...
--- re-building 'introduction.Rmd' using rmarkdown
Loading required package: sysfonts
Loading required package: showtextdb
Quitting from lines 43-57 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'curl'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Package suggested but not available for checking: 'tidyverse'
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'covr'

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.
Package required but not available: 'ggmap'

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

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').
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.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.
Packages suggested but not available for checking: 'car', 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'MoosePopR-SightabilityPopR-Demo.Rmd' using rmarkdown
Quitting from lines 17-29 (MoosePopR-SightabilityPopR-Demo.Rmd) 
Error: processing vignette 'MoosePopR-SightabilityPopR-Demo.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'MoosePopR-SightabilityPopR-Demo.Rmd'

--- re-building 'RatioEstimator.pdf.asis' using asis
--- finished re-building 'RatioEstimator.pdf.asis'

--- re-building 'SightabilityModel.Rnw' using Sweave
--- finished re-building 'SightabilityModel.Rnw'

SUMMARY: processing the following file failed:
  'MoosePopR-SightabilityPopR-Demo.Rmd'

Error: Vignette re-building failed.
Execution halted
Note: found 28 marked UTF-8 strings
Package required but not available: 'ggpubr'

Packages suggested but not available for checking: 'covr', 'UCSCXenaTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'Seurat'

Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr', 'biovizBase'

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

Package suggested but not available for checking: 'rhdf5'

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

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: 'covr'
Package required but not available: 'GSVA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'phylobase', 'phyext2', 'phyloseq'

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

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 suggested but not available for checking: 'covr'
Packages required but not available: 'car', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'MASS' 'grid'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Package required but not available: 'RPushbullet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'magick'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'secret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'digest'
  All declared Imports should be used.
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.
Errors in running code in vignettes:
when running code in 'simFrame-intro.Rnw'
  ...

> tv <- simSapply(eusilcP, "gender", function(x) gini(x$eqIncome)$value)

> print(plot(results, true = tv, xlab = "Gini coefficient"))

> library("robCompositions")

  When sourcing 'simFrame-intro.R':
Error: there is no package called 'robCompositions'
Execution halted

  'simFrame-eusilc.Rnw'... OK
  'simFrame-intro.Rnw'... failed
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 suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'pkgdown', 'covr', 'kableExtra'
Namespaces in Imports field not imported from:
  'future' 'magrittr' 'purrr' 'rlang' 'utils'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'MCSE.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 52-67 (MCSE.Rmd) 
Error: processing vignette 'MCSE.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'MCSE.Rmd'

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 49-58 (simulation_workflow.Rmd) 
Error: processing vignette 'simulation_workflow.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'simulation_workflow.Rmd'

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 41-46 (visualization.Rmd) 
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'visualization.Rmd'

SUMMARY: processing the following files failed:
  'MCSE.Rmd' 'simulation_workflow.Rmd' 'visualization.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg38'
Package suggested but not available for checking: 'covr'
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.
Namespace in Imports field not imported from: 'quadprog'
  All declared Imports should be used.
Packages required but not available: 'gRbase', 'qpgraph'

Package suggested but not available for checking: 'clipper'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'covr', 'devtools'
Namespace in Imports field not imported from: 'DBI'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'tidyverse', 'ggpubr', 'covr'
Error(s) in re-building vignettes:
  ...
--- re-building 'intro_vignette.Rmd' using rmarkdown
--- finished re-building 'intro_vignette.Rmd'

--- re-building 'reanalysis.Rmd' using rmarkdown
Quitting from lines 21-27 (reanalysis.Rmd) 
Error: processing vignette 'reanalysis.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'reanalysis.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Package suggested but not available for checking: 'VIM'
Package unavailable to check Rd xrefs: 'VIM'
'LazyData' is specified without a 'data' directory
Package required but not available: 'ontologyPlot'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'badger'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

Package suggested but not available for checking: 'INLA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'crqa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'Effect-size-definitions.Rmd' using rmarkdown
--- finished re-building 'Effect-size-definitions.Rmd'

--- re-building 'Using-SingleCaseES.Rmd' using rmarkdown
Quitting from lines 23-29 (Using-SingleCaseES.Rmd) 
Error: processing vignette 'Using-SingleCaseES.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'Using-SingleCaseES.Rmd'

SUMMARY: processing the following file failed:
  'Using-SingleCaseES.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'pracma'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Packages required but not available:
  'PNADcIBGE', 'POFIBGE', 'PNSIBGE', 'COVIDIBGE', 'tidyverse'

Packages suggested but not available for checking: 'projmgr', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
assimilation: no visible global function definition for 'as.im'
assimilation: no visible global function definition for 'as.mask'
assimilation: no visible global function definition for 'coords'
assimilation: no visible global function definition for 'npoints'
assimilation: no visible global function definition for 'marks<-'
assimilation_pix: no visible global function definition for 'as.im'
assimilation_pix: no visible global function definition for 'as.mask'
assimilation_pix: no visible global function definition for 'coords'
assimilation_pix: no visible global function definition for 'npoints'
assimilation_pix: no visible global function definition for 'eval.im'
assimilation_pix: no visible global function definition for
  'integral.im'
assimilation_pix: no visible global function definition for 'marks<-'
core: no visible global function definition for 'inside.owin'
core: no visible global function definition for 'erosion'
core: no visible global function definition for 'as.owin'
edges: no visible global function definition for 'erosion'
edges: no visible global function definition for 'as.owin'
edges: no visible global function definition for 'periodify'
edges: no visible global function definition for 'dilation'
pairwise : cindexf: no visible global function definition for 'npoints'
pairwise : cindexf: no visible global function definition for 'marks'
pairwise: no visible global function definition for 'marks'
pairwise: no visible global function definition for 'marks<-'
pairwise: no visible global function definition for 'applynbd'
Undefined global functions or variables:
  applynbd as.im as.mask as.owin coords dilation erosion eval.im
  inside.owin integral.im marks marks<- npoints periodify
'LazyData' is specified without a 'data' directory
Package required but not available: 'systemfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Rgraphviz'
Package unavailable to check Rd xrefs: 'Rgraphviz'
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stringi'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggpubr'

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

Package suggested but not available for checking: 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'libgeos'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'brms', 'car', 'httr', 'rstanarm'
Packages suggested but not available for checking: 'brms', 'car', 'rstan'
Package unavailable to check Rd xrefs: 'brms'
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
Packages suggested but not available for checking:
  'devtools', 'car', 'tseries'
Namespaces in Imports field not imported from:
  'CompQuadForm' 'Hmisc' 'boot' 'mvtnorm'
  All declared Imports should be used.
Packages unavailable to check Rd xrefs: 'car', 'tseries'
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'dplyr' 'methods'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Package required but not available: 'modeltime'

Package suggested but not available for checking: 'timetk'

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

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

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

Packages suggested but not available for checking: 'kableExtra', 'covr'

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

Packages suggested but not available for checking: 'covr', 'texPreview'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'forecast', 'imputeTS', 'TSclust', 'tsoutliers'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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 unavailable to check Rd xrefs: 'RcmdrPlugin.SLC'
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'car'
Package suggested but not available for checking: 'car'
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rcrossref'
Error(s) in re-building vignettes:
  ...
--- re-building 'slgf_vignette.Rmd' using rmarkdown
Quitting from lines 20-28 (slgf_vignette.Rmd) 
Error: processing vignette 'slgf_vignette.Rmd' failed with diagnostics:
there is no package called 'rcrossref'
--- failed re-building 'slgf_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'pdftools', 'covr'
Error(s) in re-building vignettes:
--- re-building 'basics.Rmd' using rmarkdown
--- finished re-building 'basics.Rmd'

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

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

--- re-building 'pdfs.Rmd' using rmarkdown
Quitting from lines 11-18 (pdfs.Rmd) 
Error: processing vignette 'pdfs.Rmd' failed with diagnostics:
there is no package called 'pdftools'
--- failed re-building 'pdfs.Rmd'

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'viridisLite'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'nonlinearTseries'

Package suggested but not available for checking: 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'candisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'spatstat'
  All declared Imports should be used.
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'Introduction_to_SmallCountRounding.Rmd' using rmarkdown
Quitting from lines 18-52 (Introduction_to_SmallCountRounding.Rmd) 
Error: processing vignette 'Introduction_to_SmallCountRounding.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'Introduction_to_SmallCountRounding.Rmd'

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

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
Packages required but not available: 'httr', 'rhdf5', 'rvest'

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'sva'

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.
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.
Packages required but not available: 'GSVA', 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'lintr'
'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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'rvest'

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: 'pkgdown'
Namespaces in Imports field not imported from:
  'Rdpack' 'rmarkdown'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'demography'
Namespaces in Imports field not imported from:
  'compiler' 'lmtest'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'TTR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Package required but not available: 'greybox'

Packages suggested but not available for checking: 'Mcomp', 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'rgeos'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'nlme'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'devtools'
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'Rdpack' 'ggplot2'
  All declared Imports should be used.
Packages required but not available: 'httr', 'rvest', 'wdman', 'RSelenium'

Packages suggested but not available for checking: 'covr', '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: 'snow'
  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: 'nws'
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 suggested but not available for checking: 'biomaRt'
Namespace in Imports field not imported from: 'BiocStyle'
  All declared Imports should be used.
Package required but not available: 'biomaRt'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Note: found 833 marked UTF-8 strings
Packages required but not available: 'curl', 'httr', 'oai'

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: 'censusapi', 'tidycensus'

Package suggested but not available for checking: 'tigris'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

Packages suggested but not available for checking: 'httr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'mvoutlier'
Namespaces in Imports field not imported from:
  'R6' 'lgr'
  All declared Imports should be used.
Running examples in 'solitude-Ex.R' failed
The error most likely occurred in:

> ### 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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'crul'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: 'rlist'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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.
Packages suggested but not available for checking:
  'covr', 'devtools', 'googleCloudStorageR', 'googleLanguageR'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Packages suggested but not available for checking: 'devtools', 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'tutorial.Rmd' using rmarkdown
Sotkanet R tools (C) 2013-2021 rOpenGov
http://ropengov.org
Quitting from lines 46-50 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
Package required but not available: 'Seurat'

Packages suggested but not available for checking: 'rstan', 'DropletUtils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'gtools' 'reshape2'
  All declared Imports should be used.
Package required but not available: 'gRbase'

Packages suggested but not available for checking:
  'Rgraphviz', 'r2cytoscape', 'graphite', 'hgu95av2.db'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'quantmod', 'covr'
Error(s) in re-building vignettes:
  ...
--- re-building 'getting_started.Rmd' using rmarkdown
Quitting from lines 44-46 (getting_started.Rmd) 
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
there is no package called 'quantmod'
--- failed re-building 'getting_started.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cshapes'
Errors in running code in vignettes:
when running code in 'jss816.Rnw'
  ...

> sttdf = as(l2, "STTDF")

> print(stplot(sttdf, by = "time*id"))

> library(cshapes)

  When sourcing 'jss816.R':
Error: there is no package called 'cshapes'
Execution halted

  'stgvis.Rmd'... OK
  'jss816.Rnw' using 'UTF-8'... failed
  'sto.Rnw' using 'UTF-8'... OK
  'stpg.Rnw' using 'UTF-8'... OK
  'stsubs.Rnw' using 'UTF-8'... OK
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'googledrive', 'httr'
Package unavailable to check Rd xrefs: 'covr'
Packages suggested but not available for checking: 'covr', 'SpaDES.addins'
Packages suggested but not available for checking:
  'animation', 'googledrive', 'covr'
Namespace in Imports field not imported from: 'Require'
  All declared Imports should be used.
Packages suggested but not available for checking: 'covr', 'earlywarnings'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'earlywarnings'
'LazyData' is specified without a 'data' directory
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 required but not available: 'car'

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

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 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: 'sparklyr'

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

Package suggested but not available for checking: 'arrow'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'arrow'
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'gtable' 'rlang' 'testthat'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RCy3'
Package unavailable to check Rd xrefs: 'RCy3'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'FactoMineR', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'spatstat.linnet'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'irlba' 'knitr' 'rmarkdown'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'lubridate'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'exactextractr', 'GeNetIt'
Running examples in 'spatialEco-Ex.R' failed
The error most likely occurred in:

> ### Name: zonal.stats
> ### Title: zonal.stats
> ### Aliases: zonal.stats
> 
> ### ** Examples
> 
> library(raster)
Loading required package: sp

Attaching package: 'raster'

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

    shift

> library(sp)                                                                          
> 
> # skewness function
> skew <- function(x, na.rm = FALSE) { 
+    if (na.rm) x <- x[!is.na(x)]
+    sum( (x - mean(x)) ^ 3) / ( length(x) * sd(x) ^ 3 )  
+   }   
> 
> # percent x >= p function
> pct <- function(x, p=0.30, na.rm = FALSE) {
+   if ( length(x[x >= p]) < 1 )  return(0) 
+     if ( length(x[x >= p]) == length(x) ) return(1) 
+      else return( length(x[x >= p]) / length(x) ) 
+ }
> 
> # create some example data
> p <- raster(nrow=10, ncol=10)
>   p[] <- runif(ncell(p)) * 10
>     p <- rasterToPolygons(p, fun=function(x){x > 9})
>       r <- raster(nrow=100, ncol=100)
>         r[] <- runif(ncell(r)) 
> plot(r)
>   plot(p, add=TRUE, lwd=4) 
> 
> # run zonal statistics using skew and pct functions   
> z.skew <- zonal.stats(x = p, y = r, stats = "skew") 
Error in zonal.stats(x = p, y = r, stats = "skew") : 
  please install exactextractr before running this function
Execution halted
Package suggested but not available for checking: 'INLA'
Namespaces in Imports field not imported from:
  'RColorBrewer' 'SpatialEpi' 'dplyr' 'dygraphs' 'ggplot2'
  'htmlwidgets' 'knitr' 'leaflet' 'mapproj' 'maptools' 'rgdal' 'rgeos'
  'rmarkdown' 'shinyjs' 'spdep' 'xts'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rstan', 'SDraw'

Package suggested but not available for checking: 'INLA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cartography'
Error(s) in re-building vignettes:
  ...
--- re-building 'SpatialPosition.Rmd' using rmarkdown
--- finished re-building 'SpatialPosition.Rmd'

--- re-building 'StewartExample.Rmd' using rmarkdown
Quitting from lines 29-68 (StewartExample.Rmd) 
Error: processing vignette 'StewartExample.Rmd' failed with diagnostics:
there is no package called 'cartography'
--- failed re-building 'StewartExample.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Note: found 281 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'tibble' 'viridisLite'
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'doParallel' 'ggplot2' 'parallel'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.core', 'spatstat.linnet', 'spatstat.data',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Namespace in Imports field not imported from: 'spatstat'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'
Note: found 56 marked UTF-8 strings
Note: found 34 marked Latin-1 strings
Package suggested but not available for checking: 'covr'
Package required but not available: 'forecast'

