Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EstimateProbability: no visible global function definition for
  ‘predict’
LOGICOIL: no visible binding for global variable ‘pssm’
LOGICOIL: no visible binding for global variable ‘LOGICOILfit’
LOGICOIL: no visible binding for global variable ‘Model_Parameters’
plot_LOGICOIL: no visible global function definition for ‘png’
plot_LOGICOIL: no visible global function definition for ‘par’
plot_LOGICOIL: no visible global function definition for ‘lines’
plot_LOGICOIL: no visible global function definition for ‘axis’
plot_LOGICOIL: no visible global function definition for ‘mtext’
plot_LOGICOIL: no visible global function definition for ‘legend’
plot_LOGICOIL: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par png
  predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par")
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following files/directories:
  ‘GCN4wt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘logisticRR.Rmd’ using rmarkdown
Quitting from lines 162-169 (logisticRR.Rmd) 
Error: processing vignette 'logisticRR.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘logisticRR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
LogitNet.weight: no visible global function definition for ‘lowess’
LogitNet.weight: no visible global function definition for ‘median’
Undefined global functions or variables:
  lowess median
Consider adding
  importFrom("stats", "lowess", "median")
to your NAMESPACE file.
rloglognorm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LogrankA: no visible global function definition for ‘is.Surv’
LogrankA: no visible global function definition for ‘na.omit’
LogrankA: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  is.Surv na.omit pchisq
Consider adding
  importFrom("stats", "na.omit", "pchisq")
to your NAMESPACE file.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘main.tex’ ‘scene.asy’
Package suggested but not available for checking: ‘ElemStatLearn’
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
fplot: no visible global function definition for ‘rnorm’
fplot: no visible global function definition for ‘segments’
fplot: no visible global function definition for ‘points’
fplot: no visible global function definition for ‘text’
fplot.foodweb: no visible global function definition for ‘segments’
fplot.foodweb: no visible global function definition for ‘points’
fplot.foodweb: no visible global function definition for ‘text’
gplot: no visible global function definition for ‘runif’
groupplot: no visible global function definition for ‘rnorm’
groupplot: no visible global function definition for ‘segments’
groupplot: no visible global function definition for ‘points’
groupplot: no visible global function definition for ‘text’
groupplot.foodweb: no visible global function definition for ‘rnorm’
groupplot.foodweb: no visible global function definition for ‘segments’
groupplot.foodweb: no visible global function definition for ‘points’
groupplot.foodweb: no visible global function definition for ‘text’
Undefined global functions or variables:
  points rnorm runif segments text
Consider adding
  importFrom("graphics", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
amendColumns: no visible global function definition for ‘setNames’
fillColumns: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Overview.Rmd’
lpint : <anonymous>: no visible global function definition for
  ‘integrate’
lpint: no visible global function definition for ‘integrate’
lpint : lpint : <anonymous>: no visible global function definition for
  ‘integrate’
lplikint : lplikint.fun : <anonymous>: no visible global function
  definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
'library' or 'require' call to ‘Rsymphony’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
mipSolve.Rsymphony: no visible global function definition for
  ‘Rsymphony_solve_LP’
Undefined global functions or variables:
  Rsymphony_solve_LP
learnPattern.default: no visible global function definition for ‘runif’
plot.learnPattern: no visible global function definition for ‘matplot’
plotMDS: no visible global function definition for ‘par’
plotMDS: no visible global function definition for ‘rainbow’
plotMDS: no visible global function definition for ‘pairs’
visualizePattern: no visible global function definition for ‘par’
visualizePattern: no visible global function definition for ‘points’
visualizePattern: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend matplot pairs par points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
LP.comoment: no visible global function definition for ‘cor’
LP.comoment: no visible global function definition for ‘cov’
LP.moment: no visible global function definition for ‘cor’
LPTrans: no visible global function definition for ‘ecdf’
VAR: no visible global function definition for ‘embed’
VAR: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cor cov ecdf embed lm
Consider adding
  importFrom("stats", "cor", "cov", "ecdf", "embed", "lm")
to your NAMESPACE file.
associate: no visible global function definition for ‘cor’
textmatrix: no visible global function definition for ‘xtabs’
textvector: no visible global function definition for ‘data’
Undefined global functions or variables:
  cor data xtabs
Consider adding
  importFrom("stats", "cor", "xtabs")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following files/directories:
  ‘homer.bmp’ ‘homer.jpeg’ ‘homer.pdf’ ‘homer.png’ ‘homer.ps’
  ‘homer.tiff’
Lsdv.formula: no visible global function definition for ‘model.frame’
Lsdv.formula: no visible global function definition for ‘model.matrix’
Lsdv.formula: no visible global function definition for
  ‘model.response’
lsdv: no visible global function definition for ‘pf’
summary.Lsdv: no visible global function definition for ‘coef’
summary.Lsdv: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pf pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pf", "pt")
to your NAMESPACE file.
legend.lshorth: no visible global function definition for ‘legend’
legend.lshorth: no visible global function definition for ‘strwidth’
legend.lshorth: no visible global function definition for ‘text’
plot.lshorth: no visible global function definition for ‘plot.new’
plot.lshorth: no visible global function definition for ‘plot.window’
plot.lshorth: no visible global function definition for ‘axis’
plot.lshorth: no visible global function definition for ‘title’
plot.lshorth: no visible global function definition for ‘box’
plot.lshorth: no visible global function definition for ‘lines’
plot.lshorth: no visible global function definition for ‘legend’
plot.lshorth: no visible global function definition for ‘strwidth’
plot.lshorth: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box legend lines plot.new plot.window strwidth text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot.new",
             "plot.window", "strwidth", "text", "title")
to your NAMESPACE file.
OC : Lnapprox: no visible global function definition for ‘pnorm’
OC : Lnapprox: no visible global function definition for ‘qnorm’
OC : Lt: no visible global function definition for ‘pt’
OC : Lt: no visible global function definition for ‘qnorm’
OC : OC_emwa2: no visible global function definition for ‘pnorm’
OC : OC_emwa2: no visible global function definition for ‘qnorm’
OC: no visible global function definition for ‘pnorm’
OC: no visible global function definition for ‘qnorm’
cmBE : LAtHy: no visible global function definition for ‘phyper’
cmBE: no visible global function definition for ‘uniroot’
planAOQL : Gderivacex: no visible global function definition for
  ‘pnorm’
planAOQL : Mnk: no visible global function definition for ‘uniroot’
planAOQL : k0AOQL : delta: no visible global function definition for
  ‘pnorm’
planAOQL : alpha0: no visible global function definition for ‘pnorm’
planAOQL : alpha0: no visible global function definition for ‘qnorm’
planAOQL : fMSmodq2: no visible global function definition for
  ‘optimize’
planAOQL : kAOQL: no visible global function definition for ‘uniroot’
planLTPD : nAPPROXL : k0L : g: no visible global function definition
  for ‘qnorm’
planLTPD : nAPPROXL : k0L : h: no visible global function definition
  for ‘qnorm’
planLTPD : nAPPROXL : k0L: no visible global function definition for
  ‘qnorm’
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  ‘pnorm’
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  ‘qnorm’
planLTPD : nAPPROXL: no visible global function definition for
  ‘uniroot’
planLTPD : kEWMA: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  optimize phyper pnorm pt qnorm uniroot
Consider adding
  importFrom("stats", "optimize", "phyper", "pnorm", "pt", "qnorm",
             "uniroot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘robustbase’
  Please remove these calls from your code.
ltsbase: no visible global function definition for ‘lm’
ltsbase: no visible global function definition for ‘lines’
ltsbase: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines lm
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "lm")
to your NAMESPACE file.
terrestrial.season: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘test’
generate.clonal.data : pcr.rpareto.func: no visible global function
  definition for ‘runif’
generate.clonal.data : get.readcount.given.cellcount: no visible global
  function definition for ‘rlnorm’
generate.clonal.data: no visible global function definition for
  ‘rmultinom’
generate.clonal.data: no visible global function definition for ‘rpois’
infer.clonality: no visible global function definition for ‘cov’
infer.clonality: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output cov rlnorm rmultinom rpois runif
Consider adding
  importFrom("stats", "cov", "rlnorm", "rmultinom", "rpois", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
project.M3.1.to.M3.2: no visible global function definition for
  ‘coordinates<-’
project.M3.1.to.M3.2: no visible global function definition for
  ‘proj4string<-’
project.M3.1.to.M3.2: no visible global function definition for ‘CRS’
project.M3.1.to.M3.2: no visible global function definition for
  ‘spTransform’
project.M3.1.to.M3.2: no visible global function definition for
  ‘coordinates’
Undefined global functions or variables:
  CRS coordinates coordinates<- proj4string<- spTransform
maboost.default: no visible global function definition for
  ‘flush.console’
maboost.default: no visible binding for global variable ‘na.pass’
maboost.default : predict.type: no visible global function definition
  for ‘predict’
maboost.formula: no visible global function definition for
  ‘model.extract’
maboost.machine.bin: no visible global function definition for ‘runif’
maboost.machine.bin: no visible binding for global variable ‘na.pass’
maboost.machine.multi: no visible global function definition for
  ‘runif’
maboost.machine.multi: no visible binding for global variable ‘na.pass’
projsplx_k: no visible global function definition for ‘tail’
varplot.maboost: no visible global function definition for ‘dotchart’
Undefined global functions or variables:
  dotchart flush.console model.extract na.pass predict runif tail
Consider adding
  importFrom("graphics", "dotchart")
  importFrom("stats", "model.extract", "na.pass", "predict", "runif")
  importFrom("utils", "flush.console", "tail")
to your NAMESPACE file.
logistic_z: no visible global function definition for ‘glm’
logistic_z: no visible binding for global variable ‘binomial’
logistic_z: no visible global function definition for ‘predict’
plsrf_x: no visible global function definition for ‘qnorm’
plsrf_x: no visible global function definition for ‘predict’
plsrf_x_pv: no visible global function definition for ‘qnorm’
plsrf_x_pv: no visible global function definition for ‘predict’
plsrf_xz: no visible global function definition for ‘qnorm’
plsrf_xz: no visible global function definition for ‘predict’
plsrf_xz_pv: no visible global function definition for ‘qnorm’
plsrf_xz_pv: no visible global function definition for ‘predict’
rf_z: no visible global function definition for ‘qnorm’
rf_z: no visible global function definition for ‘predict’
simuldata_list: no visible global function definition for ‘rnorm’
simuldatacluster_list: no visible global function definition for
  ‘rnorm’
svm_x: no visible global function definition for ‘predict’
Undefined global functions or variables:
  binomial glm predict qnorm rnorm
Consider adding
  importFrom("stats", "binomial", "glm", "predict", "qnorm", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘R2wd’
'library' or 'require' calls in package code:
  ‘R2wd’ ‘ggplot2’ ‘metafor’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘maddison_project_database.Rmd’
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-package-majesticr--rmd.Rmd’
Found the following files/directories:
  ‘MyMetadata.Rdata’ ‘MyMetadata.csv’ ‘MyintMatrix.Rdata’
  ‘MyintMatrix.csv’ ‘int.Rdata’ ‘int.binary.nex’
Package in Depends field not imported from: ‘rJava’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MalletLDA: no visible global function definition for ‘.jnew’
mallet.doc.topics: no visible global function definition for
  ‘.jevalArray’
mallet.import: no visible global function definition for ‘J’
mallet.import: no visible global function definition for ‘.jnew’
mallet.import: no visible global function definition for ‘.jcast’
mallet.subset.topic.words: no visible global function definition for
  ‘.jevalArray’
mallet.topic.hclust: no visible global function definition for ‘hclust’
mallet.topic.hclust: no visible global function definition for ‘dist’
mallet.topic.words: no visible global function definition for
  ‘.jevalArray’
mallet.word.freqs: no visible global function definition for
  ‘.jevalArray’
Undefined global functions or variables:
  .jcast .jevalArray .jnew J dist hclust
Consider adding
  importFrom("stats", "dist", "hclust")
to your NAMESPACE file.
cf1.sample: no visible global function definition for ‘rexp’
cf1.sample: no visible global function definition for ‘rmultinom’
dherlang : <anonymous> : <anonymous>: no visible global function
  definition for ‘dgamma’
erhmm.param.kmeans: no visible global function definition for ‘kmeans’
erhmm.param.kmeans: no visible global function definition for ‘var’
erhmm.param.kmeans: no visible global function definition for ‘runif’
gmmpp.param.kmeans: no visible global function definition for ‘kmeans’
gmmpp.param.kmeans: no visible global function definition for ‘runif’
herlang.param.kmeans: no visible global function definition for
  ‘kmeans’
herlang.param.kmeans: no visible global function definition for ‘var’
map.param.kmeans: no visible global function definition for ‘kmeans’
map.param.kmeans: no visible global function definition for ‘runif’
ph.param.random: no visible global function definition for ‘runif’
ph.sample: no visible global function definition for ‘rmultinom’
ph.sample: no visible global function definition for ‘rexp’
pherlang : <anonymous> : <anonymous>: no visible global function
  definition for ‘pgamma’
rherlang: no visible global function definition for ‘rmultinom’
rherlang : <anonymous>: no visible global function definition for
  ‘rgamma’
Undefined global functions or variables:
  dgamma kmeans pgamma rexp rgamma rmultinom runif var
Consider adding
  importFrom("stats", "dgamma", "kmeans", "pgamma", "rexp", "rgamma",
             "rmultinom", "runif", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘mgcv’ which was already attached by Depends.
  Please remove these calls from your code.
ageprofile: no visible global function definition for ‘model.frame’
ageprofile: no visible binding for global variable ‘poisson’
ageprofile: no visible global function definition for ‘predict.gam’
ageprofile: no visible global function definition for ‘as.formula’
ageprofile: no visible global function definition for ‘summary.gam’
ageprofile: no visible global function definition for ‘contrasts<-’
ageprofile: no visible global function definition for ‘anova.gam’
plotap: no visible global function definition for ‘dev.new’
plotap: no visible global function definition for ‘lines’
plotap: no visible global function definition for ‘points’
plotap: no visible global function definition for ‘legend’
splitter: no visible global function definition for ‘reshape’
tabm: no visible global function definition for ‘coef’
tabm: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC anova.gam as.formula coef contrasts<- dev.new legend lines
  model.frame points poisson predict.gam reshape summary.gam
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "points")
  importFrom("stats", "AIC", "as.formula", "coef", "contrasts<-",
             "model.frame", "poisson", "reshape")
to your NAMESPACE file.
calcStats: no visible global function definition for ‘as.formula’
calcStats: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  as.formula na.omit
Consider adding
  importFrom("stats", "as.formula", "na.omit")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘RArcInfo’
Running examples in ‘mapview-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: +
> ### Title: mapview + mapview adds data from the second map to the first
> ### Aliases: + +,mapview,mapview-method +,mapview,ANY-method
> ###   +,mapview,NULL-method +,mapview,character-method
> 
> ### ** Examples
> 
> m1 <- mapView(franconia, col.regions = "red")
Warning: st_crs<- : replacing crs does not reproject data; use st_transform for that
> m2 <- mapView(breweries)
Warning: st_crs<- : replacing crs does not reproject data; use st_transform for that
> 
> ### add two mapview objects
> m1 + m2
Error in if (!is.na(getProjection(lst[[i]]))) { : 
  argument is of length zero
Calls: + -> + -> combineExtent -> do.call -> lapply -> FUN
Execution halted
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mapview)
  > 
  > test_check("mapview")
  ── 1. Failure: getProjection() runs without issues (@test-mapviewControls.R#108)
  getProjection(franconia) has type `NULL`, not `character`.
  
  ── 2. Failure: getProjection() runs without issues (@test-mapviewControls.R#109)
  getProjection(franconia) not equal to "+proj=longlat +datum=WGS84 +no_defs".
  target is NULL, current is character
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 63 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Failure: getProjection() runs without issues (@test-mapviewControls.R#108) 
  2. Failure: getProjection() runs without issues (@test-mapviewControls.R#109) 
  
  Error: testthat unit tests failed
  Execution halted
negbin.rel.clust: no visible global function definition for ‘kmeans’
negbin.rel.clust: no visible global function definition for ‘matplot’
negbin.rel.pca: no visible global function definition for ‘princomp’
negbin.rel.pca: no visible global function definition for ‘biplot’
pois.rel.clust: no visible global function definition for ‘kmeans’
pois.rel.clust: no visible global function definition for ‘matplot’
pois.rel.pca: no visible global function definition for ‘princomp’
pois.rel.pca: no visible global function definition for ‘biplot’
sim.negbin: no visible global function definition for ‘rnbinom’
sim.pois: no visible global function definition for ‘rpois’
wt.rel.negbin: no visible global function definition for ‘var’
wt.rel.negbin: no visible global function definition for ‘optimize’
wt.rel.negbin: no visible global function definition for ‘integrate’
wt.rel.pois: no visible global function definition for ‘optimize’
wt.rel.pois: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  biplot integrate kmeans matplot optimize princomp rnbinom rpois var
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "biplot", "integrate", "kmeans", "optimize",
             "princomp", "rnbinom", "rpois", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
mAr.pca: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘WhatIf’
Found the following possibly unsafe calls:
File ‘matlab/R/zzz.R’:
  unlockBinding("savedTime", .MatlabNamespaceEnv)