Packages suggested but not available for checking: 'covr', 'devtools'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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'
'LazyData' is specified without a 'data' directory
Package required but not available: 'xcms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'speaq', 'genefilter', 'imputeTS', 'specmine.datasets', 'plotly'

Packages suggested but not available for checking:
  'qdap', 'qpdf', 'MAIT', 'xcms', 'KEGGREST', 'rcytoscapejs', 'curl',
  'pins'

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 'custom-plot.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 'custom-plot.rmd'

--- re-building 'decompose_var.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: Matrix
boundary (singular) fit: see ?isSingular
--- finished re-building 'decompose_var.rmd'

--- re-building 'invest-spec.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 'invest-spec.rmd'

--- re-building 'progress.rmd' using rmarkdown
--- finished re-building 'progress.rmd'

--- re-building 'specr.rmd' using rmarkdown
Quitting from lines 25-28 (specr.rmd) 
Error: processing vignette 'specr.rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'specr.rmd'

SUMMARY: processing the following file failed:
  'specr.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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 5 marked Latin-1 strings
Package required but not available: 'pdftools'

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.
Package suggested but not available for checking: 'pdftools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: 'covr'
Namespace in Imports field not imported from: 'mathjaxr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'class' 'mlbench'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Packages suggested but not available for checking: 'covr', 'robotstxt'
Packages required but not available: 'httr', 'rgbif'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package required but not available: 'plotly'

Package suggested but not available for checking: 'covr'

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.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'pkgdown', 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'httr', 'stevedore', 'magick'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'httr'
Packages suggested but not available for checking: 'covr', 'antaresViz'
Package unavailable to check Rd xrefs: 'antaresViz'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: 'kableExtra'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'KNetworkFunctions.Rmd' using rmarkdown
--- finished re-building 'KNetworkFunctions.Rmd'

--- re-building 'NKDE.Rmd' using rmarkdown
Quitting from lines 131-154 (NKDE.Rmd) 
Error: processing vignette 'NKDE.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'NKDE.Rmd'

--- re-building 'NKDEdetailed.Rmd' using rmarkdown
Loading required package: sp
rgeos version: 0.5-5, (SVN revision 640)
 GEOS runtime version: 3.6.2-CAPI-1.10.2 
 Linking to sp version: 1.4-5 
 Polygon checking: TRUE 

Checking rgeos availability: TRUE
--- finished re-building 'NKDEdetailed.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'rgbif', 'rbison', 'rebird', 'rvertnet', 'ridigbio', 'crul'

Packages suggested but not available for checking: 'taxize', 'vcr'

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pkgdown'
Note: found 7587 marked UTF-8 strings
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.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
Packages required but not available: 'smoof', 'SPOT', 'plotly'

Packages suggested but not available for checking: 'shinytest', 'devtools'

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

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

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

Package suggested but not available for checking: 'babsim.hospital'

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

Packages suggested but not available for checking:
  'babsim.hospital', 'car', 'OpenML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'sampling'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'extrafont' 'ggplot2'
  All declared Imports should be used.
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.
Package suggested but not available for checking: 'spsUtil'
Package unavailable to check Rd xrefs: 'spsUtil'
Package required but not available: 'car'

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

Package suggested but not available for checking: 'devtools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'matrixcalc' 'mvtnorm' 'sp'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'sp'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'spatstat' 'spatstat.data' 'spatstat.linnet' 'spatstat.sparse'
  'spatstat.utils' 'testthat'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
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: 'rvest', 'polite'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'r4ss'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'TTR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'shinyFiles'
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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
Package required but not available: 'BIGDAWG'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'tidyverse', 'factoextra', 'covr'
Running examples in 'SSLR-Ex.R' failed
The error most likely occurred in:

> ### Name: EMLeastSquaresClassifierSSLR
> ### Title: General Interface for EMLeastSquaresClassifier model
> ### Aliases: EMLeastSquaresClassifierSSLR
> 
> ### ** Examples
> 
> library(tidyverse)
Error in library(tidyverse) : there is no package called 'tidyverse'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   1. \-base::library(tidyverse) test-selfTraining.R:1:0
  -- Error (test-setred.R:1:1): (code run outside of `test_that()`) --------------
  Error: there is no package called 'tidyverse'
  Backtrace:
      x
   1. \-base::library(tidyverse) test-setred.R:1:0
  -- Error (test-tritraining.R:1:1): (code run outside of `test_that()`) ---------
  Error: there is no package called 'tidyverse'
  Backtrace:
      x
   1. \-base::library(tidyverse) test-tritraining.R:1:0
  
  [ FAIL 15 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'classification.Rmd' using rmarkdown
--- finished re-building 'classification.Rmd'

--- re-building 'clustering.Rmd' using rmarkdown
Quitting from lines 24-29 (clustering.Rmd) 
Error: processing vignette 'clustering.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'clustering.Rmd'

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

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

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

--- re-building 'regression.Rmd' using rmarkdown
-- Attaching packages -------------------------------------- tidymodels 0.1.3 --
v broom        0.7.7      v recipes      0.1.16
v dials        0.0.9      v rsample      0.1.0 
v dplyr        1.0.7      v tibble       3.1.2 
v ggplot2      3.3.4      v tidyr        1.1.3 
v infer        0.5.4      v tune         0.1.5 
v modeldata    0.1.0      v workflows    0.2.2 
v parsnip      0.1.6      v workflowsets 0.0.2 
v purrr        0.3.4      v yardstick    0.0.8 
-- Conflicts ----------------------------------------- tidymodels_conflicts() --
x purrr::discard() masks scales::discard()
x dplyr::filter()  masks stats::filter()
x dplyr::lag()     masks stats::lag()
x recipes::step()  masks stats::step()
* Use tidymodels_prefer() to resolve common conflicts.
--- finished re-building 'regression.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'sampleSelection'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'scanstatistics'
Namespace in Imports field not imported from: 'e1071'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'shinydashboard'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 123 marked UTF-8 strings
Namespace in Imports field not imported from: 'stabledist'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'butcher'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
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.
File
  LICENCE
is not mentioned in the DESCRIPTION file.
'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.
Package suggested but not available for checking: 'afex'
Error(s) in re-building vignettes:
  ...
--- re-building 'using-standardize.Rmd' using rmarkdown
Quitting from lines 362-367 (using-standardize.Rmd) 
Error: processing vignette 'using-standardize.Rmd' failed with diagnostics:
there is no package called 'afex'
--- failed re-building 'using-standardize.Rmd'

SUMMARY: processing the following file failed:
  'using-standardize.Rmd'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rstan'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pdftools'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'iterators' 'methods' 'rgdal'
  All declared Imports should be used.
Packages required but not available: 'drc', 'httr'

Packages suggested but not available for checking: 'plotly', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking:
  'AER', 'dynlm', 'erer', 'sampleSelection', 'Zelig'
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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.
Namespaces in Imports field not imported from:
  'pander' 'readr' 'tidyselect'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'covr', 'exactextractr', 'httr', 'starsdata'
Package unavailable to check Rd xrefs: 'exactextractr'
Running examples in 'stars-Ex.R' failed
The error most likely occurred in:

> ### Name: st_warp
> ### Title: Warp (resample) grids in stars objects to a new grid, possibly
> ###   in an new coordinate reference system
> ### Aliases: st_warp
> 
> ### ** Examples
> 
> geomatrix = system.file("tif/geomatrix.tif", package = "stars")
> (x = read_stars(geomatrix))
stars object with 2 dimensions and 1 attribute
attribute(s):
               Min. 1st Qu. Median    Mean 3rd Qu. Max.
geomatrix.tif    74     107    123 126.765     132  255
dimension(s):
  from to  offset delta                refsys point values x/y
x    1 20 1841002   1.5 WGS 84 / UTM zone 11N  TRUE   NULL [x]
y    1 20 1144003  -1.5 WGS 84 / UTM zone 11N  TRUE   NULL [y]
sheared raster with parameters: -5 -5 
> new_crs = st_crs(4326)
> y = st_warp(x, crs = new_crs)
> plot(st_transform(st_as_sfc(st_bbox(x)), new_crs), col = NA, border = 'red')
> plot(st_as_sfc(y, as_points=FALSE), col = NA, border = 'green', axes = TRUE, add = TRUE)
> image(y, add = TRUE, nbreaks = 6)
> plot(st_as_sfc(y, as_points=TRUE), pch=3, cex=.5, col = 'blue', add = TRUE)
> plot(st_transform(st_as_sfc(x, as_points=FALSE), new_crs), add = TRUE)
> # warp 0-360 raster to -180-180 raster:
> r = read_stars(system.file("nc/reduced.nc", package = "stars"))
trying to read file: C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\stars\stars.Rcheck\stars\nc\reduced.nc
Error in CPL_read_gdal(as.character(x), as.character(options), as.character(driver),  : 
  file not found
Calls: read_stars ... is_big -> read_stars -> <Anonymous> -> CPL_read_gdal
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'quantmod'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  'Hmisc' 'corrgram' 'datasets' 'dplyr' 'psych' 'psycho' 'rpivotTable'
  'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'covr', 'pkgdown'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'asreml'
Packages required but not available: 'animation', 'factoextra'

Package suggested but not available for checking: 'asreml'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'asreml'
Namespace in Imports field not imported from: 'mapproj'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 suggested but not available for checking: 'covr'
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package required but not available: 'tergm'

Packages suggested but not available for checking: 'EpiModel', 'ndtv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'httr', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Hmisc' 'corrgram' 'datasets' 'dplyr' 'psych' 'psycho' 'rpivotTable'
  'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'curl', 'pkgdown', 'kableExtra', 'pct', 'osmdata', 'covr'
Running 'skip-download.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   4.     \-base:::withOneRestart(expr, restarts[[1L]])
   5.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test-utils.R:36:3): locate_files & locate_one_file works -------------
  Error: there is no package called 'curl'
  Backtrace:
      x
   1. +-global::skip_download() test-utils.R:36:2
   2. \-base::loadNamespace(x)
   3.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     \-base:::withOneRestart(expr, restarts[[1L]])
   5.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 8 | WARN 2 | SKIP 6 | PASS 33 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking: 'afex', 'metaBMA'
Packages required but not available: 'httr', 'curl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'covr'
'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.
Packages suggested but not available for checking:
  'covr', 'devtools', 'lintr', 'pkgdown', 'rhub'
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

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

> ### Name: StepwiseTest-package
> ### Title: Multiple Testing Method to Control Generalized Family-Wise Error
> ###   Rate and False Discovery Proportion
> ### Aliases: StepwiseTest-package StepwiseTest FWERkControl FDPControl
> 
> ### ** Examples
> 
> # Specify the model parameters
> m_null = 3
> m_alt  = 7
> m = m_null + m_alt
> mu = c( rep(0, m_null), rep(0.5,m_alt) )
> rho = 0.25
> omega= (1-rho)*diag(1,m) + rho*matrix(1,m,m)
> v=t(chol(omega))
> 
> # generate the data
> n = 100
> y = mu%*%matrix(1,1,n)+ v %*% matrix(rnorm(m*n),m,n)
> 
> # calculate the test statistics and bootstrap statistics
> library(foreach)
> library(tseries)
Error in library(tseries) : there is no package called 'tseries'
Execution halted
Note: found 42 marked UTF-8 strings
Package required but not available: 'curl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rvest'

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'nnfor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'SnowballC' 'tm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'huge' 'readr' 'scales' 'shinyjs'
  All declared Imports should be used.
Package required but not available: 'forecast'

Package suggested but not available for checking: 'demography'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > # Since the tests are supposed to guarantee that the bundled version installed
  > # correctly, they are skipped.
  > if (!is_solaris()) {
  +   test_check("stockfish")
  + }
  == Failed tests ================================================================
  -- Failure (test-fish.R:12:3): engine works ------------------------------------
  engine$isready() is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'quantmod', 'TTR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'lintr'
Note: found 22474 marked UTF-8 strings
Running 'lint.R'
Running the tests in 'tests/lint.R' failed.
Complete output:
  > library("lintr")
  Error in library("lintr") : there is no package called 'lintr'
  Execution halted
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 327 marked UTF-8 strings
Packages required but not available: 'curl', 'httr'

Packages suggested but not available for checking:
  'dodgr', 'cyclestreets', 'pct', 'osrm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'arrow'

Package suggested but not available for checking: 'plotly'

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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'sna'
  All declared Imports should be used.
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'bnlearn'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tidyverse'
Namespace in Imports field not imported from: 'ks'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'HDoutliers'
Package suggested but not available for checking: 'animation'
Namespace in Imports field not imported from: 'dbscan'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'animation'
Package required but not available: 'drc'

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: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'usethis'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  icu69/common/cstring.h:43:70: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 156 bytes from a string of length 156 [-Wstringop-truncation]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/stringi/stringi.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'covr'
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'STRaitRazoR'
Package suggested but not available for checking: 'tidycensus'
Packages required but not available: 'car', 'phia'

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

Packages suggested but not available for checking: 'demography', 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'car', 'dynlm', 'tseries'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
Package unavailable to check Rd xrefs: 'tseries'
Packages suggested but not available for checking:
  'car', 'dynlm', 'tseries', 'bfast'
Packages unavailable to check Rd xrefs: 'tseries', 'bfast'
Package suggested but not available for checking: 'MplusAutomation'
'LazyData' is specified without a 'data' directory
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'kableExtra'
Note: found 2 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building 'stylest-vignette.Rmd' using rmarkdown
Quitting from lines 22-23 (stylest-vignette.Rmd) 
Error: processing vignette 'stylest-vignette.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'stylest-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'UpSetR' 'alluvial' 'gridBase'
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'DT' 'bsplus' 'colourpicker' 'grDevices' 'graphics' 'jsonlite'
  'purrr' 'shinyWidgets' 'shinyjs'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'GSVA', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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.
Namespace in Imports field not imported from: 'tidyselect'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'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.
Package required but not available: 'rmapshaper'

Package suggested but not available for checking: 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'plotly'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'magick'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'INLA', 'rdhs'
'LazyData' is specified without a 'data' directory
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.
Packages required but not available: 'rmapshaper', 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Package suggested but not available for checking: 'car'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > test_check("superb")
  Loading required package: superb
  ==> THIS IS A TEST OF runDebug <==
  == Failed tests ================================================================
  -- Error (test_GRD.R:59:5): A complete test with plots and anova ---------------
  Error: there is no package called 'car'
  Backtrace:
      x
   1. \-base::library(car) test_GRD.R:59:4
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 163 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'devtools', 'genefilter', 'sva'
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.
Packages suggested but not available for checking: 'car', 'covr', 'lintr'
Namespaces in Imports field not imported from:
  'backports' 'methods'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Backtrace:
      x
   1. +-supernova:::expect_supernova(two_way) test-supernova.r:316:2
   2. | \-supernova:::expect_partials(object, type, ...) test-supernova.r:80:4
   3. |   \-supernova:::get_partials(object$fit, type = type) test-supernova.r:130:2
   4. |     \-base::suppressMessages(car::Anova) test-supernova.r:25:2
   5. |       \-base::withCallingHandlers(...)
   6. \-base::loadNamespace(x) test-supernova.r:25:2
   7.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     \-base:::withOneRestart(expr, restarts[[1L]])
   9.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 3 | WARN 1 | SKIP 11 | PASS 204 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'covr'
Package required but not available: 'afex'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'rcrossref'