colorbar : colorbar.EO: no visible global function definition for ‘par’
colorbar : colorbar.EO: no visible global function definition for
  ‘axis’
colorbar : colorbar.EO: no visible global function definition for
  ‘axTicks’
colorbar : colorbar.EO: no visible global function definition for ‘box’
colorbar : colorbar.NO: no visible global function definition for
  ‘axis’
colorbar : colorbar.NO: no visible global function definition for
  ‘axTicks’
colorbar : colorbar.NO: no visible global function definition for ‘box’
imagesc : pretty.axp: no visible global function definition for ‘par’
imagesc: no visible global function definition for ‘axis’
imagesc: no visible global function definition for ‘box’
jet.colors: no visible global function definition for ‘rgb’
multiline.plot.colors : get.gca.colororder: no visible global function
  definition for ‘rgb’
std: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axTicks axis box par rgb sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axTicks", "axis", "box", "par")
  importFrom("stats", "sd")
to your NAMESPACE file.
'library' or 'require' call to ‘bigmemory’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
MAT: no visible global function definition for ‘dev.new’
MAT: no visible global function definition for ‘points’
MAT: no visible global function definition for ‘abline’
MAT: no visible global function definition for ‘text’
MAT: no visible global function definition for ‘legend’
MAT: no visible global function definition for ‘lines’
MAT: no visible global function definition for ‘par’
MAT: no visible global function definition for ‘barplot’
MAT: no visible global function definition for ‘cor’
print.MAT: no visible global function definition for ‘sd’
print.MAT: no visible global function definition for ‘cor’
simM3PL: no visible global function definition for ‘rnorm’
simM3PL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par points rnorm runif sd
  text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘utilities.R’
GSTplot : <anonymous>: no visible global function definition for
  ‘t.test’
GSTplot: no visible global function definition for ‘rt’
GSTplot: no visible global function definition for ‘layout’
GSTplot: no visible global function definition for ‘par’
GSTplot: no visible global function definition for ‘text’
GSTplot: no visible global function definition for ‘lines’
GSTplot: no visible global function definition for ‘polygon’
GSTplot: no visible global function definition for ‘abline’
GSTplot: no visible global function definition for ‘ecdf’
GSTplot: no visible global function definition for ‘knots’
GSTplot : <anonymous>: no visible global function definition for ‘aov’
GSTplot: no visible global function definition for ‘qf’
MAVTn : <anonymous>: no visible global function definition for ‘aov’
MAVTn: no visible global function definition for ‘p.adjust’
MAVTn: no visible global function definition for ‘par’
MAVTn: no visible global function definition for ‘abline’
MAVTn: no visible global function definition for ‘legend’
MAVTn: no visible global function definition for ‘locator’
Tols : olsf: no visible global function definition for ‘t.test’
Tols: no visible global function definition for ‘cor’
Undefined global functions or variables:
  abline aov cor ecdf knots layout legend lines locator p.adjust par
  polygon qf rt t.test text
Consider adding
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "locator", "par", "polygon", "text")
  importFrom("stats", "aov", "cor", "ecdf", "knots", "p.adjust", "qf",
             "rt", "t.test")
to your NAMESPACE file.
Package in Depends field not imported from: ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catt.test: no visible global function definition for ‘pnorm’
fnorm2: no visible global function definition for ‘sadmvn’
fnorm3: no visible global function definition for ‘sadmvn’
Undefined global functions or variables:
  pnorm sadmvn
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
MI.2: no visible global function definition for ‘xtabs’
RNASeq.Data: no visible binding for global variable ‘quantile’
loc.node: no visible global function definition for ‘head’
loc.node: no visible global function definition for ‘tail’
plotHybrid.Tree: no visible global function definition for ‘par’
plotHybrid.Tree: no visible global function definition for ‘text’
plotHybrid.Tree: no visible global function definition for ‘image’
plotHybrid.Tree: no visible global function definition for ‘grey’
plotHybrid.Tree: no visible global function definition for
  ‘heat.colors’
plotHybrid.Tree: no visible global function definition for ‘head’
plotHybrid.Tree: no visible global function definition for ‘segments’
plotbr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  grey head heat.colors image par quantile segments tail text xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
cfull: no visible global function definition for ‘combn’
cl: no visible global function definition for ‘combn’
cn: no visible global function definition for ‘combn’
crep: no visible global function definition for ‘combn’
crich: no visible global function definition for ‘combn’
ct: no visible global function definition for ‘combn’
mjaccard: no visible global function definition for ‘combn’
ml: no visible global function definition for ‘combn’
mn: no visible global function definition for ‘combn’
mrep: no visible global function definition for ‘combn’
mrich: no visible global function definition for ‘combn’
msorensen: no visible global function definition for ‘combn’
mt: no visible global function definition for ‘combn’
wnodf: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Found the following files/directories:
  ‘fireFracs.csv’ ‘fireProbabilityMultipliers.txt’
  ‘vegChangeProbabilityMultipliers.txt’
Package in Depends field not imported from: ‘lpSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
laugreen: no visible global function definition for ‘combn’
laugreen: no visible global function definition for ‘lp’
maxpear: no visible global function definition for ‘hclust’
maxpear: no visible global function definition for ‘as.dist’
maxpear : <anonymous>: no visible global function definition for
  ‘cutree’
medv: no visible global function definition for ‘cutree’
medv: no visible global function definition for ‘hclust’
medv: no visible global function definition for ‘as.dist’
minbinder: no visible global function definition for ‘hclust’
minbinder: no visible global function definition for ‘as.dist’
minbinder : <anonymous>: no visible global function definition for
  ‘cutree’
relabel : min.perm.labels: no visible global function definition for
  ‘lp.transport’
Undefined global functions or variables:
  as.dist combn cutree hclust lp lp.transport
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
  importFrom("utils", "combn")
to your NAMESPACE file.
getbetap.A: no visible global function definition for ‘pbeta’
getbetap.A: no visible global function definition for ‘cor.test’
Undefined global functions or variables:
  cor.test pbeta
Consider adding
  importFrom("stats", "cor.test", "pbeta")
to your NAMESPACE file.
mcgibbsit: no visible global function definition for ‘is.mcmc.list’
mcgibbsit: no visible global function definition for ‘start’
mcgibbsit: no visible global function definition for ‘end’
mcgibbsit: no visible global function definition for ‘thin’
mcgibbsit: no visible global function definition for ‘nvar’
mcgibbsit: no visible global function definition for ‘mcmc’
mcgibbsit: no visible global function definition for ‘mcmc.list’
mcgibbsit: no visible global function definition for ‘varnames’
mcgibbsit: no visible global function definition for ‘qnorm’
mcgibbsit: no visible global function definition for ‘niter’
mcgibbsit: no visible global function definition for ‘quantile’
mcgibbsit : to.table: no visible global function definition for
  ‘window’
mcgibbsit: no visible global function definition for ‘var’
read.mcmc: no visible global function definition for ‘mcmc.list’
read.mcmc: no visible global function definition for ‘mcmc’
Undefined global functions or variables:
  end is.mcmc.list mcmc mcmc.list niter nvar qnorm quantile start thin
  var varnames window
Consider adding
  importFrom("stats", "end", "qnorm", "quantile", "start", "var",
             "window")
to your NAMESPACE file.
Found the following files/directories:
  ‘dnzcY3e.1’ ‘dnzcY3e.2’ ‘dnzcY3e.3’ ‘mcmc.1.csv’ ‘mcmc.10.csv’
  ‘mcmc.11.csv’ ‘mcmc.12.csv’ ‘mcmc.13.csv’ ‘mcmc.14.csv’ ‘mcmc.15.csv’
  ‘mcmc.16.csv’ ‘mcmc.17.csv’ ‘mcmc.18.csv’ ‘mcmc.19.csv’ ‘mcmc.2.csv’
  ‘mcmc.20.csv’ ‘mcmc.3.csv’ ‘mcmc.4.csv’ ‘mcmc.5.csv’ ‘mcmc.6.csv’
  ‘mcmc.7.csv’ ‘mcmc.8.csv’ ‘mcmc.9.csv’
call_localoptim: no visible global function definition for ‘optim’
call_localoptim: no visible global function definition for ‘nlminb’
call_localoptim: no visible global function definition for
  ‘txtProgressBar’
call_localoptim: no visible global function definition for
  ‘setTxtProgressBar’
call_localoptim : <anonymous>: no visible global function definition
  for ‘optim’
call_localoptim : <anonymous>: no visible global function definition
  for ‘nlminb’
multiStartoptim: no visible global function definition for ‘median’
Undefined global functions or variables:
  median nlminb optim setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "median", "nlminb", "optim")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
mcheatmaps : coscolorFun: no visible global function definition for
  ‘rgb’
mcheatmaps : halfcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : fullcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘hclust’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘as.dist’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘sd’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘cophenetic’
mcheatmaps : printDiag: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘strwidth’
mcheatmaps: no visible global function definition for ‘pdf’
mcheatmaps: no visible global function definition for ‘plot.new’
mcheatmaps: no visible global function definition for ‘as.dendrogram’
mcheatmaps: no visible global function definition for ‘reorder’
mcheatmaps: no visible global function definition for ‘par’
mcheatmaps: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘heat.colors’
mcheatmaps: no visible global function definition for ‘terrain.colors’
mcheatmaps: no visible global function definition for ‘as.dist’
mcheatmaps: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  as.dendrogram as.dist cophenetic dev.off hclust heat.colors
  order.dendrogram par pdf plot.new reorder rgb sd strwidth
  terrain.colors
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
             "terrain.colors")
  importFrom("graphics", "par", "plot.new", "strwidth")
  importFrom("stats", "as.dendrogram", "as.dist", "cophenetic", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘CarStats.pdf’ ‘CarStats_labels.pdf’
lik_locfit: no visible global function definition for ‘predict’
mcll_coeff: no visible global function definition for ‘optim’
mcll_est: no visible global function definition for ‘cov’
mcll_est: no visible global function definition for ‘optim’
mcll_se: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optim predict
Consider adding
  importFrom("stats", "cov", "optim", "predict")
to your NAMESPACE file.
do.linear.conjoint: no visible global function definition for
  ‘as.formula’
do.linear.conjoint: no visible global function definition for ‘lm’
do.linear.conjoint: no visible global function definition for
  ‘coefficients’
is.close.to.orthogonal: no visible global function definition for ‘cor’
mc.add.to.design: no visible global function definition for ‘combn’
mc.good.designs: no visible global function definition for ‘combn’
Undefined global functions or variables:
  as.formula coefficients combn cor lm
Consider adding
  importFrom("stats", "as.formula", "coefficients", "cor", "lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to ‘scatterplot3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.nsga2: no visible global function definition for ‘lines’
plot.nsga2: no visible global function definition for ‘pairs’
plot.nsga2.collection: no visible global function definition for
  ‘devAskNewPage’
Undefined global functions or variables:
  devAskNewPage lines pairs
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "lines", "pairs")
to your NAMESPACE file.
src/Makevars: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘coda’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘car’ ‘spatstat’ ‘spdep’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RANN’ ‘maptools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Non-standard file/directory found at top level:
  ‘AUTHORS’
Authors information should be in file inst/AUTHORS
conf.interval: no visible global function definition for ‘pbinom’
conf.statement: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  pbinom
Consider adding
  importFrom("stats", "pbinom")
to your NAMESPACE file.
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
.df: no visible global function definition for ‘logLik’
coef_simple: no visible global function definition for ‘coef’
fitall: no visible binding for global variable ‘as.formula’
fitbest: no visible binding for global variable ‘as.formula’
lmboot: no visible global function definition for ‘lm’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘resid’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘rstudent’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘fitted’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘influence.measures’
stdcoef: no visible global function definition for ‘coef’
stdcoef: no visible global function definition for ‘update’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘logLik’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘AIC’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘fitted’
summary.resid_ensemble: no visible binding for global variable
  ‘rstudent’
summary.resid_ensemble: no visible global function definition for ‘sd’
summary.variable_ensemble: no visible global function definition for
  ‘sd’
Undefined global functions or variables:
  AIC as.formula coef fitted influence.measures lm logLik resid
  rstudent sd update
Consider adding
  importFrom("stats", "AIC", "as.formula", "coef", "fitted",
             "influence.measures", "lm", "logLik", "resid", "rstudent",
             "sd", "update")
to your NAMESPACE file.
Found the following files/directories:
  ‘meme_data2.jpg’
'library' or 'require' calls in package code:
  ‘adegenet’ ‘geosphere’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
codomToPropShared: no visible global function definition for
  ‘df2genind’
codomToPropShared: no visible global function definition for
  ‘propShared’
mgLandscape: no visible global function definition for ‘SpatialPoints’
mgQuick: no visible global function definition for ‘distm’
mgQuick: no visible binding for global variable ‘distMeeus’
Undefined global functions or variables:
  SpatialPoints df2genind distMeeus distm propShared
Package vignette with placeholder title ‘Vignette Title’:
  ‘README.Rmd’
Found the following files/directories:
  ‘Absolute Positions.txt’ ‘Epidemics 1.tiff’ ‘Epidemics 1.txt’
  ‘Epidemics 2.tiff’ ‘Epidemics 2.txt’ ‘Epidemics 3.tiff’ ‘Epidemics
  3.txt’ ‘Epidemics 4.tiff’ ‘Epidemics 4.txt’ ‘Epidemics 5.tiff’
  ‘Epidemics 5.txt’ ‘Epidemics 6.tiff’ ‘Epidemics 6.txt’ ‘Epidemics
  7.tiff’ ‘Epidemics 7.txt’ ‘Epidemics 8.tiff’ ‘Epidemics 8.txt’ ‘MAP
  Curve 1.tiff’ ‘MAP Curve 1.txt’ ‘MAP Curve 2.tiff’ ‘MAP Curve 2.txt’
  ‘MAP Curve 3.tiff’ ‘MAP Curve 3.txt’ ‘MAP Curve 4.tiff’ ‘MAP Curve
  4.txt’ ‘MAP Curve 5.tiff’ ‘MAP Curve 5.txt’ ‘MAP Curve 6.tiff’ ‘MAP
  Curve 6.txt’ ‘MAP Curve 7.tiff’ ‘MAP Curve 7.txt’ ‘MAP Curve 8.tiff’
  ‘MAP Curve 8.txt’ ‘MAP Curve Slope 1.tiff’ ‘MAP Curve Slope 1.txt’
  ‘MAP Curve Slope 2.tiff’ ‘MAP Curve Slope 2.txt’ ‘MAP Curve Slope
  3.tiff’ ‘MAP Curve Slope 3.txt’ ‘MAP Curve Slope 4.tiff’ ‘MAP Curve
  Slope 4.txt’ ‘MAP Curve Slope 5.tiff’ ‘MAP Curve Slope 5.txt’ ‘MAP
  Curve Slope 6.tiff’ ‘MAP Curve Slope 6.txt’ ‘MAP Curve Slope 7.tiff’
  ‘MAP Curve Slope 7.txt’ ‘MAP Curve Slope 8.tiff’ ‘MAP Curve Slope
  8.txt’ ‘MEM Model v1.tiff’ ‘MEM Model v1.txt’ ‘MEM Model v2.tiff’
  ‘MEM Model v2.txt’ ‘Moving Epidemics.tiff’ ‘Moving Epidemics.txt’
  ‘Relative Positions.txt’ ‘Summary.txt’ ‘graph 1.tiff’ ‘graph 2.tiff’
  ‘graph 3.tiff’ ‘graph 4.tiff’ ‘graph 5.tiff’ ‘series graph.png’
Package suggested but not available for checking: ‘GenABEL’
dometa: no visible global function definition for ‘qchisq’
dometa: no visible global function definition for ‘median’
dometa: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘qnorm’
forestplot: no visible global function definition for ‘points’
forestplot: no visible global function definition for ‘text’
metagwa.files: no visible global function definition for ‘read.csv’
metagwa.files: no visible global function definition for ‘write.csv’
metagwa.tables: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  median pchisq points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Running ‘testthat.R’ [113s/186s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  ── 1. Failure: Summing counts per taxon (@test--calculations.R#103)  ───────────
  sum(x$data$tax_data$`700035949`) not equal to result$`700035949`[1].
  names for current but not for target
  
  ── 2. Failure: Summing counts per taxon (@test--calculations.R#126)  ───────────
  `total_counts` not equal to result$total[1].
  names for current but not for target
  
  ── 3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_write
  result$data$tax_data$unite_seq[5] not equal to "CCAAATCATGTCTCCCGGCCGCAAGGCAGGTGCAGGCGTTTAACCCTTTGTGAACCAAAAAACCTTTCGCTTCGGCAGCAGCTCGGTTGGAGACAGCCTCTGTGTCAGCCTGCCGCTAGCACCAATTATCAAAACTTGCGGTTAGCAACATTGTCTGATTACCAAATTTTCGAATGAAAATCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAACGCGATAGTTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCATTGGTATTCCATTGGGCATGTCTGTTTGAGCGTCATTACAACCCTCGGTCACCACCGGTTTTGAGCGAGCAGGGTCTTCGGATCCAGCTGGCTTTAAAGTTGTAAGCTCTGCTGGCTGCTCGGCCCAACCAGAACATAGTAAAATCATGCTTGTTCAAGGTTCGCGGTCGAAGCGGTACGGCCTGAACAATACCTACCACCTCTTAGG".
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 93 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Summing counts per taxon (@test--calculations.R#103) 
  2. Failure: Summing counts per taxon (@test--calculations.R#126) 
  3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_writers.R#119) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
bcgVaccineData: no visible global function definition for ‘data’
bcgVaccineData: no visible global function definition for ‘qnorm’
hConfidence: no visible global function definition for ‘qchisq’
intervalEstimates_OneSgnf : crt: no visible global function definition
  for ‘qt’
intervalEstimates_OneSgnf: no visible binding for global variable
  ‘qnorm’
metagenGeneralised: no visible binding for global variable ‘quantile’
performancePointH : property: no visible global function definition for
  ‘var’
performancePointR : property: no visible global function definition for
  ‘var’
pfunc : pfun: no visible global function definition for ‘uniroot’
pivotalStream: no visible global function definition for ‘rchisq’
pivotalStream : <anonymous>: no visible global function definition for
  ‘rchisq’
pivotalStream: no visible global function definition for ‘rnorm’
rBinomGauss: no visible global function definition for ‘rnorm’
rBinomGauss: no visible global function definition for ‘rbinom’
rD: no visible global function definition for ‘rchisq’
rY: no visible global function definition for ‘rnorm’
render: no visible global function definition for ‘pdf’
render: no visible global function definition for ‘dev.off’
renderSVG: no visible global function definition for ‘svg’
renderSVG: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  data dev.off pdf qchisq qnorm qt quantile rbinom rchisq rnorm svg
  uniroot var
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "svg")
  importFrom("stats", "qchisq", "qnorm", "qt", "quantile", "rbinom",
             "rchisq", "rnorm", "uniroot", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
EScombination: no visible global function definition for ‘model.matrix’
EScombination: no visible global function definition for ‘p.adjust’
EScombination: no visible global function definition for ‘pt’
EScombination.paired: no visible global function definition for
  ‘p.adjust’
EScombination.paired: no visible global function definition for ‘pt’
calcfit2Diffrep: no visible global function definition for
  ‘model.matrix’
directEScombi: no visible global function definition for ‘pnorm’
directEScombi: no visible global function definition for ‘p.adjust’
directpvalcombi : fstatmeta: no visible global function definition for
  ‘qnorm’
directpvalcombi: no visible global function definition for ‘pnorm’
directpvalcombi: no visible global function definition for ‘p.adjust’
pvalcombination: no visible global function definition for
  ‘model.matrix’
pvalcombination: no visible global function definition for ‘p.adjust’
pvalcombination: no visible global function definition for ‘pt’
pvalcombination.paired: no visible global function definition for
  ‘p.adjust’
pvalcombination.paired: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.matrix p.adjust pnorm pt qnorm
Consider adding
  importFrom("stats", "model.matrix", "p.adjust", "pnorm", "pt", "qnorm")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘metan_start.Rmd’ using rmarkdown
[]=====================================================[]
[] Multi-Environment Trial Analysis (metan) v1.4.0     []
[] Author: Tiago Olivoto                               []
[] Type citation('metan') to know how to cite metan    []
[] Type vignette('metan_start') for a short tutorial   []
[] Visit http://bit.ly/2TIq6JE for a complete tutorial []
[]=====================================================[]
No issues detected while inspecting data.
Quitting from lines 133-134 (metan_start.Rmd) 
Error: processing vignette 'metan_start.Rmd' failed with diagnostics:
No common type for `..1$Y` <character> and `..2$Y` <integer>.
--- failed re-building ‘metan_start.Rmd’