Packages suggested but not available for checking: 'covr', 'fulltext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'doParallel' 'pROC'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'learnr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rootSolve'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'plyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: 'survival'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'animation', 'INLA'
Package unavailable to check Rd xrefs: 'animation'
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 suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'AER'
Package unavailable to check Rd xrefs: 'AER'
Running '3stage2phase.R'
  Running 'DBIcheck.R'
  Running 'api.R'
  Running 'badcal.R'
  Comparing 'badcal.Rout' to 'badcal.Rout.save' ... OK
  Running 'bycovmat.R'
  Running 'caleg.R'
  Running 'check.R'
  Comparing 'check.Rout' to 'check.Rout.save' ... OK
  Running 'deff.R'
  Comparing 'deff.Rout' to 'deff.Rout.save' ... OK
  Running 'domain.R'
  Comparing 'domain.Rout' to 'domain.Rout.save' ... OK
  Running 'fpc.R'
  Running 'glm-scoping.R'
  Running 'kalton.R'
  Comparing 'kalton.Rout' to 'kalton.Rout.save' ... OK
  Running 'lonely.psu.R'
  Comparing 'lonely.psu.Rout' to 'lonely.psu.Rout.save' ... OK
  Running 'multistage.R'
  Running 'nwts-cch.R'
  Running 'nwts.R'
  Comparing 'nwts.Rout' to 'nwts.Rout.save' ... OK
  Running 'pps.R'
  Running 'quantile.R'
  Comparing 'quantile.Rout' to 'quantile.Rout.save' ... OK
  Running 'rakecheck.R'
  Comparing 'rakecheck.Rout' to 'rakecheck.Rout.save' ... OK
  Running 'raowuboot.R'
  Comparing 'raowuboot.Rout' to 'raowuboot.Rout.save' ... OK
  Running 'regpredict.R'
  Comparing 'regpredict.Rout' to 'regpredict.Rout.save' ... OK
  Running 'scoping.R'
  Running 'survcurve.R'
  Comparing 'survcurve.Rout' to 'survcurve.Rout.save' ... OK
  Running 'svyivreg.R'
Running the tests in 'tests/svyivreg.R' failed.
Last 13 lines of output:
  > library(survey)
  Loading required package: grid
  Loading required package: Matrix
  Loading required package: survival
  
  Attaching package: 'survey'
  
  The following object is masked from 'package:graphics':
  
      dotchart
  
  > library(AER)
  Error in library(AER) : there is no package called 'AER'
  Execution halted
'LazyData' is specified without a 'data' directory
'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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

Packages suggested but not available for checking: 'shinystan', 'INLA'

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

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.
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.
Package required but not available: 'survminer'

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.
Namespace in Imports field not imported from: 'quadprog'
  All declared Imports should be used.
Note: found 525 marked UTF-8 strings
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'base'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'survminer'
Error(s) in re-building vignettes:
  ...
--- re-building 'survParamSim.Rmd' using rmarkdown
Quitting from lines 53-58 (survParamSim.Rmd) 
Error: processing vignette 'survParamSim.Rmd' failed with diagnostics:
there is no package called 'survminer'
--- failed re-building 'survParamSim.Rmd'

SUMMARY: processing the following file failed:
  'survParamSim.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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'survminer'

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tsDyn'
Package suggested but not available for checking: 'covr'
Malformed Description field: should contain one or more complete sentences.
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'covr'
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.
Package suggested but not available for checking: 'plumber'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'timetk'

Packages suggested but not available for checking:
  'robets', 'tidyquant', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'swephRdata'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'mapdata' 'utils'
  All declared Imports should be used.
Packages required but not available: 'rvest', 'pdftools'

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()`:
'ewcdf' is not an exported object from 'namespace:spatstat'
Warning: Computation failed in `stat_ecdf()`:
'ewcdf' is not an exported object from 'namespace:spatstat'
Warning: Computation failed in `stat_ecdf()`:
'ewcdf' is not an exported object from 'namespace:spatstat'
Warning: Computation failed in `stat_ecdf()`:
'ewcdf' is not an exported object from 'namespace:spatstat'
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: 'swirl'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
Running 'winpath.R'
Running the tests in 'tests/winpath.R' failed.
Last 13 lines of output:
  > trace(lazyRepo, stop)
  Tracing function "lazyRepo" in environment <namespace:switchr>
  Warning: Tracing only in the namespace; to untrace you will need:
  untrace("lazyRepo", where = getNamespace("switchr"))
  [1] "lazyRepo"
  attr(,"package")
  [1] "switchr"
  > install_packages("switchr", repos = defaultRepos(), lib = tmplib)
  caught error: Error: Bioconductor does not yet build and check packages for R version 4.2; see
    https://bioconductor.org/install
  
  Error in getStringType(repos) : 
    Got mixed string types (likely in seed). This shouldn't happen.
  Calls: install_packages -> install_packages -> getStringType
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'SWMPr'

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

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: 'cplexAPI'
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: 'cplexAPI'
Package suggested but not available for checking: 'cplexAPI'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
Package required but not available: 'RSDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
---- unloading
'LazyData' is specified without a 'data' directory
Running examples in 'symengine-Ex.R' failed
The error most likely occurred in:

> ### Name: D,SymEngineDataType-method
> ### Title: Derivatives of a Symbolic Expression
> ### Aliases: D,SymEngineDataType-method
> 
> ### ** Examples
> 
> expr <- S(~ exp(x))
> D(expr) == expr
[1] TRUE
> expr <- S(~ x^2 + 2*x + 1)
> D(expr)
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(symengine)
  SymEngine Version: 0.4.1
   _____           _____         _         
  |   __|_ _ _____|   __|___ ___|_|___ ___ 
  |__   | | |     |   __|   | . | |   | -_|
  |_____|_  |_|_|_|_____|_|_|_  |_|_|_|___|
        |___|               |___|          
  > 
  > test_check("symengine")
Error(s) in re-building vignettes:
  ...
--- re-building 'odesystem.Rmd' using rmarkdown
--- re-building 'quick_start.Rmd' using rmarkdown
SUMMARY: processing the following files failed:
  'odesystem.Rmd' 'quick_start.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'library' or 'require' calls to packages already attached by Depends:
  'tcltk' 'tkrplot'
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'metR'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'acs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'devtools'
Package suggested but not available for checking: 'ChainLadder'
Error(s) in re-building vignettes:
  ...
--- re-building 'SynthETIC-demo.Rmd' using rmarkdown
Quitting from lines 981-996 (SynthETIC-demo.Rmd) 
Error: processing vignette 'SynthETIC-demo.Rmd' failed with diagnostics:
there is no package called 'ChainLadder'
--- failed re-building 'SynthETIC-demo.Rmd'

SUMMARY: processing the following file failed:
  'SynthETIC-demo.Rmd'

Error: Vignette re-building failed.
Execution halted
'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.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'curl'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'unix'
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.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.
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'table1-examples.Rmd' using rmarkdown

Attaching package: 'table1'

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

    units, units<-

--- finished re-building 'table1-examples.Rmd'

--- re-building 'table1-latex.Rmd' using rmarkdown
Quitting from lines 34-59 (table1-latex.Rmd) 
Error: processing vignette 'table1-latex.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'table1-latex.Rmd'

SUMMARY: processing the following file failed:
  'table1-latex.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
    1. +-testthat::expect_equal(...) test-modules-print.R:538:8
    2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
    3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
    4. \-tableone:::ModuleConvertNonNormal(...)
    5.   +-base::data.frame(...)
    6.   +-base::paste0(...)
    7.   \-tableone:::ModuleFormatNumericVector(...)
    8.     +-base::do.call(...)
    9.     +-(function (x, ...) ...
   10.     \-base::format.default(...)
   11.       \-base::prettyNum(...)
  
  [ FAIL 7 | WARN 135 | SKIP 0 | PASS 531 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'jsonvalidate'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'kableExtra'
Package unavailable to check Rd xrefs: 'kableExtra'
Errors in running code in vignettes:
when running code in 'tables.Rnw'
  ...
\bottomrule 
\end{tabular}

> library(magrittr)

> library(kableExtra)

  When sourcing 'tables.R':
Error: there is no package called 'kableExtra'
Execution halted

  'HTML.Rmd' using 'UTF-8'... OK
  'knitrTables.Rmd'... OK
  'tables.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'HTML.Rmd' using rmarkdown
Quitting from lines 142-150 (HTML.Rmd) 
Error: processing vignette 'HTML.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'HTML.Rmd'

--- re-building 'knitrTables.Rmd' using rmarkdown
Quitting from lines 1277-1282 (knitrTables.Rmd) 
Error: processing vignette 'knitrTables.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'knitrTables.Rmd'

--- re-building 'tables.Rnw' using Sweave
Loading required namespace: Hmisc

Error: processing vignette 'tables.Rnw' failed with diagnostics:
 chunk 61 
Error in library(kableExtra) : there is no package called 'kableExtra'

--- failed re-building 'tables.Rnw'

SUMMARY: processing the following files failed:
  'HTML.Rmd' 'knitrTables.Rmd' 'tables.Rnw'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'gee' 'survival'
  All declared Imports should be used.
Packages suggested but not available for checking: 'covr', 'kableExtra'
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Note: found 81 marked UTF-8 strings
Namespaces in Imports field not imported from:
  'stringr' 'tibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'covr', 'forecast'
Package unavailable to check Rd xrefs: 'forecast'
Error(s) in re-building vignettes:
  ...
--- re-building 'new-high-level-functions.Rmd' using rmarkdown
--- finished re-building 'new-high-level-functions.Rmd'

--- re-building 'new-methods.Rmd' using rmarkdown
Quitting from lines 100-103 (new-methods.Rmd) 
Error: processing vignette 'new-methods.Rmd' failed with diagnostics:
there is no package called 'forecast'
--- failed re-building 'new-methods.Rmd'

--- re-building 'new-panel-functions.Rmd' using rmarkdown
--- finished re-building 'new-panel-functions.Rmd'

--- re-building 'tactile-theme.Rmd' using rmarkdown
--- finished re-building 'tactile-theme.Rmd'

SUMMARY: processing the following file failed:
  'new-methods.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'readr'
  All declared Imports should be used.
Package suggested but not available for checking: 'tidyverse'
'LazyData' is specified without a 'data' directory
Package required but not available: 'smoother'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'jiebaR'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'curl'
Packages suggested but not available for checking:
  'arrow', 'aws.s3', 'curl', 'usethis'
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'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.
Namespaces in Imports field not imported from:
  'SnowballC' 'dplyr' 'igraph' 'tm' 'wordcloud2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tashudata'
Namespaces in Imports field not imported from:
  'drat' 'plyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Package unavailable to check Rd xrefs: 'kableExtra'
'LazyData' is specified without a 'data' directory
Running examples in 'tatoo-Ex.R' failed
The error most likely occurred in:

> ### Name: as_latex
> ### Title: Convert a Table to Latex Code
> ### Aliases: as_latex save_pdf view_pdf
> 
> ### ** Examples
> 
>   as_latex(iris)
Error in loadNamespace(x) : there is no package called 'kableExtra'
Calls: as_latex ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'covr'

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

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

Package suggested but not available for checking: 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'bold', 'rredlist', 'rotl', 'ritis', 'worrms', 'natserv',
  'wikitaxa'

Package suggested but not available for checking: 'vcr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'ggalt'
Error(s) in re-building vignettes:
  ...
--- re-building 'intro_to_tbrf.Rmd' using rmarkdown
Quitting from lines 123-138 (intro_to_tbrf.Rmd) 
Error: processing vignette 'intro_to_tbrf.Rmd' failed with diagnostics:
there is no package called 'ggalt'
--- failed re-building 'intro_to_tbrf.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'Matrix' 'quadprog'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tcgsaseq', 'GEOquery'
Unknown package 'tcgsaseq' in Rd xrefs
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
Packages required but not available: 'plotly', 'ggpubr', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'colorspace' 'psych'
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'Mcomp', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lintr'
Namespace in Imports field not imported from: 'scales'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'covr'
Package required but not available: 'SPOT'

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

Package suggested but not available for checking: 'plotly'

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

Warning in file(con, "r") :
  cannot open file 'C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\tealeaves\tmp\RtmpkXWLZM\file61704527792c': Permission denied
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> readLines -> file
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
'LazyData' is specified without a 'data' directory
Running examples in 'telemac-Ex.R' failed
The error most likely occurred in:

> ### Name: tin
> ### Title: TIN object
> ### Aliases: tin tin.character tin.matrix tin.list print.t2d_tin
> 
> ### ** Examples
> 
> 
> ### BASIC FUNCTIONALITY ###
> library(sf)
Linking to GEOS 3.6.2, GDAL 3.0.4, PROJ 7.0.0
> 
> # load boundary as sf linestring
> bnd <- st_read(system.file("dem/boundary_lagos.gpkg", package = "telemac"))
Reading layer `aoi_line_small' from data source 
  `C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\telemac\telemac.Rcheck\telemac\dem\boundary_lagos.gpkg' 
  using driver `GPKG'
Simple feature collection with 1 feature and 1 field
Geometry type: LINESTRING
Dimension:     XY
Bounding box:  xmin: 530280 ymin: 729900 xmax: 536310 ymax: 744300
Projected CRS: WGS 84 / UTM zone 31N
> 
> # create t2d_tin object
> tin_obj <- tin(list(boundary = bnd), s = 90, a = 100^2, q = 30)
> 
> # inspection
> tin_obj
Object of class t2d_tin: TELEMAC mesh (TIN)
The mesh is composed of 7991 elements (triangles) and 4257 points.
> str(tin_obj)
List of 5
 $ points    : num [1:4257, 1:2] 531990 531910 531843 531780 531691 ...
 $ triangles : int [1:7991, 1:3] 526 22 878 23 522 630 22 1270 2085 25 ...
 $ edges     : int [1:12247, 1:2] 526 1153 911 22 21 19 878 751 618 23 ...
 $ boundaries: int [1:521] 21 20 19 18 17 16 15 14 13 12 ...
 $ breaklines: NULL
 - attr(*, "class")= chr [1:2] "t2d_tin" "list"
> plot(tin_obj, pch = ".")
> 
> ### DEALING WITH INTERSECTING BREAKLINES ###
> library(sf)
> library(tidyverse)
Error in library(tidyverse) : there is no package called 'tidyverse'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 't2d_basics.Rmd' using rmarkdown
Loading required package: sp
Linking to GEOS 3.6.2, GDAL 3.0.4, PROJ 7.0.0
Quitting from lines 31-35 (t2d_basics.Rmd) 
Error: processing vignette 't2d_basics.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 't2d_basics.Rmd'