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

Error: Vignette re-building failed.
Execution halted
MAPE: no visible global function definition for ‘is’
MAPE: no visible global function definition for ‘new’
Undefined global functions or variables:
  is new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘doSMP’
Package in Depends field not imported from: ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘pcaPP:::l1median_HoCr’ ‘pcaPP:::l1median_VaZh’
  See the note in ?`:::` about the use of this operator.
Package vignette with placeholder title ‘Vignette Title’:
  ‘how_to_use_crosshairs.Rmd’
fishercomb: no visible global function definition for ‘pchisq’
fishercomb: no visible global function definition for ‘p.adjust’
invnorm : <anonymous>: no visible global function definition for
  ‘qnorm’
invnorm: no visible global function definition for ‘pnorm’
invnorm: no visible global function definition for ‘p.adjust’
sim.function : <anonymous>: no visible global function definition for
  ‘rnorm’
sim.function : <anonymous>: no visible global function definition for
  ‘rnbinom’
Undefined global functions or variables:
  p.adjust pchisq pnorm qnorm rnbinom rnorm
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
             "rnorm")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  ‘SKAT:::Get_Davies_PVal’ ‘SKAT:::Get_Lambda’ ‘SKAT:::Get_Liu_PVal’
  ‘SKAT:::SKAT_Check_Method’ ‘SKAT:::SKAT_Optimal_Each_Q’
  ‘SKAT:::SKAT_Optimal_PValue_Davies’ ‘SKAT:::SKAT_Optimal_PValue_Liu’
  See the note in ?`:::` about the use of this operator.
fit.bivar: no visible binding for global variable ‘binomial’
summary.fit.bivar: no visible global function definition for ‘qt’
summary.fit.bivar: no visible global function definition for ‘pt’
Undefined global functions or variables:
  binomial pt qt
Consider adding
  importFrom("stats", "binomial", "pt", "qt")
to your NAMESPACE file.
crosssection: no visible global function definition for
  ‘colorRampPalette’
crosssection: no visible global function definition for
  ‘filled.contour’
crosssection: no visible global function definition for ‘axis’
crosssection: no visible global function definition for ‘par’
crosssection: no visible global function definition for ‘contour’
temperatures: no visible binding for global variable ‘time’
Undefined global functions or variables:
  axis colorRampPalette contour filled.contour par time
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "contour", "filled.contour", "par")
  importFrom("stats", "time")
to your NAMESPACE file.
getdata: no visible global function definition for ‘read.csv’
plotdata: no visible global function definition for ‘head’
Undefined global functions or variables:
  head read.csv
Consider adding
  importFrom("utils", "head", "read.csv")
to your NAMESPACE file.
RUVRand: no visible global function definition for ‘barplot’
RUVRand: no visible global function definition for ‘prcomp’
RuvRandIter: no visible global function definition for ‘kmeans’
RuvRandIter: no visible global function definition for ‘barplot’
RuvRandIter: no visible global function definition for ‘prcomp’
opt: no visible global function definition for ‘optim’
printdata: no visible global function definition for ‘head’
Undefined global functions or variables:
  barplot head kmeans optim prcomp
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "kmeans", "optim", "prcomp")
  importFrom("utils", "head")
to your NAMESPACE file.
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
MetSizeR : sim.pilot.data: no visible global function definition for
  ‘rnorm’
MetSizeR : sim.pilot: no visible global function definition for
  ‘rgamma’
MetSizeR : sim.pilot: no visible global function definition for ‘rnorm’
MetSizeR : samp.dist: no visible global function definition for ‘var’
MetSizeR : metsize: no visible global function definition for ‘qnorm’
MetSizeR : metsize: no visible global function definition for
  ‘quantile’
MetSizeR : metsize: no visible global function definition for ‘lm’
MetSizeR : metsize: no visible global function definition for ‘par’
MetSizeR : metsize: no visible global function definition for ‘lines’
MetSizeR : metsize: no visible global function definition for ‘abline’
MetSizeR : metsize: no visible global function definition for ‘legend’
MetSizeR : metsize: no visible global function definition for ‘arrows’
MetSizeR : metsize: no visible global function definition for ‘title’
MetSizeR : metsize: no visible global function definition for ‘text’
MetSizeR : pilot.open: no visible global function definition for
  ‘read.table’
MetSizeR : cov.open: no visible global function definition for
  ‘read.table’
MetSizeR : demo.pilot.open: no visible global function definition for
  ‘read.table’
MetSizeR : ssize.est : up.size: no visible global function definition
  for ‘pdf’
MetSizeR : ssize.est : up.size: no visible global function definition
  for ‘dev.off’
MetSizeR : <anonymous>: no visible global function definition for
  ‘help’
Undefined global functions or variables:
  abline arrows dev.off help legend lines lm par pdf qnorm quantile
  read.table rgamma rnorm text title var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "arrows", "legend", "lines", "par",
             "text", "title")
  importFrom("stats", "lm", "qnorm", "quantile", "rgamma", "rnorm",
             "var")
  importFrom("utils", "help", "read.table")
to your NAMESPACE file.
show,mewTyp: no visible global function definition for ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
Running examples in ‘mfe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: infotheo
> ### Title: Information-theoretic meta-features
> ### Aliases: infotheo infotheo.default infotheo.formula
> 
> ### ** Examples
> 
> ## Extract all metafeatures
> infotheo(Species ~ ., iris)
Error in `[.data.frame`(x, , j) : undefined columns selected
Calls: infotheo ... concentration.coefficient -> table -> [ -> [.data.frame
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mfe-vignette.Rmd’ using rmarkdown
Quitting from lines 55-66 (mfe-vignette.Rmd) 
Error: processing vignette 'mfe-vignette.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘mfe-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
maglm: no visible global function definition for ‘combn’
maglm: no visible global function definition for ‘glm’
maglm: no visible global function definition for ‘logLik’
mamglm: no visible global function definition for ‘combn’
mamglm: no visible global function definition for ‘logLik’
ses.maglm: no visible global function definition for ‘rnorm’
ses.maglm: no visible binding for global variable ‘sd’
ses.mamglm: no visible global function definition for ‘rnorm’
ses.mamglm: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  combn glm logLik rnorm sd
Consider adding
  importFrom("stats", "glm", "logLik", "rnorm", "sd")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘mglm_vignette.rmd’
Packages in Depends field not imported from:
  ‘corpcor’ ‘evd’ ‘fields’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to ‘RJSONIO’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for ‘packageVersion’
.onAttach: no visible binding for global variable ‘.MGRAST’
build.MGRAST: no visible binding for global variable ‘.MGRAST’
build.MGRAST: no visible global function definition for ‘fromJSON’
call.MGRAST: no visible binding for global variable ‘.MGRAST’
call.MGRAST: no visible global function definition for ‘download.file’
call.MGRAST: no visible global function definition for ‘isValidJSON’
call.MGRAST: no visible global function definition for ‘fromJSON’
doc.MGRAST: no visible binding for global variable ‘.MGRAST’
doc.MGRAST: no visible global function definition for ‘str’
load.MGRAST: no visible binding for global variable ‘.MGRAST’
parse.MGRAST: no visible binding for global variable ‘.MGRAST’
this.package: no visible binding for global variable ‘.MGRAST’
Undefined global functions or variables:
  .MGRAST download.file fromJSON isValidJSON packageVersion str
Consider adding
  importFrom("utils", "download.file", "packageVersion", "str")
to your NAMESPACE file.
calc_z_var: no visible binding for global variable ‘median’
diffScore: no visible global function definition for ‘new’
diffScore: no visible global function definition for ‘model.matrix’
logNORMcdf: no visible global function definition for ‘pnorm’
mGSZ.adj.mean.std: no visible binding for global variable ‘sd’
pick.data.cols: no visible binding for global variable ‘var’
plotProfile: no visible binding for global variable ‘quantile’
plotProfile: no visible global function definition for ‘lines’
plotProfile: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines median model.matrix new pnorm quantile sd var
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("methods", "new")
  importFrom("stats", "median", "model.matrix", "pnorm", "quantile",
             "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
BCI: no visible global function definition for ‘quantile’
Metro_Hastings: no visible global function definition for ‘optim’
Metro_Hastings: no visible global function definition for ‘runif’
Metro_Hastings: no visible global function definition for ‘var’
plotMH: no visible global function definition for ‘hist’
plotMH: no visible global function definition for ‘frame’
plotMH: no visible global function definition for ‘text’
Undefined global functions or variables:
  frame hist optim quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "text")
  importFrom("stats", "optim", "quantile", "runif", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘structSSI’
Found the following files/directories:
  ‘Ex01-WFLung-2000-2004-State-Dot-County-Box.pdf’
  ‘Ex02-WmLung50-70-Arrow-Bar.pdf’ ‘Ex03-Time-Series-with-Conf.pdf’
  ‘Ex04-Scatter-Dots.pdf’ ‘Ex05-Stkd-Bar-var-height.pdf’
  ‘Ex06-Stkd-Bar-fixedheight-nodot.pdf’ ‘Ex07-Educ-Centered-Bar.pdf’
  ‘Ex08-DotSignificants.pdf’ ‘Ex09-Kansas Population and
  Inc-8.5x14-sn.pdf’ ‘Ex10-Kansas Population and Inc-11x17.pdf’
  ‘Ex11-New York Pop 2010 and Change-sn colSize.pdf’ ‘Ex12-MD Pop 1970
  and 2010 plus change-map.pdf’ ‘Ex13-China 2013 Population.pdf’
  ‘Ex14-Seoul 2012 Population.pdf’ ‘Ex15-Utah Population.pdf’
  ‘Ex16_state.x77_no_DC.pdf’ ‘Ex17_state.x77_DCasNA_D.pdf’ ‘Ex18_Africa
  Micromap-11x17.pdf’
Running examples in ‘micropan-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binomixEstimate
> ### Title: Binomial mixture model estimates
> ### Aliases: binomixEstimate
> 
> ### ** Examples
> 
> # Loading an example pan-matrix
> data(xmpl.panmat)
> 
> # Estimating binomial mixture models
> binmix.lst <- binomixEstimate(xmpl.panmat, K.range = 3:8)
binomixEstimate: Fitting 3 component model...
Error: Assigned data `lst[[1]]` must be compatible with row subscript `i`.
✖ 1 row must be assigned.
✖ Assigned data has 3 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─micropan::binomixEstimate(xmpl.panmat, K.range = 3:8)
 2.   ├─base::`[<-`(...)
 3.   └─tibble:::`[<-.tbl_df`(...)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
Running ‘testthat.R’ [18s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  Loading required package: Rcpp
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 cores── 1. Failure: fastRank schemes , default fixed options identcal results  (@test
  all.equal(getRanking(origExample), getRanking(fastExample)) isn't true.
  
  ── 2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@t
  rankedSetOfSchemesOrig@ranking not equal to rankedSetOfSchemesNew@ranking.
  Component "name": 'current' is not a factor
  
  start Ranking Schemes on cluster with  2 cores── 3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47)  ────────────
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 19 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: fastRank schemes , default fixed options identcal results  (@testRankSetOfSchemes.R#87) 
  2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@testRankSetOfSchemes.R#95) 
  3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Non-standard file/directory found at top level:
  ‘MicroStrategyR-Ex.R’
'library' or 'require' call to ‘gWidgetsRGtk2’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘gWidgetsRGtk2’
  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:
  ‘Summary.csv’ ‘Summary.txt’ ‘Summary.xlsx’ ‘groupSKM.csv’
  ‘groupSKM.txt’ ‘groupSKM.xlsx’ ‘groupTM.csv’ ‘groupTM.txt’
  ‘groupTM.xlsx’
migration.cv.in : <anonymous>: no visible global function definition
  for ‘sd’
migration.cv.out : <anonymous>: no visible global function definition
  for ‘sd’
migration.field.diagram: no visible global function definition for
  ‘lines’
migration.field.diagram: no visible global function definition for
  ‘text’
migration.field.diagram: no visible global function definition for
  ‘polygon’
migration.field.diagram: no visible global function definition for ‘lm’
migration.field.diagram: no visible global function definition for
  ‘predict’
migration.field.diagram: no visible global function definition for
  ‘points’
migration.field.diagram: no visible global function definition for
  ‘resid’
migration.field.diagram: no visible global function definition for
  ‘coef’
migration.field.diagram: no visible global function definition for
  ‘mtext’
migration.field.diagram: no visible global function definition for
  ‘density’
migration.field.diagram: no visible global function definition for
  ‘rug’
migration.gini.col : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.in : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.out : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.row : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.total: no visible global function definition for ‘dist’
Undefined global functions or variables:
  coef density dist lines lm mtext points polygon predict resid rug sd
  text
Consider adding
  importFrom("graphics", "lines", "mtext", "points", "polygon", "rug",
             "text")
  importFrom("stats", "coef", "density", "dist", "lm", "predict",
             "resid", "sd")
to your NAMESPACE file.
.default_model: no visible global function definition for ‘is’
.guess_type: no visible global function definition for ‘is.ts’
.parse_trans: no visible binding for global variable ‘qnorm’
do_get_data_from_disk: no visible global function definition for
  ‘read.csv’
do_get_data_from_mi: no visible global function definition for ‘data’
do_get_data_from_r : <anonymous>: no visible global function definition
  for ‘is’
do_parametric_eval : <anonymous>: no visible global function definition
  for ‘dev.off’
do_parametric_eval : <anonymous>: no visible global function definition
  for ‘title’
do_var_options : varHandler2: no visible global function definition for
  ‘is’
do_var_options : varHandler3: no visible global function definition for
  ‘getClass’
do_var_options : varHandler3: no visible global function definition for
  ‘is’
do_var_options : changeHandler: no visible global function definition
  for ‘is’
do_var_options : <anonymous>: no visible global function definition for
  ‘title’
do_var_options: no visible global function definition for ‘getClass’
do_var_options: no visible global function definition for ‘is’
helpHandler: no visible global function definition for ‘browseURL’
is.method_in_mi: no visible global function definition for
  ‘selectMethod’
is.method_in_mi: no visible global function definition for ‘signature’
Undefined global functions or variables:
  browseURL data dev.off getClass is is.ts qnorm read.csv selectMethod
  signature title
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "title")
  importFrom("methods", "getClass", "is", "selectMethod", "signature")
  importFrom("stats", "is.ts", "qnorm")
  importFrom("utils", "browseURL", "data", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
nat_hist: no visible global function definition for ‘data’
nat_hist: no visible binding for global variable ‘current.other’
t_mal: no visible global function definition for ‘uniroot’
t_prog: no visible global function definition for ‘rlnorm’
tdeath_lung: no visible global function definition for ‘data’
tdeath_lung: no visible binding for global variable ‘ci.lung’
tdeath_lung: no visible binding for global variable ‘current.other’
tdeath_lung: no visible binding for global variable ‘former.other’
tdeath_lung: no visible binding for global variable ‘never.other’
tdeath_other: no visible global function definition for ‘data’
tdeath_other: no visible binding for global variable ‘ci.lung’
tdeath_other: no visible binding for global variable ‘current.other’
tdeath_other: no visible binding for global variable ‘former.other’
tdeath_other: no visible binding for global variable ‘never.other’
Undefined global functions or variables:
  ci.lung current.other data former.other never.other rlnorm uniroot
Consider adding
  importFrom("stats", "rlnorm", "uniroot")
  importFrom("utils", "data")
to your NAMESPACE file.
MImix.default: no visible binding for global variable ‘coef’
MImix.default: no visible binding for global variable ‘vcov’
MImix.one: no visible global function definition for ‘qnorm’
MImix.one: no visible global function definition for ‘uniroot’
mixcdf.target: no visible global function definition for ‘pnorm’
print.MImixresult: no visible global function definition for ‘coef’
print.MImixresult: no visible global function definition for ‘vcov’
summary.MImixresult: no visible global function definition for ‘coef’
summary.MImixresult: no visible global function definition for ‘vcov’
summary.MImixresult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  coef pnorm qnorm qt uniroot vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "qt", "uniroot", "vcov")
to your NAMESPACE file.
Running examples in ‘MIMSunit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: import_mhealth_csv
> ### Title: Import raw multi-channel accelerometer data stored in mHealth
> ###   Specification
> ### Aliases: import_mhealth_csv
> 
> ### ** Examples
> 
>   default_ops = options()
>   options(digits.secs=3)
>   # Use the sample mhealth csv file provided by the package
>   filepath = system.file('extdata', 'mhealth.csv', package='MIMSunit')
>   filepath
[1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MIMSunit/extdata/mhealth.csv"
> 
>   # Load the file
>   df = import_mhealth_csv(filepath)
Error: Assigned data `as.character(df[, factor_cols])` must be compatible with existing data.
✖ Existing data has 5000 rows.
✖ Assigned data has 0 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─MIMSunit::import_mhealth_csv(filepath)
 2.   ├─base::`[<-`(`*tmp*`, , factor_cols, value = character(0))
 3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, , factor_cols, value = character(0))
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
miney : plot.initial.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘text’
miney: no visible global function definition for ‘locator’
miney: no visible global function definition for ‘rect’
miney: no visible global function definition for ‘title’
Undefined global functions or variables:
  locator rect text title
Consider adding
  importFrom("graphics", "locator", "rect", "text", "title")
to your NAMESPACE file.
rminimax: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
read_design: no visible global function definition for ‘model.frame’
read_design: no visible global function definition for ‘read.table’
read_design: no visible global function definition for ‘model.matrix’
read_response: no visible global function definition for ‘read.table’
update_beta: no visible global function definition for ‘update’
update_beta: no visible global function definition for ‘glm’
update_beta: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  glm model.frame model.matrix poisson read.table update
Consider adding
  importFrom("stats", "glm", "model.frame", "model.matrix", "poisson",
             "update")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘glycolysis.xml’ ‘glycolysis_desc.tsv’ ‘glycolysis_met.tsv’
  ‘glycolysis_react.tsv’
minxent.multiple: no visible global function definition for ‘cov.wt’
minxent.single: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  cov.wt optimize
Consider adding
  importFrom("stats", "cov.wt", "optimize")
to your NAMESPACE file.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.