--- re-building 't2d_rainfall_runoff.Rmd' using rmarkdown
Quitting from lines 30-35 (t2d_rainfall_runoff.Rmd) 
Error: processing vignette 't2d_rainfall_runoff.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 't2d_rainfall_runoff.Rmd'

SUMMARY: processing the following files failed:
  't2d_basics.Rmd' 't2d_rainfall_runoff.Rmd'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'tsBSS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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
Package required but not available: 'tergm'

Package suggested but not available for checking: 'EpiModel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/tergm/tergm.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'magick'

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'gurobi', 'kableExtra', 'pkgdown'
Error(s) in re-building vignettes:
  ...
--- re-building 'constraints.Rmd' using rmarkdown
Quitting from lines 20-28 (constraints.Rmd) 
Error: processing vignette 'constraints.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'constraints.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking:
  'covr', 'curl', 'usethis'
Package unavailable to check Rd xrefs: 'curl'
Packages required but not available: 'devtools', 'usethis'

Package suggested but not available for checking: 'covr'

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

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

Packages suggested but not available for checking:
  'covr', 'kableExtra', 'pdftools', 'texreg'

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

Packages which this enhances but not available for checking:
  'AER', 'brms', 'btergm', 'dynlm', 'forecast', 'Zelig'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'googleAuthR', 'googleLanguageR', 'httr', 'mscstts'

Packages suggested but not available for checking: 'aws.polly', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: 'lexicon'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'pdftools'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ggpubr'
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:
  'Rgraphviz', 'concaveman'
Packages suggested but not available for checking: 'rio', 'covr'
Note: found 3 marked UTF-8 strings
Packages required but not available: 'curl', 'pdftools', 'rvest'

Package suggested but not available for checking: 'tesseract'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'stringr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'textreadr'
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'pins', 'magick'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'ggm'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'curl'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   6.   \-thematic:::update_gfonts()
  -- Error (test-lattice.R:7:1): (code run outside of `test_that()`) -------------
  Error: Using an updated set of google fonts requires the curlpackage to be installed
  Backtrace:
      x
   1. +-thematic::thematic_theme(...) test-lattice.R:7:0
   2. | +-base::structure(...)
   3. | \-thematic:::as_font_spec(font)
   4. |   \-thematic:::is_font_spec(font)
   5. \-thematic::font_spec("Rock Salt", update = TRUE)
   6.   \-thematic:::update_gfonts()
  
  [ FAIL 3 | WARN 0 | SKIP 8 | PASS 25 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'plotly', 'rstan'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'hts'

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: 'devtools'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'curl'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rstan', 'MplusAutomation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
.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.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
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').
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'rstan', 'rstanarm', 'brms', 'covr', 'pkgdown'
Packages unavailable to check Rd xrefs: 'brms', 'rstanarm', 'rstan'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building 'tidyBdE.Rmd' using rmarkdown
Quitting from lines 60-68 (tidyBdE.Rmd) 
Error: processing vignette 'tidyBdE.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'tidyBdE.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'tidyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr', 'tigris', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'grDevices' 'graphics' 'utils'
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'qpdf', 'covr'
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'MplusAutomation'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'modeldata' 'workflowsets'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'europepmc', 'covr'
Package required but not available: 'rstanarm'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages required but not available:
  'quantmod', 'httr', 'curl', 'Quandl', 'riingo', 'alphavantager',
  'timetk', 'TTR'

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: 'covr'
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'redcapAPI'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 24 marked UTF-8 strings
Package required but not available: 'httr'

Packages suggested but not available for checking: 'httptest', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'MplusAutomation'

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'SingleR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 113 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Packages suggested but not available for checking: 'covr', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'tigris', 'usethis', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'googledrive', 'googlesheets4', 'httr', 'rvest'

Package suggested but not available for checking: 'covr'

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

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: 'httr'

Package suggested but not available for checking: 'tidycensus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'curl'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/tiledb/tiledb.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'sp'
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: 'lwgeom'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'rgdal'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'base'
  All declared Imports should be used.
Package suggested but not available for checking: 'httr'
'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
Namespace in Imports field not imported from: 'lubridate'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'tseries'

Package suggested but not available for checking: 'devtools'

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

Packages suggested but not available for checking:
  'tidyquant', 'modeltime', 'tidyverse', 'robets', 'tseries'

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.
Namespace in Imports field not imported from: 'lubridate'
  All declared Imports should be used.
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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Packages required but not available: 'curl', 'rvest'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'cpp11' 'dplyr' 'magrittr' 'stringi'
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'snow'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'jsonvalidate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'rmapshaper', 'osmdata', 'covr'
Packages suggested but not available for checking: 'rmapshaper', 'osmdata'
Package unavailable to check Rd xrefs: 'rmapshaper'
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 134043 marked UTF-8 strings
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'curl'
'LazyData' is specified without a 'data' directory
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'pdftools', 'Rcampdf', 'Rgraphviz', 'Rpoppler',
  'tm.lexicon.GeneralInquirer'
Packages unavailable to check Rd xrefs: 'readtext', 'pdftools', 'Rpoppler'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Namespace in Imports field not imported from: 'rjson'
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Note: found 1 marked UTF-8 string
Packages suggested but not available for checking:
  'cancensus', 'tidycensus'
Namespaces in Imports field not imported from:
  'geojsonsf' 'lwgeom'
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Package required but not available: 'robCompositions'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'cowplot' 'ggplot2' 'jsonlite'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'OAIHarvester', 'corpus.JSS.papers'
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'httr'
Namespaces in Imports field not imported from:
  'rappdirs' 'withr'
  All declared Imports should be used.
Package required but not available: 'pins'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'magick'
Package unavailable to check Rd xrefs: 'magick'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'WikipediR'

Packages suggested but not available for checking: 'toscaData', 'devtools'

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.
Namespaces in Imports field not imported from:
  'R6' 'jmvcore'
  All declared Imports should be used.
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tidyverse', 'kableExtra'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Tplyr.Rmd' using rmarkdown
Quitting from lines 20-27 (Tplyr.Rmd) 
Error: processing vignette 'Tplyr.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'Tplyr.Rmd'

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

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

--- re-building 'desc.Rmd' using rmarkdown
Quitting from lines 20-26 (desc.Rmd) 
Error: processing vignette 'desc.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'desc.Rmd'

--- re-building 'options.Rmd' using rmarkdown
Quitting from lines 20-28 (options.Rmd) 
Error: processing vignette 'options.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'options.Rmd'

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

--- re-building 'table.Rmd' using rmarkdown
Quitting from lines 20-26 (table.Rmd) 
Error: processing vignette 'table.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'table.Rmd'

SUMMARY: processing the following files failed:
  'Tplyr.Rmd' 'desc.Rmd' 'options.Rmd' 'table.Rmd'

Error: Vignette re-building failed.
Execution halted
Subdirectory 'tpr/src' contains apparent object files/libraries
  approx.o
Object files/libraries should not be included in a source package.
Package required but not available: 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'move', 'moveVis', 'moveHMM'
Packages unavailable to check Rd xrefs: 'moveVis', 'moveHMM'
Packages required but not available: 'trackeR', 'plotly', 'V8'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'httr'
Packages suggested but not available for checking: 'covr', 'animation'
Namespaces in Imports field not imported from:
  'ggplot2' 'jpeg' 'pastecs' 'plyr' 'raster'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'neuralnet'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages required but not available: 'httr', 'crul', 'taxize', 'rvest'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'forecast', 'taxidata'
Package unavailable to check Rd xrefs: 'forecast'
Running examples in 'trajectories-Ex.R' failed
The error most likely occurred in:

> ### Name: auto.arima.Track
> ### Title: Fitting arima model to a track
> ### Aliases: auto.arima.Track
> 
> ### ** Examples
> 
> X <- rTrack()
> auto.arima.Track(X)
Error in auto.arima.Track(X) : 
  package forecast required, please install it first
Execution halted
Errors in running code in vignettes:
when running code in 'article.Rnw'
  ...

> plot(w, lwd = 2, main = "w")

> plot(z, lwd = 2, main = "z")

> library("forecast")

  When sourcing 'article.R':
Error: there is no package called 'forecast'
Execution halted

  'article.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'article.Rnw' using Sweave

Error: processing vignette 'article.Rnw' failed with diagnostics:
 chunk 14 
Error in library("forecast") : there is no package called 'forecast'

--- failed re-building 'article.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mlrMBO', 'smoof'

Package suggested but not available for checking: 'kableExtra'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'httr'

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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'animation'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
rtrapezoid: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggpubr', 'TSA'

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

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

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

Package suggested but not available for checking: 'adaptiveGPCA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'tree'
  All declared Imports should be used.
Package suggested but not available for checking: 'TreeDistData'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
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.
Packages required but not available: 'adephylo', 'RLumShiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'maptools'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'plotly', 'covr'
Running examples in 'trelliscopejs-Ex.R' failed
The error most likely occurred in:

> ### Name: cog
> ### Title: Cast Column as a Cognostic
> ### Aliases: cog
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(tidyr)
> library(purrr)
> library(ggplot2)
> library(plotly)
Error in library(plotly) : there is no package called 'plotly'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(trelliscopejs)
  > 
  > test_check("trelliscopejs")
  == Failed tests ================================================================
  -- Error (test-trelliscope.R:8:3): examples run without barfing ----------------
  Error: there is no package called 'plotly'
  Backtrace:
      x
   1. +-base::suppressPackageStartupMessages(library(plotly)) test-trelliscope.R:8:2
   2. | \-base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
   3. \-base::library(plotly)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'trelliscopejs.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 174-192 (trelliscopejs.Rmd) 
Error: processing vignette 'trelliscopejs.Rmd' failed with diagnostics:
there is no package called 'plotly'
--- failed re-building 'trelliscopejs.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'brms', 'covr'
Package unavailable to check Rd xrefs: 'brms'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'forecast', 'Rssa', 'tseries', 'imputeTS'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plotly'
Namespaces in Imports field not imported from:
  'boot' 'chron' 'randtoolbox'
  All declared Imports should be used.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggtern'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'ez'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'countrycode' 'haven' 'readstata13' 'stringr' 'tibble' 'tidyr'
  All declared Imports should be used.
Note: found 118 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
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: 'httr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'forecast', 'tseries'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- Error (test_nonstandard_cnames.R:43:3): first object determines col order and col names (#166) --
  Error: Additional packages needed. To install, use:
  
    install.packages("forecast")
  Backtrace:
      x
   1. +-testthat::expect_identical(names(ts_forecast(ts2)), names(ts2)) test_nonstandard_cnames.R:43:2
   2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
   3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
   4. \-tsbox::ts_forecast(ts2)
   5.   \-tsbox::load_suggested("forecast")
  
  [ FAIL 2 | WARN 0 | SKIP 13 | PASS 416 ]
  Error: Test failures
  Execution halted
Package required but not available: 'forecast'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'TSmisc', 'tseries'
Packages unavailable to check Rd xrefs: 'TSmisc', 'tseries'
Errors in running code in vignettes:
when running code in 'Guide.Stex'
  ...
> z <- TSget("ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT", 
+     eurostat)
Jun 22, 2021 4:30:12 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest
Jun 22, 2021 4:30:12 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: Internal Server Error

  When sourcing 'Guide.R':
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
when running code in 'GuideAppendix.Stex'
  ...

> options(continue = "  ")

> user <- Sys.getenv("MYSQL_USER")

> setup <- RMySQL::dbConnect(RMySQL::MySQL(), dbname = "test")

  When sourcing 'GuideAppendix.R':
Error: Failed to connect to database: Error: Can't connect to MySQL server on 'localhost' (10061)
Execution halted

  'Guide.Stex'... failed
  'GuideAppendix.Stex'... failed
  'GuideDevel.Stex'... OK
Package suggested but not available for checking: 'tseries'
'LazyData' is specified without a 'data' directory
Package required but not available: 'TSclust'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'quantmod'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Package suggested but not available for checking: 'tseries'
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.
Packages required but not available: 'forecast', 'tseries'

Package suggested but not available for checking: 'Mcomp'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'tsibble'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package required but not available: 'plotly'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
Packages required but not available: 'tseries', 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'covr'
GNU make is a SystemRequirements.
Running 'fontconfig-helper.R'
  Running 'spelling.R'
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if (requireNamespace("spelling", quietly = TRUE)) {
  +   if (!covr::in_covr()) {
  +     spelling::spell_check_test(
  +       vignettes = TRUE, error = FALSE,
  +       skip_on_cran = TRUE
  +     )
  +   }
  + }
  Error in loadNamespace(x) : there is no package called 'covr'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tseries'
Package suggested but not available for checking: 'tseries'
Package required but not available: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tseries'
Package required but not available: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'forecast'

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

Package suggested but not available for checking: 'car'

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

Packages suggested but not available for checking: 'devtools', 'quantmod'

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

Package suggested but not available for checking: 'thief'

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

> ### Name: TSVC
> ### Title: Tree-Structured Modelling of Varying Coefficients
> ### Aliases: TSVC print.TSVC
> 
> ### ** Examples
> 
> # Swiss Labour Market 
> library(AER)
Error in library(AER) : there is no package called 'AER'
Execution halted
Packages required but not available: 'plotly', 'forecast'

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'dplyr' 'shinyAce' 'shinyjs'
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: 'latticeExtra'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

Package which this enhances but not available for checking: 'quantmod'

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

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

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

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Package required but not available: 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
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.
Packages required but not available: 'httr', 'tidyverse', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'systemfit'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
Package suggested but not available for checking: 'OVtool'
Errors in running code in vignettes:
when running code in 'twang.rnw'
  ...


> glm5 <- lm(sqrt(re78) ~ treat + age + educ + black + 
+     hispan + nodegree + married + sqrt(re74) + sqrt(re75), data = lalonde)

> library(OVtool)

  When sourcing 'twang.R':
Error: there is no package called 'OVtool'
Execution halted

  'iptw.rnw' using 'UTF-8'... OK
  'mnps.rnw' using 'UTF-8'... OK
  'twang.rnw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
--- re-building 'iptw.rnw' using Sweave
To reproduce results from prior versions of the twang package, please see the version="legacy" option described in the documentation.
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

--- finished re-building 'iptw.rnw'

--- re-building 'mnps.rnw' using Sweave
To reproduce results from prior versions of the twang package, please see the version="legacy" option described in the documentation.
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

--- finished re-building 'mnps.rnw'

--- re-building 'twang.rnw' using Sweave
To reproduce results from prior versions of the twang package, please see the version="legacy" option described in the documentation.
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

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

    dotchart


Error: processing vignette 'twang.rnw' failed with diagnostics:
 chunk 24 
Error in library(OVtool) : there is no package called 'OVtool'

--- failed re-building 'twang.rnw'

SUMMARY: processing the following file failed:
  'twang.rnw'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
TwoCop: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'onewaytests', 'car'

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

Package which this enhances but not available for checking: 'sl3'
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'exifr', 'link2GI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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 suggested but not available for checking: 'DMwR2'
Package required but not available: 'rstan'

Packages suggested but not available for checking:
  'covr', 'devtools', 'pkgdown'

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

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'curl'
GNU make is a SystemRequirements.
Packages required but not available: 'ggpubr', 'UCSCXenaTools'

Packages suggested but not available for checking:
  'covr', 'plotly', 'survminer'

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

Package suggested but not available for checking: 'covr'

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

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

Packages suggested but not available for checking: 'car', 'rio'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'TSstudio'
Packages required but not available: 'curl', 'httr'

Package suggested but not available for checking: 'covr'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'DiagrammeRsvg', 'kableExtra'

Package suggested but not available for checking: 'devtools'

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.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'car'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'Rgraphviz'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rstan'
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: 'covr'
Note: found 548 marked UTF-8 strings
Packages required but not available:
  'httr', 'magick', 'tidyverse', 'ggpubr', 'curl', 'gprofiler2'

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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Running 'aunitizer.R'
  Running 'runtt.R'
Running the tests in 'tests/runtt.R' failed.
Last 13 lines of output:
  
  v |  15       | Unitize 2 [18.5 s]
  
  / |   0       | testthat.zzrunlast                                              ALL TESTS COMPLETED!
  
  == Results =====================================================================
  Duration: 132.5 s
  
  -- Skipped tests  --------------------------------------------------------------
  * empty test (4)
  * fails CRAN (2)
  
  [ FAIL 3 | WARN 15 | SKIP 6 | PASS 832 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Running 'test_non_interactive.R'
  Running 'test_ok.R'
  Running 'test_ok_group.R'
  Running 'test_ut_cmp.R'
Running the tests in 'tests/test_ut_cmp.R' failed.
Last 13 lines of output:
  +     ok(cmp_lines(ut_cmp_identical(as.integer(4), 4),
  +         '--- as.integer(4)',
  +         ' int 4',
  +         '+++ 4',
  +         ' num 4',
  +         NULL), "Equivalent objects do not, unlike ut_cmp_equal(). We also fall back to using str(), as print() will produce identical output")
  + }))
  # ut_cmp_identical:nogit
  ok - Identical objects return true
  ok - Equivalent objects do not, unlike ut_cmp_equal(). We also fall back to using str(), as print() will produce identical output
  > 
  > proc.time()
     user  system elapsed 
     0.43    0.20    2.12 
  # Looks like you failed 1 of 15 tests.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'extraDistr' 'logitnorm' 'nakagami' 'tibble'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rvest', 'covr'
Error(s) in re-building vignettes:
  ...
--- re-building 'html.Rmd' using rmarkdown
Quitting from lines 21-25 (html.Rmd) 
Error: processing vignette 'html.Rmd' failed with diagnostics:
there is no package called 'rvest'
--- failed re-building 'html.Rmd'

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

--- re-building 'small-multiples.Rmd' using rmarkdown
--- finished re-building 'small-multiples.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in 'unrtf-Ex.R' failed
The error most likely occurred in:

> ### Name: unrtf
> ### Title: Convert rtf Documents
> ### Aliases: unrtf
> 
> ### ** Examples
> 
> library(unrtf)
> text <- unrtf("https://jeroen.github.io/files/sample.rtf", format = "text")
No config directories. Searched: ../share/
Error: System call to 'unrtf' failed
Execution halted
Note: found 3345 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'kableExtra', 'covr'
Namespaces in Imports field not imported from:
  'lavaan' 'lifecycle' 'patchwork' 'ragg' 'scales' 'simstandard'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'tutorial_unusualprofile.Rmd' using rmarkdown
Quitting from lines 32-61 (tutorial_unusualprofile.Rmd) 
Error: processing vignette 'tutorial_unusualprofile.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'tutorial_unusualprofile.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'devtools'
Note: found 7872 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'RcppProgress'
  All declared Imports should be used.
Package suggested but not available for checking: 'qpdf'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'sampleSelection'
Error(s) in re-building vignettes:
  ...
--- re-building 'ExtendedAppendix.Rnw' using knitr
--- finished re-building 'ExtendedAppendix.Rnw'

--- re-building 'Manuscript.Rnw' using knitr
Quitting from lines 159-160 (Manuscript.Rnw) 
Error: processing vignette 'Manuscript.Rnw' failed with diagnostics:
there is no package called 'sampleSelection'
--- failed re-building 'Manuscript.Rnw'

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

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

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

Packages suggested but not available for checking: 'covr', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'httr'
Note: found 488 marked UTF-8 strings
Packages suggested but not available for checking:
  'USAboundariesData', 'covr'
Package suggested but not available for checking: 'covr'
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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'tidyverse'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'cli'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'gert', 'gh'

Packages suggested but not available for checking: 'covr', 'magick'

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:
  'devtools', 'plotly', 'usethis'
Namespace in Imports field not imported from: 'tsibble'
  All declared Imports should be used.
Running examples in 'USgrid-Ex.R' failed
The error most likely occurred in:

> ### 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 suggested but not available for checking: 'covr'
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ggdag'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'RCurl' 'stringdist' 'utils'
  All declared Imports should be used.
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.
Package required but not available: 'rio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggpubr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'dbplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'covr', 'curl', 'devtools'
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'testthat'
  All declared Imports should be used.
Package suggested but not available for checking: 'Seurat'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'curl'
Error(s) in re-building vignettes:
  ...
--- re-building 'cd.Rmd' using rmarkdown
--- finished re-building 'cd.Rmd'

--- re-building 'cfw.Rmd' using rmarkdown
Quitting from lines 27-30 (cfw.Rmd) 
Error: processing vignette 'cfw.Rmd' failed with diagnostics:
there is no package called 'curl'
--- failed re-building 'cfw.Rmd'

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

--- re-building 'leukemia.Rmd' using rmarkdown
Loading required package: Matrix
Loaded glmnet 4.1-1
--- finished re-building 'leukemia.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'car'
Packages unavailable to check Rd xrefs: 'car', 'candisc'
Running examples in 'VARSEDIG-Ex.R' failed
The error most likely occurred in:

> ### Name: VARSEDIG
> ### Title: Variable selection to discriminate among taxonomic groups
> ### Aliases: VARSEDIG
> ### Keywords: VARSEDIG
> 
> ### ** Examples
> 
> 
> data(characiformes)
> 
> VARSEDIG(data = characiformes , variables = c("M2","M3","M4","M5","M6","M7","M8","M9","M10",
+ "M11","M12","M13","M14","M15","M16","M17","M18","M19","M20","M21","M22","M23",
+ "M24","M25","M26","M27","M28"), group="Species" , group1= "Moenkhausia oligolepis",
+ group2="Moenkhausia dichroura", LEGENDd=c("x='topright'", "legend = dati",
+ "col = COLORB", "lty=lty", "bty='n'", "cex=1.2", "text.font= 3"),
+ LEGENDs=c("x='topright'", "legend=unique(datosF[,'Group'])", "col = color1",
+ "pch = pcht", "bty='n'", "cex=1.2", "text.font=3"), LEGENDr=c("x='topright'",
+ "legend = dati", "col=col", "pch= c(16,16)", "bty='n'", "cex=1.2", "text.font=3"),
+ XLIMs=c(-1.2,1.2), YLIMs=c(-1.3,1.3), BIVTEST12=c("br=br", "cex=1.1",
+ "col=colbiv", "sub=sub", "Pcol=Pcol"), BIVTEST21=c("br=br", "cex=1.1",
+ "col=colbiv", "sub=sub", "Pcol=Pcol"), colbiv="blue", ellipse=TRUE, convex=FALSE)
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
dev.new(): using pdf(file="Rplots3.pdf")
Error in loadNamespace(x) : there is no package called 'car'
Calls: VARSEDIG ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'rio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'kableExtra'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'article_html_varshrink.Rmd' using rmarkdown
Quitting from lines 149-160 (article_html_varshrink.Rmd) 
Error: processing vignette 'article_html_varshrink.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'article_html_varshrink.Rmd'

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

Error: Vignette re-building failed.
Execution halted
black_scholes: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: 'matrixcalc'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mlrMBO', 'smoof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'car', 'AER'
Packages required but not available: 'crul', 'httr', 'webmockr'

Package suggested but not available for checking: 'curl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggtern'
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.
Package suggested but not available for checking: 'covr'
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 suggested but not available for checking: 'devtools'
Namespace in Imports field not imported from: 'pander'
  All declared Imports should be used.
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: 'devtools'
Namespaces in Imports field not imported from:
  'Rcpp' 'foreach' 'iterators' 'maps' 'spam'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'httr', 'usethis', 'rsconnect'
Package suggested but not available for checking: 'smacof'
Package suggested but not available for checking: 'curl'
Package required but not available: 'taxlist'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Checking should be performed on sources prepared by 'R CMD build'.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'nlme'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'car'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package required but not available: 'crul'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Package required but not available: 'ggpubr'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 60 marked UTF-8 strings
Namespaces in Imports field not imported from:
  'plotrix' 'sp' 'viridis'
  All declared Imports should be used.
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.
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.
Namespaces in Imports field not imported from:
  'mclust' 'rlang'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package required but not available: 'car'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'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: 'covr', 'sparklyr'
Package unavailable to check Rd xrefs: 'sparklyr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mgarchBEKK', 'matlib'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'httr', 'covr'
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'intro-to-viridis.Rmd' using rmarkdown

Attaching package: 'scales'

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

    viridis_pal

Loading required package: raster
Loading required package: sp

Attaching package: 'raster'

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

    RGB

Loading required package: terra
terra version 1.3.4

Attaching package: 'terra'

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

    rescale

Loading required package: lattice
Loading required package: latticeExtra

Attaching package: 'latticeExtra'

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

    layer

Quitting from lines 251-260 (intro-to-viridis.Rmd) 
Error: processing vignette 'intro-to-viridis.Rmd' failed with diagnostics:
there is no package called 'httr'
--- failed re-building 'intro-to-viridis.Rmd'

SUMMARY: processing the following file failed:
  'intro-to-viridis.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'devtools', 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'using_virtualPollen.Rmd' using rmarkdown
Installing packages into 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/virtualPollen/virtualPollen.Rcheck'
(as 'lib' is unspecified)
Quitting from lines 14-44 (using_virtualPollen.Rmd) 
Error: processing vignette 'using_virtualPollen.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building 'using_virtualPollen.Rmd'

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

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

Packages suggested but not available for checking: 'covr', 'jsonld'

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

Package suggested but not available for checking: 'lintr'

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

> ### Name: alluvial_diagram
> ### Title: alluvial_diagram
> ### Aliases: alluvial_diagram
> 
> ### ** Examples
> 
> library(tidyverse)
Error in library(tidyverse) : there is no package called 'tidyverse'
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'plotly'
Namespaces in Imports field not imported from:
  'ggplot2' 'reshape2'
  All declared Imports should be used.
Package required but not available: 'rstan'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

Packages suggested but not available for checking: 'covr', 'highcharter'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'rpart'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Packages required but not available: 'cranlogs', 'plotly'

Package suggested but not available for checking: 'devtools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'rorcid'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ggalt'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'glue' 'tidyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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: 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

Package suggested but not available for checking: 'ssh'

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

Packages suggested but not available for checking: 'kableExtra', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 4954 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'devtools'
Packages required but not available: 'httr', 'vosonSML'

Package suggested but not available for checking: 'rtweet'

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

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

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'magick', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to 'misc3d' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages suggested but not available for checking: 'covr', 'curl'
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.
Packages required but not available: 'survminer', 'ggpubr'

Package suggested but not available for checking: 'plotly'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Hmisc' 'XML' 'checkmate' 'gstat' 'intervals'
  All declared Imports should be used.
Package required but not available: 'DiagrammeRsvg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'EnvStats' 'shiny' 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
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.
Note: found 358074 marked UTF-8 strings
Package required but not available: 'curl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'Matrix' 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

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

Package suggested but not available for checking: 'rgbif'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'R6' 'WRS2' 'ggplot2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'kableExtra'
Namespace in Imports field not imported from: 'stringi'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'nlme'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package required but not available: 'dataRetrieval'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'qpdf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'rgdal' 'vctrs'
  All declared Imports should be used.
Package suggested but not available for checking: 'rPeaks'
Namespaces in Imports field not imported from:
  'raster' 'reshape2'
  All declared Imports should be used.
Package suggested but not available for checking: 'lintr'
Package required but not available: 'forecast'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Namespaces in Imports field not imported from:
  'Matrix' 'zoo'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'checkpoint'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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.
Note: found 1537 marked UTF-8 strings
Package required but not available: 'binman'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'arcpullr', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'httr', 'wdman', 'RSelenium'

Package suggested but not available for checking: 'ggmap'

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

Packages suggested but not available for checking: 'devtools', 'vcr'

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.
Packages required but not available: 'httr', 'rvest'

Packages suggested but not available for checking:
  'covr', 'robotstxt', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'curl', 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'curl', 'httr'
Package unavailable to check Rd xrefs: 'httr'
Running examples in 'webfakes-Ex.R' failed
The error most likely occurred in:

> ### Name: httpbin_app
> ### Title: Generic web app for testing HTTP clients
> ### Aliases: httpbin_app
> 
> ### ** Examples
> 
> app <- httpbin_app()
> proc <- new_app_process(app)
> url <- proc$url("/get")
> resp <- curl::curl_fetch_memory(url)
Error in loadNamespace(x) : there is no package called 'curl'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  -- Error (test-tmpl-glue.R:16:3): glue templating ------------------------------
  Error: there is no package called 'curl'
  Backtrace:
      x
   1. \-base::loadNamespace(x) test-tmpl-glue.R:16:2
   2.   \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     \-base:::withOneRestart(expr, restarts[[1L]])
   4.       \-base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 58 | WARN 0 | SKIP 2 | PASS 84 ]
  Error: Test failures
  Execution halted
Package required but not available: 'httr'

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

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

Packages suggested but not available for checking: 'vcr', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rgeolocate'
Package required but not available: 'rrtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package required but not available: 'httr'

Package suggested but not available for checking: 'devtools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  'here' 'rgeos' 'tibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

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: 'EdSurvey'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'rgdal'
  All declared Imports should be used.
Package suggested but not available for checking: 'org.Mm.eg.db'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'kableExtra', 'covr'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'counters.Rmd' using rmarkdown
--- finished re-building 'counters.Rmd'