Found the following calls to attach():
File ‘MIPHENO/R/cdf.pval.R’:
  attach(sample.cdf)
See section ‘Good practice’ in ‘?attach’.
.FCLoess: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘median’
.Import.Luminex: no visible global function definition for ‘read.csv’
.Intra.Me: no visible global function definition for ‘sd’
.Intra.Me: no visible global function definition for ‘quantile’
.Intra.Me: no visible global function definition for ‘qchisq’
.Intra.Median: no visible global function definition for ‘median’
.boxplot.rtprofile: no visible global function definition for ‘boxplot’
.denplot: no visible global function definition for ‘density’
.denplot: no visible global function definition for ‘abline’
.normalize.Luminex: no visible global function definition for ‘sd’
.normalize.qrtpcr: no visible global function definition for ‘density’
.validate.default: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  abline boxplot density loess median qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘GGplots.pdf’ ‘Heatmap.pdf’
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
fisher.combination: no visible global function definition for ‘pchisq’
gs.test: no visible global function definition for ‘ks.test’
gs.test: no visible global function definition for ‘wilcox.test’
gs.test: no visible global function definition for ‘fisher.test’
inverse.normal.combination: no visible global function definition for
  ‘qnorm’
inverse.normal.combination: no visible global function definition for
  ‘pnorm’
limma.one.sided: no visible global function definition for ‘pt’
Undefined global functions or variables:
  fisher.test ks.test pchisq pnorm pt qnorm wilcox.test
Consider adding
  importFrom("stats", "fisher.test", "ks.test", "pchisq", "pnorm", "pt",
             "qnorm", "wilcox.test")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘rgl’ ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘canonicalizeAndMergeScene’ ‘colorScene’ ‘t2ve’ ‘vertexNormals’
  ‘vertexTriangles’
Found the following files/directories:
  ‘nmix.off’
missForest: no visible global function definition for ‘predict’
missForest: no visible global function definition for ‘idiv’
missForest: no visible global function definition for ‘var’
nrmse: no visible global function definition for ‘var’
Undefined global functions or variables:
  idiv predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
AndersonDarling: no visible global function definition for ‘spline’
Hawkins: no visible global function definition for ‘cov’
Hawkins: no visible global function definition for ‘pf’
Impute: no visible global function definition for ‘cov’
Mimpute: no visible global function definition for ‘rnorm’
SimNey: no visible global function definition for ‘runif’
TestMCARNormality: no visible global function definition for ‘cov’
TestMCARNormality: no visible global function definition for ‘pchisq’
TestUNey: no visible global function definition for ‘pchisq’
boxplot.testhomosc: no visible global function definition for ‘par’
boxplot.testhomosc: no visible global function definition for ‘title’
boxplot.testhomosc: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov par pchisq pf rnorm runif spline title
Consider adding
  importFrom("graphics", "abline", "par", "title")
  importFrom("stats", "cov", "pchisq", "pf", "rnorm", "runif", "spline")
to your NAMESPACE file.
'library' or 'require' call to ‘CompQuadForm’ which was already attached by Depends.
  Please remove these calls from your code.
linear.test: no visible global function definition for ‘lm’
linear.test: no visible global function definition for ‘pchisq’
linear.weight.test: no visible global function definition for ‘lm’
linear.weight.test: no visible global function definition for ‘dbeta’
linear.weight.test: no visible global function definition for ‘pchisq’
logit.test: no visible global function definition for ‘glm’
logit.test: no visible global function definition for ‘binomial’
logit.test: no visible binding for global variable ‘logit’
logit.test: no visible global function definition for ‘pchisq’
logit.weight.test: no visible global function definition for ‘glm’
logit.weight.test: no visible global function definition for ‘binomial’
logit.weight.test: no visible binding for global variable ‘logit’
logit.weight.test: no visible global function definition for ‘dbeta’
logit.weight.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  binomial dbeta glm lm logit pchisq
Consider adding
  importFrom("stats", "binomial", "dbeta", "glm", "lm", "pchisq")
to your NAMESPACE file.
Found the following files/directories:
  ‘imputation.R’ ‘imputation.dat’ ‘imputation.inp’ ‘imputation.sav’
  ‘imputation.sps’ ‘imputation1.dat’ ‘imputation2.dat’
  ‘imputation3.dat’ ‘imputation4.dat’ ‘imputation5.dat’
  ‘imputationlist.dat’
Packages in Depends field not imported from:
  ‘MASS’ ‘RODBC’ ‘tcltk’ ‘tcltk2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.mixtNB: no visible global function definition for ‘dnbinom’
fit.mixtNB: no visible global function definition for ‘nlminb’
wald.test: no visible global function definition for ‘pnorm’
wald.test: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  dnbinom nlminb p.adjust pnorm
Consider adding
  importFrom("stats", "dnbinom", "nlminb", "p.adjust", "pnorm")
to your NAMESPACE file.
computeContourValues: no visible global function definition for
  ‘na.omit’
deselectNonMovementSteps : coOccurProb: no visible global function
  definition for ‘dnorm’
deselectNonMovementSteps: no visible global function definition for
  ‘pnorm’
estVarMKDE: no visible global function definition for ‘na.omit’
estVarMKDE: no visible global function definition for ‘qnorm’
estVarMKDE: no visible global function definition for ‘optimize’
plotMKDE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  dnorm na.omit optimize pnorm qnorm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "dnorm", "na.omit", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘ascii3d.txt’ ‘condor_3dMKDE.dat’ ‘condor_3dMKDE.vtk’
  ‘condor_3dMKDE.xdmf’ ‘condor_dem.dat’ ‘condor_dem.vtk’
  ‘condor_dem.xdmf’ ‘condor_locations.vtk’ ‘condor_path.vtk’
mkle: no visible global function definition for ‘sd’
mkle: no visible global function definition for ‘density’
mkle: no visible global function definition for ‘optimize’
mkle.ci: no visible global function definition for ‘sd’
mkle.ci: no visible binding for global variable ‘var’
mkle.ci: no visible global function definition for ‘quantile’
mkle.ci: no visible global function definition for ‘qnorm’
opt.bw: no visible global function definition for ‘sd’
opt.bw : mse: no visible global function definition for ‘var’
opt.bw: no visible global function definition for ‘optimize’
opt.bw: no visible global function definition for ‘var’
Undefined global functions or variables:
  density optimize qnorm quantile sd var
Consider adding
  importFrom("stats", "density", "optimize", "qnorm", "quantile", "sd",
             "var")
to your NAMESPACE file.
mkssd: no visible global function definition for ‘txtProgressBar’
mkssd: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘developing-with-mlapi.Rmd’
Non-standard file/directory found at top level:
  ‘Data-Administration.R’
Unexported objects imported by ':::' calls:
  ‘MASS:::lda.default’ ‘MASS:::qda.default’
  ‘e1071:::naiveBayes.default’ ‘e1071:::svm.default’
  ‘randomForest:::randomForest.default’
  See the note in ?`:::` about the use of this operator.
confusionBarplot: no visible global function definition for ‘par’
confusionBarplot: no visible global function definition for ‘barplot’
confusionBarplot: no visible global function definition for ‘lines’
confusionBarplot: no visible global function definition for ‘text’
confusionBarplot: no visible global function definition for ‘legend’
confusionBarplot: no visible global function definition for ‘axis’
confusionImage: no visible global function definition for ‘par’
confusionImage: no visible global function definition for ‘image’
confusionImage: no visible global function definition for ‘text’
confusionImage: no visible global function definition for ‘abline’
confusionImage: no visible global function definition for ‘axis’
confusionImage: no visible global function definition for ‘mtext’
confusionStars: no visible global function definition for ‘par’
confusionStars: no visible global function definition for ‘stars’
confusionStars: no visible global function definition for ‘rect’
Undefined global functions or variables:
  abline axis barplot image legend lines mtext par rect stars text
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "mtext", "par", "rect", "stars", "text")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
plotCDF1: no visible global function definition for ‘lines’
plotCDF2: no visible global function definition for ‘gray’
plotCDF2: no visible global function definition for ‘image’
plotCDF2: no visible global function definition for ‘box’
plotCDF2: no visible global function definition for ‘par’
plotCDF2: no visible global function definition for ‘rect’
plotCDF2: no visible global function definition for ‘text’
plotCM: no visible global function definition for ‘image’
plotCM: no visible global function definition for ‘axis’
plotCM: no visible global function definition for ‘box’
plotDens1: no visible global function definition for ‘lines’
plotDens2: no visible global function definition for ‘gray’
plotDens2: no visible global function definition for ‘rect’
plotDens2: no visible global function definition for ‘axis’
plotDens2: no visible global function definition for ‘text’
plotHM: no visible global function definition for ‘terrain.colors’
plotHM: no visible global function definition for ‘image’
plotHM: no visible global function definition for ‘box’
plotHM: no visible global function definition for ‘abline’
plotHM: no visible global function definition for ‘text’
plotHM: no visible global function definition for ‘par’
plotHM: no visible global function definition for ‘rect’
plotRects: no visible global function definition for ‘rainbow’
plotRects: no visible global function definition for ‘abline’
plotRects: no visible global function definition for ‘rect’
Undefined global functions or variables:
  abline axis box gray image lines par rainbow rect terrain.colors text
Consider adding
  importFrom("grDevices", "gray", "rainbow", "terrain.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "lines",
             "par", "rect", "text")
to your NAMESPACE file.
dftest: no visible global function definition for ‘slot’
mctest: no visible global function definition for ‘rnorm’
mleurDiag: no visible global function definition for ‘acf’
mleurDiag: no visible global function definition for ‘pchisq’
mleurDiag: no visible global function definition for ‘par’
mleurDiag: no visible global function definition for ‘boxplot’
mleurDiag: no visible global function definition for ‘shapiroTest’
mleurDiag: no visible global function definition for ‘title’
mleurDiag: no visible global function definition for ‘abline’
mleurDiag: no visible global function definition for ‘lines’
simar1: no visible global function definition for ‘rnorm’
simar1: no visible global function definition for ‘rt’
simar1: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  abline acf boxplot convolve lines par pchisq rnorm rt shapiroTest
  slot title
Consider adding
  importFrom("graphics", "abline", "boxplot", "lines", "par", "title")
  importFrom("methods", "slot")
  importFrom("stats", "acf", "convolve", "pchisq", "rnorm", "rt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘CHANGELOG.txt’
Packages in Depends field not imported from:
  ‘methods’ ‘seqinr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CheckStability: no visible global function definition for ‘cor’
CheckStability: no visible global function definition for ‘var’
PriorNormPCA: no visible global function definition for ‘barplot’
SortModes: no visible global function definition for ‘rnorm’
mlicaMAIN: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot cor rnorm runif var
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "cor", "rnorm", "runif", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘BMA’ ‘abind’ ‘maxLik’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy

Found the following assignments to the global environment:
File ‘mlPhaser/R/mlPhaser.R’:
  assign("validHaploGroups", c(get("validHaploGroups", globalenv()), 
    groupStoreList), globalenv())
  assign("validHaploGroups", list(), globalenv())
Running ‘testthat.R’ [380s/463s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("checkmate")
  > library("testthat")
  > library("mlr3")
  > library("paradox")
  > library("mlr3pipelines")
  > 
  > test_check("mlr3pipelines")
  Training debug.multi with input list(input_1 = 1, input_2 = 1)
  ── 1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12)  ───────────
  <TaskClassif:tsk> has the following unsupported feature types: character
  Backtrace:
   1. lrn$train(tsk)
   2. mlr3::assert_learnable(task, self)
   3. mlr3misc::stopf(...)
  