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

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

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

--- re-building 'tables.Rmd' using rmarkdown
Quitting from lines 18-21 (tables.Rmd) 
Error: processing vignette 'tables.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'tables.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'covr'
Note: found 4102 marked UTF-8 strings
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plotly'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

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.
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.
Packages required but not available: 'httr', 'WikipediR'

Package suggested but not available for checking: 'lintr'

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

Packages suggested but not available for checking: 'tidyverse', 'pageviews'

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

Package suggested but not available for checking: 'covr'

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

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

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

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

Packages suggested but not available for checking: 'WikidataR', 'pageviews'

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

Package suggested but not available for checking: 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'plotly', 'DESeq2', 'FactoMineR', 'factoextra', 'heatmaply'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  trace_back_backtrace.c:87:19: warning: too many arguments for format [-Wformat-extra-args]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/winch/winch.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'drc', 'imputeTestbench'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'curl'
Note: found 1 marked UTF-8 string
Packages suggested but not available for checking: 'rnrfa', 'httr', 'curl'
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Package required but not available: 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'lintr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'scales'
  All declared Imports should be used.
Package suggested but not available for checking: 'AER'
Error(s) in re-building vignettes:
  ...
--- re-building 'Introductory-Econometrics-Examples.Rmd' using rmarkdown

Please cite as: 

 Hlavac, Marek (2018). stargazer: Well-Formatted Regression and Summary Statistics Tables.
 R package version 5.2.2. https://CRAN.R-project.org/package=stargazer 

Quitting from lines 946-948 (Introductory-Econometrics-Examples.Rmd) 
Error: processing vignette 'Introductory-Econometrics-Examples.Rmd' failed with diagnostics:
there is no package called 'AER'
--- failed re-building 'Introductory-Econometrics-Examples.Rmd'

SUMMARY: processing the following file failed:
  'Introductory-Econometrics-Examples.Rmd'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'dbplyr'
  All declared Imports should be used.
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 6738 marked UTF-8 strings
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
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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 suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Package required but not available: 'httr'

Packages suggested but not available for checking: 'covr', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Packages suggested but not available for checking: 'butcher', 'covr'
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Package required but not available: 'httr'

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

Package suggested but not available for checking: 'vcr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tidyverse', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'factoextra', 'FactoMineR'
Error(s) in re-building vignettes:
  ...
--- re-building 'wrGraphVignette1.Rmd' using rmarkdown
Quitting from lines 27-33 (wrGraphVignette1.Rmd) 
Error: processing vignette 'wrGraphVignette1.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building 'wrGraphVignette1.Rmd'

SUMMARY: processing the following file failed:
  'wrGraphVignette1.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'fdadensity' 'locfit' 'locpol' 'modeest'
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: 'vsn'
Package unavailable to check Rd xrefs: 'vsn'
Package suggested but not available for checking: 'ROTS'
Package suggested but not available for checking: 'car'
Package suggested but not available for checking: 'knitcitations'
'LazyData' is specified without a 'data' directory
Package required but not available: 'forecast'

Packages suggested but not available for checking: 'EGRET', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'magick'
Package unavailable to check Rd xrefs: 'magick'
Namespaces in Imports field not imported from:
  'dplyr' 'magrittr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
Package required but not available: 'httr'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plotly'
Namespace in Imports field not imported from: 'simts'
  All declared Imports should be used.
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.
Package required but not available: 'ftsa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/x13binary/x13binary.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'covr', 'magick'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found a 'configure.in' file: 'configure.ac' has long been preferred.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'pak', 'curl'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lintr'
GNU make is a SystemRequirements.
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: 'pkgdown'
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.
Namespace in Imports field not imported from: 'psychTools'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
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.
Packages suggested but not available for checking: 'covr', 'curl', 'httr'
Packages unavailable to check Rd xrefs: 'curl', 'httr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > if (!is_solaris) {
  +   test_check("xml2")
  + }
  This is libxml2 version 2.9.10 
  == Skipped tests ===============================================================
  * On CRAN (3)
  
  == Failed tests ================================================================
  -- Failure (test-write_xml.R:6:3): write_xml errors for incorrect directory and with invalid inputs --
  `write_xml(x, filename)` did not throw an error.
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 398 ]
  Error: Test failures
  Execution halted
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'curl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

Package suggested but not available for checking: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'blorr', 'highcharter', 'kableExtra', 'olsrr', 'plotly', 'rbokeh'
Package required but not available: 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package suggested but not available for checking: 'plotly'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   \-ggplot2::ggsave(...)
   3.     \-ggplot2:::plot_dim(...)
   4.       \-base::match.arg(units)
  -- Error (test-xpose_save.R:80:3): mutlitple pages are properly saved ----------
  Error: 'arg' must be of length 1
  Backtrace:
      x
   1. \-xpose::xpose_save(...) test-xpose_save.R:80:2
   2.   \-ggplot2::ggsave(...)
   3.     \-ggplot2:::plot_dim(...)
   4.       \-base::match.arg(units)
  
  [ FAIL 4 | WARN 0 | SKIP 7 | PASS 516 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'plotly'
Package suggested but not available for checking: 'factorMerger'
'LazyData' is specified without a 'data' directory
Running examples in 'xspliner-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_variable_transition
> ### Title: Plot variable profile
> ### Aliases: plot_variable_transition
> 
> ### ** Examples
> 
> library(randomForest)
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
> set.seed(1)
> data <- iris
> # regression model
> iris.rf <- randomForest(Petal.Width ~  Sepal.Length + Petal.Length + Species, data = data)
> iris.xs <- xspline(iris.rf)
Error in loadNamespace(x) : there is no package called 'factorMerger'
Calls: xspline ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
Some Unix compilers require LF line endings.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tseries'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Packages suggested but not available for checking: 'covr', 'devtools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'animation'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: 'lubridate'
  All declared Imports should be used.
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').
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.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.
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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'usethis', 'whoami'

Packages suggested but not available for checking: 'covr', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'rstan'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'quantmod', 'plotly'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'RNRCS', 'rnoaa', 'neonUtilities'
'LazyData' is specified without a 'data' directory
Package required but not available: 'crul'

Package suggested but not available for checking: 'vcr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'usethis'
Package suggested but not available for checking: 'covr'
Package required but not available: 'AER'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking: 'Rgraphviz', 'qrmtools'
Running examples in 'zenplots-Ex.R' failed
The error most likely occurred in:

> ### Name: graph_pairs
> ### Title: Turn pairs or paths into a graph
> ### Aliases: graph_pairs
> 
> ### ** Examples
> 
> ## Get some pairs
> pairs <- matrix(c(1,2, 5,1, 3,4, 2,3, 4,2), ncol = 2, byrow = TRUE)
> g <- graph_pairs(pairs)
> ## which can be displayed using plot(g) 
> ## if the graph package is installed.
> library(graph) 
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

> plot(g) 
Error: package required but not installed: 'Rgraphviz'
Execution halted
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'TSA'
Package unavailable to check Rd xrefs: 'TSA'
Package suggested but not available for checking: 'covr'
Note: found 47 marked UTF-8 strings
Package required but not available: 'tidycensus'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
Namespaces in Imports field not imported from:
  'ggplot2' 'testthat'
  All declared Imports should be used.
Package suggested but not available for checking: 'covr'
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'vignette.Rmd' using knitr
Quitting from lines 44-51 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building 'zlog.Rmd' using rmarkdown
Quitting from lines 65-105 (zlog.Rmd) 
Error: processing vignette 'zlog.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'zlog.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'zdat'
Packages suggested but not available for checking: 'pct', 'covr'
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Packages required but not available: 'magick', 'paws'

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: 'rfigshare'

Package suggested but not available for checking: 'SDMTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'AER', 'tseries'
Package unavailable to check Rd xrefs: 'tseries'
Running 'as.Date.R'
  Comparing 'as.Date.Rout' to 'as.Date.Rout.save' ... OK
  Running 'bugfixes.R'
  Comparing 'bugfixes.Rout' to 'bugfixes.Rout.save' ... OK
  Running 'na.fill.R'
  Comparing 'na.fill.Rout' to 'na.fill.Rout.save' ... OK
  Running 'na.locf.R'
  Comparing 'na.locf.Rout' to 'na.locf.Rout.save' ... OK
  Running 'vignette-zoo-quickref.R'
Running the tests in 'tests/vignette-zoo-quickref.R' failed.
Last 13 lines of output:
  > ###################################################
  > ### chunk number 1: preliminaries
  > ###################################################
  > library("zoo")
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  > library("tseries")
  Error in library("tseries") : there is no package called 'tseries'
  Execution halted
Errors in running code in vignettes:
when running code in 'zoo-quickref.Rnw'
  ...
The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


> library("tseries")

  When sourcing 'zoo-quickref.R':
Error: there is no package called 'tseries'
Execution halted
when running code in 'zoo.Rnw'
  ...
The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


> library("tseries")

  When sourcing 'zoo.R':
Error: there is no package called 'tseries'
Execution halted

  'zoo-design.Rnw'... OK
  'zoo-faq.Rnw'... OK
  'zoo-quickref.Rnw'... failed
  'zoo-read.Rnw'... OK
  'zoo.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'zoo-design.Rnw' using Sweave

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

--- finished re-building 'zoo-design.Rnw'

--- re-building 'zoo-faq.Rnw' using Sweave

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'timeSeries'

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

    time<-

--- finished re-building 'zoo-faq.Rnw'

--- re-building 'zoo-quickref.Rnw' using Sweave

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


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

--- failed re-building 'zoo-quickref.Rnw'

--- re-building 'zoo-read.Rnw' using Sweave

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

--- finished re-building 'zoo-read.Rnw'

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

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


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

--- failed re-building 'zoo.Rnw'

SUMMARY: processing the following files failed:
  'zoo-quickref.Rnw' 'zoo.Rnw'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'rvest'

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

Package suggested but not available for checking: 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘acceldata2.RData’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘AdaptFit’ in Rd xrefs
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 suggested but not available for checking: ‘gsDesign’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Bestmatches.csv’ ‘ID.csv’ ‘listsp.csv’ ‘mylabels.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘About.Rmd’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘myplot.pdf’ ‘myplot.png’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ALA4R.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: maps
Quitting from lines 185-188 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
HTTP status code 500 received.
  Either there was an error with the
                                       request, or the servers may be down
                                       (try again later). If this problem persists please notify the ALA4R
            maintainers by lodging an issue at
            https://github.com/AtlasOfLivingAustralia/ALA4R/issues/
            or emailing support@ala.org.au
--- failed re-building ‘ALA4R.Rmd’

SUMMARY: processing the following file failed:
  ‘ALA4R.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ahull_track: no visible global function definition for ‘psp’
ahull_track: no visible global function definition for ‘owin’
ahull_track: no visible global function definition for
  ‘runifpointOnLines’
dw_track: no visible global function definition for ‘psp’
dw_track: no visible global function definition for ‘owin’
dw_track: no visible global function definition for ‘runifpointOnLines’
Undefined global functions or variables:
  owin psp runifpointOnLines
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Malformed Title field: should not end in a period.
Found the following files/directories:
  ‘BM-motion-chart.html’ ‘css’ ‘images’ ‘index.html’ ‘js’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tmg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
aw_map: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MonetDBLite’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘ARTP’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MSToutput.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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: ‘asteRiskData’
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocInstaller’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘exemplary_input1.txt’ ‘exemplary_input2.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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').
'LazyData' is specified without a 'data' directory
‘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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running ‘testthat.R’ [30s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bayesAB)
  > 
  > test_check("bayesAB")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-generics.R:41:3): Success ─────────────────────────────────────
  `plot(x)` produced warnings.
  ── Failure (test-generics.R:42:3): Success ─────────────────────────────────────
  `plot(x, rep(0.5, 4))` produced warnings.
  ── Failure (test-generics.R:46:3): Success ─────────────────────────────────────
  `print(plot(x))` produced warnings.
  ── Failure (test-generics.R:47:3): Success ─────────────────────────────────────
  `print(plot(x, rep(0.5, 4)))` produced warnings.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 137 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BayesianReasoning)
  > 
  > test_check("BayesianReasoning")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-PPV_heatmap.R:117:3): PPV calculation with area overlay, low uncertainty, and decimals in y axis ──
  p$layers[[3]]$geom_params$description not identical to "40 y.o.\n2 out of 8\nFP = 4.8%\nPPV = 85%".
  target is NULL, current is character
  ── Failure (test-PPV_heatmap.R:146:3): NPV calculation with area overlay and low uncertainty ──
  p$layers[[3]]$geom_params$description not identical to "40 y.o.\n67 out of 68\nFN = 1%\nNPV = 59%".
  target is NULL, current is character
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 27 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cyjShiny’
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
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.
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’
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.
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘fabiabreast.txt’
Packages suggested but not available for checking: 'INLA', 'ldr'
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘bferrbars.eps’ ‘dataplot.eps’ ‘ppdat.eps’ ‘ppmod.eps’
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.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Found the following files/directories:
  ‘example_Initial.parameters.Robj’ ‘example_MCMC_output1.Robj’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘BiDimRegrOutput.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’.
Error(s) in re-building vignettes:
  ...
--- re-building ‘analysis.Rmd’ using rmarkdown
Quitting from lines 392-393 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
replacement has 2 rows, data has 3
--- failed re-building ‘analysis.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘outputs’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
bins.quantiles: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘biomartr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: listDatabases
> ### Title: Retrieve a List of Available NCBI Databases for Download
> ### Aliases: listDatabases listNCBIDatabases
> 
> ### ** Examples
> 
> # retrieve all versions of the NCBI 'nr' database that can be downloaded
> listNCBIDatabases(db = "nr")
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'strsplit': server response timeout
Calls: listNCBIDatabases ... <Anonymous> -> curlPerform -> <Anonymous> -> fun -> <Anonymous>
Execution halted
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘JSBP.css’ ‘JSBP.js’ ‘vizjs.js’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘BIS.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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.
GNU make is a SystemRequirements.
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘brew-test-1-1.eps’ ‘brew-test-1-2.eps’ ‘brew-test-1.tex’
  ‘brew-test-2.html’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘glmmADMB’
Package suggested but not available for checking: ‘btergm’
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'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/btergm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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-patched-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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tmp.txt’
Found the following files/directories:
  ‘MDA231_tree.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
‘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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘Vignette.Rmd’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘cartools.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spacodiR’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hotcold.csv’
'LazyData' is specified without a 'data' directory
'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’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
select_lambda: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘stepres00.txt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
Package vignette with placeholder title ‘Vignette Title’:
  ‘childhoodmortality.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘CISE_vignette.Rmd’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘desciption-ciuupi.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘clusterhap_reports’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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.
Running ‘testthat.R’ [12s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(checkmate)
  > library(coalitions)
  > 
  > test_check("coalitions")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-scrapers.R:35:1): State wide german scrapers work ─────────────
  Check on survey2 is not TRUE
  
  `actual` is a character vector ('Must have exactly 1 rows, but has 0 rows')
  `expected` is a logical vector (TRUE)
  Must have exactly 1 rows, but has 0 rows
  Backtrace:
      █
   1. └─checkmate::expect_data_frame(survey2, nrows = 1, ncols = 11) test-scrapers.R:35:0
   2.   └─checkmate::makeExpectation(x, res, info, label)
   3.     └─testthat::expect_true(...)
  ── Failure (test-scrapers.R:36:1): State wide german scrapers work ─────────────
  survey2$cdu not equal to 39.5.
  Lengths differ: 0 is not 1
  ── Failure (test-scrapers.R:37:1): State wide german scrapers work ─────────────
  survey2$respondents not equal to 1403.
  Lengths differ: 0 is not 1
  
  [ FAIL 3 | WARN 10 | SKIP 0 | PASS 83 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
‘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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggtern’

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.
Package suggested but not available for checking: ‘ggtern’
'LazyData' is specified without a 'data' directory
Running examples in ‘codalm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: codalm
> ### Title: Transformation-free Linear Regression for Compositional Outcomes
> ###   and Predictors
> ### Aliases: codalm
> 
> ### ** Examples
> 
> require(ggtern)
Loading required package: ggtern
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggtern’
> data("WhiteCells", package = 'ggtern')
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘ggtern’
Calls: data -> find.package
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘codalm_quickstart.Rmd’ using rmarkdown
Quitting from lines 21-23 (codalm_quickstart.Rmd) 
Error: processing vignette 'codalm_quickstart.Rmd' failed with diagnostics:
there is no package called 'ggtern'
--- failed re-building ‘codalm_quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Found the following files/directories:
  ‘fda7wnr6u.c’ ‘fda7wnr6u.o’ ‘fda7wnr6u.so’ ‘symbols.rds’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘collectArgs_and_iterateWithArgs.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: ‘CAM’
compareC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
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 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2005benchmark’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘countyflood.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘customsteps.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Packages which this enhances 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.
'LazyData' is specified without a 'data' directory
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').
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘GRCh38_browser’ ‘GRCh38_map’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘datadigest.Rmd’
'LazyData' is specified without a 'data' directory
Found the following assignments to the global environment:
File ‘DataEntry/R/Export.R’:
  assign(svalue(edObnm), d, envir = .GlobalEnv)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘LFC.d.jpeg’ ‘LFC.s.jpeg’ ‘TF_bridged_DCL.pdf’
  ‘TF_bridged_DCL_int.pdf’
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
test.LM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘decomposedPSF-vignette.Rmd’
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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').
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘smd_table.docx’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
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').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 which this enhances but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘csim’ ‘xyz’ ‘xyz.sav’ ‘xyz.sav.comment’
Found the following files/directories:
  ‘csim.mean’ ‘csim.mean.comment’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BOLTSSIRR’
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘documenter.Rmd’
Found the following files/directories:
  ‘annotation_file.yml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: ‘doRedis’
'LazyData' is specified without a 'data' directory
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').
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘dotdot.Rmd’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.Rmd’ using rmarkdown
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
Quitting from lines 433-435 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
replacement has 2 rows, data has 3
--- failed re-building ‘userGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘vignette.Rmd’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
'LazyData' is specified without a 'data' directory
ebSNP: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tmplp.dat’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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').
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’ ‘combined.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘PPtree’
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.
'LazyData' is specified without a 'data' directory
License components which are templates and need ‘+ file LICENSE’:
  MIT
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Found the following files/directories:
  ‘somefile’
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘plotrix’ which was already attached by Depends.
  Please remove these calls from your code.
‘library’ or ‘require’ calls in package code:
  ‘Hmisc’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘plotrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘a.alpha.ade’ ‘a.coladd.ade’ ‘a.getcol.ade’ ‘a.glc’
Rd file 'scatter.ade.Rd':
  \examples lines wider than 100 characters:
     scatter.ade(x, y, g, z, vnames=c("blue","red"), alpha=0.25, xlim=c(-5, 5), zticks=c(1, 2, 3, 4, 5), wall=3)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘epidict’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘statnet’
Packages required but not available: 'tergm', 'tergmLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘EpiSoon’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
plot.episplineDensity: no visible global function definition for
  ‘points’
postproc: no visible global function definition for ‘points’
preprocess.data: no visible global function definition for ‘sd’
Undefined global functions or variables:
  points sd
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
FCIplot: no visible global function definition for ‘na.omit’
FCIplot: no visible global function definition for ‘tail’
FCIplot: no visible global function definition for ‘grid’
FCIplot: no visible global function definition for ‘polygon’
FCIplot: no visible global function definition for ‘rgb’
linpred: no visible global function definition for ‘lm’
mplott: no visible global function definition for ‘par’
mplott: no visible global function definition for ‘na.omit’
mplott: no visible global function definition for ‘lines’
mplott: no visible global function definition for ‘legend’
mplott: no visible global function definition for ‘grid’
plott: no visible global function definition for ‘lines’
plott: no visible global function definition for ‘par’
plott: no visible global function definition for ‘grid’
tsideplot: no visible global function definition for ‘par’
tsideplot: no visible global function definition for ‘axis’
tsideplot: no visible global function definition for ‘grid’
Undefined global functions or variables:
  axis grid legend lines lm na.omit par polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
eqs2lavaan: no visible global function definition for ‘ignore.case’
eqs2lavaan: no visible global function definition for ‘str_join’
eqs2lavaan: no visible binding for global variable ‘r’
eqsCorr: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘par’
plotCov: no visible global function definition for ‘image’
plotCov: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis cov2cor ignore.case image par r str_join
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "cov2cor")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘docs’ ‘license.txt’ ‘status.txt’
'library' or 'require' call to ‘qtl’ which was already attached by Depends.
  Please remove these calls from your code.
Unexported objects imported by ‘:::’ calls:
  ‘qtl:::c.scanone’ ‘qtl:::plot.scanone’
  See the note in ?`:::` about the use of this operator.
Found the following files/directories:
  ‘CATane_4_27_.png’ ‘CATavz_4_37_.png’ ‘CATbaa_4_13_.png’
  ‘CATbko_4_36_.png’ ‘CATbuu_1_45_.png’ ‘CATbuu_4_45_.png’
  ‘CATbuu_5_45_.png’ ‘CATbzp_4_50_.png’ ‘CATbzx_4_29_.png’
  ‘CATdbn_1_18_.png’ ‘CATdbn_3_18_.png’ ‘CATdmq_4_49_.png’
  ‘CATepg_4_44_.png’ ‘CATfgb_4_7_.png’ ‘CATfgb_5_7_.png’
  ‘CATfnu_4_21_.png’ ‘CATfnu_5_21_.png’ ‘CATham_4_14_.png’
  ‘CATham_5_14_.png’ ‘CATipy_4_19_.png’ ‘CATjoj_2_22_.png’
  ‘CATjpz_4_35_.png’ ‘CATjxh_1_31_.png’ ‘CATlbg_4_40_.png’
  ‘CATlkr_4_32_.png’ ‘CATlzh_4_43_.png’ ‘CATntj_4_24_.png’
  ‘CAToti_5_28_.png’ ‘CATppt_4_4_.png’ ‘CATppt_5_4_.png’
  ‘CATpsl_4_23_.png’ ‘CATpyn_4_20_.png’ ‘CATqoq_4_8_.png’
  ‘CATrck_4_26_.png’ ‘CATrjo_4_30_.png’ ‘CATsgu_4_9_.png’
  ‘CATsgu_5_9_.png’ ‘CATtez_4_34_.png’ ‘CATudg_4_16_.png’
  ‘CATuhl_4_39_.png’ ‘CATuhl_5_39_.png’ ‘CATvbb_4_41_.png’
  ‘CATwgo_4_17_.png’ ‘CATwgo_5_17_.png’ ‘CATwrn_4_46_.png’
  ‘CATwwh_4_10_.png’ ‘CATxmc_2_48_.png’ ‘CATxni_5_6_.png’ ‘ID_5_1_.png’
  ‘ae_dotplot_traitxqtl.png’ ‘ae_siplot_traitxqtl.png’
  ‘histogram_controled_etrait.png’ ‘histogram_qtl.png’
  ‘lod_dotplot_traitxqtl.png’ ‘lod_siplot_traitxqtl.png’
The following files contain a license that requires
distribution of original sources:
  ‘upgreek.sty’
Please ensure that you have complied with it.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘aeq3.out’ ‘ste3a.out’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'statnet', 'btergm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tergm’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘errorize.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ESA: no visible binding for global variable ‘var’
plot.esabcv: no visible global function definition for ‘points’
plot.esabcv: no visible global function definition for ‘axis’
plot.esabcv: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis points title var
Consider adding
  importFrom("graphics", "axis", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ESEA.Main: no visible global function definition for ‘rnorm’
ESEA.Main: no visible global function definition for ‘sd’
ESEA.Main: no visible global function definition for ‘p.adjust’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘lines’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘colors’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘points’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘legend’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘text’
PlotPathwayGraph: no visible global function definition for ‘par’
PlotRunEnrichment: no visible global function definition for ‘lines’
PlotRunEnrichment: no visible global function definition for ‘colors’
PlotRunEnrichment: no visible global function definition for ‘text’
SavePathway2File: no visible global function definition for ‘is’
calEdgeCorScore: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colors is legend lines na.omit p.adjust par points rnorm sd text
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "legend", "lines", "par", "points", "text")
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "p.adjust", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
cv.ES: no visible binding for global variable ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘estoutstorage’
descsto: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.Transition: no visible global function definition for ‘rnorm’
.Transition.DC: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘rpois’
Simu.Cond.HR: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘hist’
Simu.Cond.HR: no visible global function definition for ‘var’
Simu.HR: no visible global function definition for ‘rpois’
Simu.HR: no visible global function definition for ‘runif’
Simu.HR: no visible global function definition for ‘hist’
Simu.HR: no visible global function definition for ‘var’
Undefined global functions or variables:
  hist rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
etc.diff: no visible global function definition for ‘model.frame’
etc.diff: no visible binding for global variable ‘sd’
etc.diff: no visible global function definition for ‘qt’
etc.diff: no visible global function definition for ‘pt’
etc.diff: no visible global function definition for ‘wilcox.test’
etc.rat: no visible global function definition for ‘model.frame’
etc.rat: no visible binding for global variable ‘sd’
etc.rat: no visible global function definition for ‘qt’
etc.rat: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.frame pt qt sd wilcox.test
Consider adding
  importFrom("stats", "model.frame", "pt", "qt", "sd", "wilcox.test")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
powerSet : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
mposterior: no visible global function definition for ‘optim’
rl.pred: no visible global function definition for ‘matplot’
rl.pst: no visible binding for global variable ‘quantile’
rl.pst: no visible global function definition for ‘matplot’
Undefined global functions or variables:
  matplot optim quantile
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘sample .nwk’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘UsingEvolutionaryGames.Rmd’
evolvabilityBetaMCMC : <anonymous>: no visible binding for global
  variable ‘median’
evolvabilityBetaMCMC: no visible binding for global variable ‘median’
evolvabilityBetaMCMC2: no visible binding for global variable ‘median’
evolvabilityMeans: no visible global function definition for ‘var’
evolvabilityMeansMCMC : <anonymous>: no visible global function
  definition for ‘var’
evolvabilityMeansMCMC: no visible binding for global variable ‘median’
randomBeta: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  median rnorm var
Consider adding
  importFrom("stats", "median", "rnorm", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘evd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DPOT: no visible global function definition for ‘optim’
mop.rho: no visible global function definition for ‘median’
Undefined global functions or variables:
  median optim
Consider adding
  importFrom("stats", "median", "optim")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
EW : PhiP : Phi: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
BinomialCIone: no visible global function definition for ‘na.omit’
PairedCIone: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
build.mcx.obj: no visible global function definition for ‘glm’
build.mcx.obj: no visible binding for global variable ‘poisson’
build.mcx.obj: no visible global function definition for ‘fitted’
cab: no visible global function definition for ‘rbinom’
cab: no visible global function definition for ‘runif’
mcexact: no visible global function definition for ‘update’
rounded.tprob: no visible global function definition for ‘pt’
simtable.cab: no visible global function definition for ‘rbinom’
simtable.cab: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fitted glm poisson pt rbinom runif update
Consider adding
  importFrom("stats", "fitted", "glm", "poisson", "pt", "rbinom",
             "runif", "update")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
plot.pgrid: no visible global function definition for ‘image’
statistic.cv: no visible global function definition for ‘quantile’
statistic.sim: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines image quantile
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "image")
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of ‘dig’ to ‘digits’
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of ‘env’ to ‘envir’
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of ‘env’ to ‘envir’
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of ‘dig’ to ‘digits’
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of ‘env’ to ‘envir’
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of ‘env’ to ‘envir’
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  ‘wid’ to ‘width’
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘Vignette.Rmd’
Malformed Description field: should contain one or more complete sentences.
index.citations: no visible global function definition for
  ‘txtProgressBar’
read.exsic: no visible global function definition for ‘read.csv’
update.pb: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  read.csv setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
extfunnel: no visible global function definition for ‘qnorm’
extfunnel: no visible global function definition for ‘meta.summaries’
extfunnel: no visible global function definition for ‘flush.console’
extfunnel: no visible global function definition for ‘qt’
extfunnel: no visible global function definition for ‘dev.new’
extfunnel: no visible global function definition for ‘par’
extfunnel: no visible global function definition for ‘polygon’
extfunnel: no visible global function definition for ‘segments’
extfunnel: no visible global function definition for ‘abline’
extfunnel: no visible global function definition for ‘axis’
extfunnel: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "polygon",
             "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
bars: no visible global function definition for ‘segments’
cv.binomial: no visible binding for global variable ‘var’
cv.binomial: no visible global function definition for ‘abline’
cv.normal: no visible binding for global variable ‘var’
cv.normal: no visible global function definition for ‘abline’
cv.poisson: no visible binding for global variable ‘var’
cv.poisson: no visible global function definition for ‘abline’
plot.extlasso: no visible global function definition for ‘matplot’
plot.extlasso: no visible global function definition for ‘axis’
Undefined global functions or variables:
  abline axis matplot segments var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments")
  importFrom("stats", "var")
to your NAMESPACE file.
exbio: no visible global function definition for ‘as.formula’
exbio: no visible global function definition for ‘glm’
exbio: no visible binding for global variable ‘gaussian’
exbio: no visible global function definition for ‘Gamma’
exbio: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  Gamma as.formula gaussian glm pchisq
Consider adding
  importFrom("stats", "Gamma", "as.formula", "gaussian", "glm", "pchisq")
to your NAMESPACE file.
Rd file 'exbio.Rd':
  \usage lines wider than 90 characters:
     exbio(R, R.alt, cc, n, tol = 0.001, a.start = 1, b.start = 1, max.it = 1000, digits = NULL, model.maf = TRUE)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
font_install: no visible global function definition for
  ‘installed.packages’
font_install: no visible global function definition for
  ‘install.packages’
fonttable_add: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  install.packages installed.packages write.csv
Consider adding
  importFrom("utils", "install.packages", "installed.packages",
             "write.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
toJavaMatrix2D: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘temp.Rdata’
bootstrapCMLE: no visible global function definition for ‘qweibull’
bootstrapCMLE: no visible binding for global variable ‘sd’
bootstrapCMLE: no visible global function definition for ‘quantile’
bootstrapCenWbMix: no visible binding for global variable ‘sd’
bootstrapCenWbMix: no visible global function definition for ‘quantile’
cenWeibullMLE: no visible global function definition for ‘sd’
expmx.p2.censor: no visible global function definition for ‘dweibull’
expmx.p2.censor: no visible global function definition for ‘pweibull’
genWbMixIni: no visible global function definition for ‘runif’
log.llh.p2.censor: no visible global function definition for ‘dweibull’
log.llh.p2.censor: no visible global function definition for ‘pweibull’
quanWbMix : t.fun: no visible global function definition for ‘pweibull’
quanWbMix: no visible global function definition for ‘uniroot’
quanWbMix.int : t.fun: no visible global function definition for
  ‘pweibull’
quanWbMix.int: no visible global function definition for ‘uniroot’
simWbMix: no visible global function definition for ‘rbinom’
simWbMix: no visible global function definition for ‘rweibull’
Undefined global functions or variables:
  dweibull pweibull quantile qweibull rbinom runif rweibull sd uniroot
Consider adding
  importFrom("stats", "dweibull", "pweibull", "quantile", "qweibull",
             "rbinom", "runif", "rweibull", "sd", "uniroot")
to your NAMESPACE file.
Package suggested but not available for checking: ‘exuberdata’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Rd file 'distance2point.Rd':
  \usage lines wider than 90 characters:
     distance2point(x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
  \examples lines wider than 100 characters:
     function( x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight ) {

Rd file 'subtendedAngle.Rd':
  \usage lines wider than 90 characters:
     subtendedAngle(x1, y1, x2, y2, viewerDistance = 58.74, viewerHeight = 4.55, resolutionX = 1280, resolutionY = 1024, screenWidth = 33.97 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     function( x1, y1, x2, y2, viewerDistance=58.74, viewerHeight=4.55, resolutionX=1280, resolutionY=1024, screenWidth=33.97, screenHeight= ... [TRUNCATED]
         d1 <- distance2point(x1, y1, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
         d2 <- distance2point(x2, y2, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
createFormula: no visible global function definition for ‘tail’
createFormula: no visible global function definition for ‘head’
createFormula: no visible global function definition for ‘as.formula’
ezsim: no visible global function definition for ‘runif’
plot.ezsim: no visible global function definition for ‘quantile’
plot.ezsim: no visible global function definition for ‘head’
plot.ezsim: no visible global function definition for ‘tail’
plot.ezsim: no visible binding for global variable ‘dnorm’
plot.ezsim: no visible binding for global variable ‘pdf’
plot.ezsim: no visible global function definition for ‘dev.off’
plot.ezsim : <anonymous>: no visible global function definition for
  ‘dev.new’
plot.summary.ezsim: no visible global function definition for ‘head’
plot.summary.ezsim: no visible global function definition for ‘tail’
plot.summary.ezsim: no visible binding for global variable ‘pdf’
plot.summary.ezsim: no visible global function definition for ‘dev.off’
plot.summary.ezsim : <anonymous>: no visible global function definition
  for ‘dev.new’
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘facilitationmovie.gif’ ‘ts.gif’
gibbs2: no visible global function definition for ‘rnorm’
gibbs_sampling: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘test_30iter.RData’ ‘test_50iter.RData’ ‘test_v2_50iter.RData’
Malformed Description field: should contain one or more complete sentences.
fma: no visible global function definition for ‘factanal’
fma: no visible global function definition for ‘runif’
fma: no visible global function definition for ‘kmeans’
fma: no visible global function definition for ‘var’
fma.em.alg: no visible global function definition for ‘var’
misc : q: no visible global function definition for ‘name’
Undefined global functions or variables:
  factanal kmeans name runif var
Consider adding
  importFrom("stats", "factanal", "kmeans", "runif", "var")
to your NAMESPACE file.
Rd file 'fma.Rd':
  \usage lines wider than 90 characters:
     fma(y, k, r, x.z = NULL, x.w = NULL, it = 15, eps = 1e-04, seed = 4, scaling = FALSE, init = NULL)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Bogota.tex’ ‘DogBreeds1.tex’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createFactualConnection: no visible global function definition for
  ‘new’
factualGetSchema: no visible global function definition for ‘fromJSON’
factualRead: no visible global function definition for ‘curlEscape’
factualRead: no visible global function definition for ‘fromJSON’
processFactualReadJSON: no visible global function definition for ‘new’
processFactualSchemaJSON: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  curlEscape fromJSON new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'factualR.Rd':
  \usage lines wider than 90 characters:
     factualRead(connection , tableID , sort = NULL , limit = NULL , offset = NULL , filters = NULL , subject_key = NULL , reformatNames , v ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
faisalconjoint: no visible global function definition for ‘barplot’
faisalconjoint: no visible global function definition for ‘text’
faisalconjoint: no visible global function definition for ‘jpeg’
faisalconjoint: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  barplot dev.off jpeg text
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "barplot", "text")
to your NAMESPACE file.
Found the following files/directories:
  ‘FCMgraph.jpg’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in '?.onAttach'.
'LazyData' is specified without a 'data' directory
coef.FAMILY: no visible global function definition for ‘glm’
coef.FAMILY: no visible global function definition for ‘lm’
fm2v: no visible global function definition for ‘na.omit’
l_inf_prox: no visible global function definition for ‘tail’
predict.FAMILY: no visible global function definition for ‘coef’
predict.FAMILY: no visible global function definition for ‘lm’
predict.FAMILY: no visible global function definition for ‘predict’
predict.FAMILY: no visible global function definition for ‘glm’
predict.FAMILY: no visible global function definition for ‘predict.glm’
v2fm: no visible global function definition for ‘tail’
Undefined global functions or variables:
  coef glm lm na.omit predict predict.glm tail
Consider adding
  importFrom("stats", "coef", "glm", "lm", "na.omit", "predict",
             "predict.glm")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘impute’ ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘default5.eps’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘quick-usage-guide-to-the-fastglm-package.Rmd’
basis_hica: no visible global function definition for ‘princomp’
energy_hica: no visible global function definition for ‘dev.new’
energy_hica: no visible global function definition for ‘points’
energy_hica: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dev.new legend points princomp
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "princomp")
to your NAMESPACE file.
Package suggested but not available for checking: ‘coxKM’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
'LazyData' is specified without a 'data' directory
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
FBN.histogramMaxima: no visible global function definition for ‘hist’
FBN.kmeans: no visible global function definition for ‘median’
FBN.kmeans: no visible global function definition for ‘kmeans’
FBNormalization: no visible global function definition for ‘read.table’
FBNormalization: no visible global function definition for ‘median’
FBNormalization: no visible global function definition for ‘hist’
FBNormalization: no visible global function definition for ‘par’
FBNormalization: no visible global function definition for ‘dev.print’
FBNormalization: no visible binding for global variable ‘bmp’
FBNormalization: no visible global function definition for ‘sd’
FBNormalization: no visible global function definition for
  ‘write.table’
medianFilter: no visible global function definition for ‘median’
Undefined global functions or variables:
  bmp dev.print hist kmeans median par read.table sd write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.print")
  importFrom("graphics", "hist", "par")
  importFrom("stats", "kmeans", "median", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Rd file 'FBNormalization.Rd':
  \usage lines wider than 90 characters:
             normDataFileName = NULL, debugFlag = FALSE, plotFlag = FALSE, plotAndSaveFlag = FALSE)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ calls in package code:
  ‘RCurl’ ‘RJSONIO’ ‘XML’ ‘glmnet’ ‘httr’ ‘speedglm’ ‘tcltk’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘glmnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fcd.cluster: no visible global function definition for ‘kmeans’
fcd.start: no visible global function definition for ‘ginv’
fcd.start: no visible global function definition for ‘glmnet’
gen.dcbm: no visible global function definition for ‘rbinom’
gen.sbm: no visible global function definition for ‘rbinom’
mis.cluster: no visible global function definition for ‘permn’
spectral.clustering: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  ginv glmnet kmeans permn rbinom
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
PTSingleAssetBarrierOption2: no visible global function definition for
  ‘new’
newton: no visible global function definition for ‘abline’
probInRange: no visible global function definition for ‘pnorm’
shortfall_risk: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline new pnorm
Consider adding
  importFrom("graphics", "abline")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘CEC’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
FDRreg: no visible global function definition for ‘dnorm’
colnormalize: no visible global function definition for ‘sd’
efron: no visible global function definition for ‘median’
efron: no visible global function definition for ‘hist’
efron: no visible global function definition for ‘glm’
efron: no visible binding for global variable ‘poisson’
efron: no visible global function definition for ‘qchisq’
efron: no visible global function definition for ‘predict’
efron: no visible global function definition for ‘quantile’
efron: no visible global function definition for ‘lm’
efron: no visible global function definition for ‘coef’
make.bspline.matrix: no visible global function definition for
  ‘quantile’
plotFDR: no visible global function definition for ‘hist’
plotFDR: no visible global function definition for ‘par’
plotFDR: no visible global function definition for ‘axis’
plotFDR: no visible global function definition for ‘lines’
plotFDR: no visible global function definition for ‘legend’
plotFDR: no visible global function definition for ‘rug’
plotFDR: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par poisson predict
  qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par", "rug",
             "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ calls in package code:
  ‘ggplot2’ ‘gridExtra’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FFieldPtRepDemo: no visible global function definition for ‘ggplot’
FFieldPtRepDemo: no visible binding for global variable ‘mtcars’
FFieldPtRepDemo: no visible global function definition for ‘aes’
FFieldPtRepDemo: no visible binding for global variable ‘mpg’
FFieldPtRepDemo: no visible global function definition for ‘geom_point’
FFieldPtRepDemo: no visible global function definition for ‘geom_text’
FFieldPtRepDemo: no visible global function definition for ‘ggtitle’
FFieldPtRepDemo: no visible global function definition for
  ‘geom_segment’
FFieldPtRepDemo: no visible global function definition for
  ‘grid.arrange’
Undefined global functions or variables:
  aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg
  mtcars
Consider adding
  importFrom("datasets", "mtcars")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ftest: no visible global function definition for ‘wilcox.test’
ftest: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  t.test wilcox.test
Consider adding
  importFrom("stats", "t.test", "wilcox.test")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘mvtnorm’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dmymvnorm: no visible global function definition for ‘dmvnorm’
dmymvt: no visible global function definition for ‘dmvt’
gof.test: no visible global function definition for ‘quantile’
gof.test : ecdf: no visible global function definition for ‘mecdf’
gof.test: no visible global function definition for ‘jacobian’
gof.test: no visible global function definition for ‘var’
gradCdfT: no visible global function definition for ‘dt’
gradCdfT: no visible global function definition for ‘pt’
gradCdfT: no visible global function definition for ‘pmvt’
influFun: no visible global function definition for ‘jacobian’
mult.sim: no visible global function definition for ‘rnorm’
plackettFormula: no visible global function definition for ‘pt’
plackettFormula: no visible global function definition for ‘pmvt’
pmymvnorm: no visible global function definition for ‘GenzBretz’
pmymvnorm: no visible global function definition for ‘TVPACK’
pmymvnorm : <anonymous>: no visible global function definition for
  ‘pmvnorm’
pmymvt: no visible global function definition for ‘GenzBretz’
pmymvt: no visible global function definition for ‘TVPACK’
pmymvt : <anonymous>: no visible global function definition for ‘pmvt’
rmymvnorm: no visible global function definition for ‘rmvnorm’
rmymvt: no visible global function definition for ‘rmvt’
Undefined global functions or variables:
  GenzBretz TVPACK dmvnorm dmvt dt jacobian mecdf pmvnorm pmvt pt
  quantile rmvnorm rmvt rnorm var
Consider adding
  importFrom("stats", "dt", "pt", "quantile", "rnorm", "var")
to your NAMESPACE file.
fgeasy: no visible global function definition for ‘dist’
fgeasy : cor.est: no visible global function definition for ‘cor.test’
fgeasy: no visible binding for global variable ‘var’
fgperm : runrand: no visible global function definition for ‘runif’
fgperm : runrand: no visible global function definition for ‘ave’
fgploc : runrand: no visible global function definition for ‘runif’
fgploc : runrand: no visible global function definition for ‘ave’
fyshuffle: no visible global function definition for ‘runif’
plot.fg: no visible global function definition for ‘par’
plot.fg: no visible global function definition for ‘segments’
plot.fg: no visible binding for global variable ‘quantile’
plot.fg: no visible global function definition for ‘abline’
plot.fg: no visible global function definition for ‘axis’
summary.fg: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  abline ave axis cor.test dist par quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
fieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘dataframe.dump’ ‘list.dump’ ‘myDB’
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘filehash’ ‘DBI’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createSQLite: no visible global function definition for ‘dbDriver’
createSQLite: no visible global function definition for ‘dbConnect’
createSQLite: no visible global function definition for
  ‘dbUnloadDriver’
createSQLite: no visible global function definition for ‘dbGetQuery’
initializeSQLite: no visible global function definition for ‘dbDriver’
initializeSQLite: no visible global function definition for ‘dbConnect’
initializeSQLite: no visible global function definition for ‘new’
dbDelete,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbDisconnect,filehashSQLite: no visible global function definition for
  ‘dbUnloadDriver’
dbFetch,filehashSQLite-character: no visible global function definition
  for ‘dbGetQuery’
dbInsert,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbList,filehashSQLite: no visible global function definition for
  ‘dbGetQuery’
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘myTestDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘tkrplot’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'POICalc.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'POIcoords_-.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'plotPOI.Rd':
  \examples lines wider than 100 characters:
          graphPOI@docs <- matrix(c(seq(1:nrow(graphPOI@objeto)), seq(1:nrow(graphPOI@objeto))), ncol = 2)
        graphPOI@objeto <- graphPOI@objeto <- rbind(c(0,.05), c(.05,0), c(0,-.05), c(-.05,0) ,round(circulo(0,0,.3,PLOT = FALSE),2))
        usaPOI@wordsInQuery <- c(paste('High', names(USArrests[,c(1,2,4)])), paste('Low', names(USArrests[,c(1,2,4)])))

These lines will be truncated in the PDF manual.