  ── 2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removecon
  Target column 'target' must have at least two levels
  Backtrace:
   1. mlr3pipelines:::test_dropping(iris, iris, list())
   2. TaskClassif$new(...)
   3. .subset2(public_bind_env, "initialize")(...)
   4. private$.update_class_property()
   5. mlr3misc::stopf(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 7497 | SKIPPED: 44 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12) 
  2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removeconstants.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
mmm2: no visible global function definition for ‘model.frame’
mmm2: no visible global function definition for ‘model.matrix’
mmm2: no visible global function definition for ‘model.response’
mmm2: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
mmm: no visible global function definition for ‘model.frame’
mmm: no visible global function definition for ‘model.matrix’
mmm: no visible global function definition for ‘model.response’
mmm: no visible global function definition for ‘as.formula’
mmm: no visible global function definition for ‘gee’
Undefined global functions or variables:
  as.formula gee model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
get.score: no visible global function definition for ‘sd’
get.score: no visible global function definition for ‘coef’
get.score: no visible global function definition for ‘as’
get.score.main: no visible global function definition for ‘sd’
get.score.main: no visible global function definition for ‘coef’
get.subgroup: no visible global function definition for ‘sd’
sample.tte: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as coef runif sd
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "runif", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
sadmvng: no visible global function definition for ‘cov2cor’
sadmvng: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov2cor pnorm
Consider adding
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
Running ‘testthat.R’ [19s/81s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modelbased)
  > 
  > test_check("modelbased")
  ── 1. Error: estimate_contrasts (@test-estimate_contrasts.R#3)  ────────────────
  Internal Server Error (HTTP 500).
  Backtrace:
   1. modelbased::estimate_contrasts(insight::download_model("stanreg_lm_6"))
   2. insight::download_model("stanreg_lm_6")
   3. insight:::.download_data_github(name, url)
   4. httr::stop_for_status(request)
  
  ── 2. Error: estimate_means (@test-estimate_means.R#8)  ────────────────────────
  Internal Server Error (HTTP 500).
  Backtrace:
   1. modelbased::estimate_means(insight::download_model("stanreg_lm_6"))
   2. insight::download_model("stanreg_lm_6")
   3. insight:::.download_data_github(name, url)
   4. httr::stop_for_status(request)
  
  ── 3. Error: estimate_response - Bayesian (@test-estimate_response.R#4)  ───────
  Internal Server Error (HTTP 500).
  Backtrace:
   1. modelbased::estimate_response(...)
   2. insight::download_model("stanreg_lm_5")
   3. insight:::.download_data_github(name, url)
   4. httr::stop_for_status(request)
  
  ── 4. Error: estimate_response - Frequentist (@test-estimate_response.R#27)  ───
  Internal Server Error (HTTP 500).
  Backtrace:
   1. modelbased::estimate_response(insight::download_model("lm_2"))
   2. insight::download_model("lm_2")
   3. insight:::.download_data_github(name, url)
   4. httr::stop_for_status(request)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 4 ]
  1. Error: estimate_contrasts (@test-estimate_contrasts.R#3) 
  2. Error: estimate_means (@test-estimate_means.R#8) 
  3. Error: estimate_response - Bayesian (@test-estimate_response.R#4) 
  4. Error: estimate_response - Frequentist (@test-estimate_response.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' call to ‘SparseM’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘glmnet’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘BIO_TCandNLCD_NLCD.jpg’ ‘BIO_TCandNLCD_TCB.jpg’
  ‘BIO_TCandNLCD_TCG.jpg’ ‘BIO_TCandNLCD_TCW.jpg’
  ‘BIO_TCandNLCD_corrplot.jpg’ ‘BIO_TCandNLCD_mask_all_predictors.jpg’
  ‘BIO_TCandNLCD_projections.txt’ ‘RF_BIO_TCandNLCD_01.img’
  ‘RF_BIO_TCandNLCD_01.img.aux.xml’
  ‘RF_BIO_TCandNLCD_01_mapmake_arguments.txt’
  ‘RF_BIO_TCandNLCD_01_projections.txt’ ‘RF_BIO_TCandNLCD_OOB.csv’
  ‘RF_BIO_TCandNLCD_OOB_corrplot.jpg’
  ‘RF_BIO_TCandNLCD_OOB_corrplot.pdf’ ‘RF_BIO_TCandNLCD_OOB_error.jpg’
  ‘RF_BIO_TCandNLCD_OOB_error.pdf’
  ‘RF_BIO_TCandNLCD_OOB_importance.jpg’
  ‘RF_BIO_TCandNLCD_OOB_importance.pdf’
  ‘RF_BIO_TCandNLCD_OOB_scatterplot.jpg’
  ‘RF_BIO_TCandNLCD_OOB_scatterplot.pdf’
  ‘RF_BIO_TCandNLCD_model_building_arguments.txt’
  ‘RF_Bio_TC_model_building_arguments.txt’ ‘example.test.csv’
  ‘example.train.csv’
'library' or 'require' calls to packages already attached by Depends:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.clustOrder: no visible global function definition for ‘hclust’
.clustOrder: no visible global function definition for ‘as.dist’
consensusMEDissimilarity: no visible global function definition for
  ‘cor’
mergeCloseModules: no visible global function definition for ‘cor’
mergeCloseModules: no visible global function definition for ‘hclust’
mergeCloseModules: no visible global function definition for ‘as.dist’
moduleEigengenes: no visible global function definition for ‘cor’
moduleEigengenes: no visible global function definition for ‘cov’
moduleNumber: no visible global function definition for ‘cutree’
orderMEs: no visible global function definition for ‘cor’
orderMEs: no visible global function definition for ‘as.dist’
plotHclustColors: no visible global function definition for ‘barplot’
plotHclustColors: no visible global function definition for ‘strwidth’
plotHclustColors: no visible global function definition for ‘rect’
plotHclustColors: no visible global function definition for ‘text’
plotHclustColors: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.dist barplot cor cov cutree hclust lines rect strwidth text
Consider adding
  importFrom("graphics", "barplot", "lines", "rect", "strwidth", "text")
  importFrom("stats", "as.dist", "cor", "cov", "cutree", "hclust")
to your NAMESPACE file.
agostino.test: no visible global function definition for
  ‘complete.cases’
agostino.test: no visible global function definition for ‘pnorm’
anscombe.test: no visible global function definition for
  ‘complete.cases’
anscombe.test: no visible global function definition for ‘pnorm’
bonett.test: no visible global function definition for ‘complete.cases’
bonett.test: no visible global function definition for ‘pnorm’
jarque.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases pchisq pnorm
Consider adding
  importFrom("stats", "complete.cases", "pchisq", "pnorm")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘mondate’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
.date.to.mondate: no visible global function definition for ‘new’
as.character.mondate: no visible global function definition for ‘slot’
Arith,array-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-array: no visible global function definition for
  ‘callGeneric’
Arith,mondate-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-numeric: no visible global function definition for
  ‘callGeneric’
Arith,numeric-mondate: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘getDataPart’
Summary,mondate: no visible global function definition for
  ‘callGeneric’
[,mondate: no visible global function definition for ‘callNextMethod’
[,mondate: no visible global function definition for ‘new’
array,mondate: no visible global function definition for
  ‘callNextMethod’
as.numeric,mondate: no visible global function definition for ‘slot’
c,mondate: no visible global function definition for ‘new’
c,mondate: no visible binding for global variable ‘getDataPart’
c,mondate: no visible global function definition for ‘getDataPart’
matrix,mondate: no visible global function definition for
  ‘callNextMethod’
mondate,Date: no visible global function definition for ‘new’
mondate,POSIXt: no visible global function definition for ‘new’
mondate,missing: no visible global function definition for ‘new’
mondate,mondate: no visible global function definition for ‘new’
mondate,numeric: no visible global function definition for ‘new’
Undefined global functions or variables:
  callGeneric callNextMethod getDataPart new slot
Consider adding
  importFrom("methods", "callGeneric", "callNextMethod", "getDataPart",
             "new", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package which this enhances but not available for checking: ‘MonetDBLite’
Missing or unexported objects:
  ‘dplyr::base_agg’ ‘dplyr::base_scalar’ ‘dplyr::build_sql’
  ‘dplyr::is.ident’ ‘dplyr::sql_infix’ ‘dplyr::sql_prefix’
  ‘dplyr::sql_translator’ ‘dplyr::sql_variant’ ‘dplyr::src_sql’
  ‘dplyr::tbl_sql’
Found the following files/directories:
  ‘MonoTaxplot.pdf’ ‘Taxplot.pdf’
Found the following files/directories:
  ‘test.csv’ ‘test1.csv’ ‘testsummary.csv’ ‘testsummary1.csv’
mopsocd : initialize_pop: no visible global function definition for
  ‘runif’
mopsocd : compute_velocity: no visible global function definition for
  ‘runif’
mopsocd : mutate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
checkTH: no visible global function definition for ‘pchisq’
getOrderPval: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
ametrine : <anonymous>: no visible global function definition for
  ‘approx’
ametrine: no visible global function definition for ‘rgb’
isolum : <anonymous>: no visible global function definition for
  ‘approx’
isolum: no visible global function definition for ‘rgb’
morgenstemning : <anonymous>: no visible global function definition for
  ‘approx’
morgenstemning: 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.
cor.gen: no visible global function definition for ‘rnorm’
cor.gen: no visible global function definition for ‘resid’
cor.gen: no visible global function definition for ‘lm’
cor.gen: no visible binding for global variable ‘sd’
cor.gen: no visible global function definition for ‘cor’
cor.gen: no visible global function definition for ‘write.table’
stat.gen: no visible global function definition for ‘rexp’
stat.gen: no visible global function definition for ‘rnorm’
stat.gen: no visible binding for global variable ‘sd’
stat.gen: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  cor lm resid rexp rnorm sd write.table
Consider adding
  importFrom("stats", "cor", "lm", "resid", "rexp", "rnorm", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘BMI BISS Correlation MorseGen Results.txt’ ‘Control MorseGen
  Results.txt’ ‘Massage MorseGen Results.txt’ ‘Variable X MorseGen
  Results.txt’ ‘Variable X Variable Y Correlation MorseGen Results.txt’
Mort1Dsmooth: no visible global function definition for ‘time’
Mort1Dsmooth: no visible global function definition for ‘glm’
Mort1Dsmooth: no visible binding for global variable ‘poisson’
Mort1Dsmooth_optimize: no visible global function definition for
  ‘median’
Mort2Dsmooth: no visible global function definition for ‘glm’
Mort2Dsmooth: no visible binding for global variable ‘poisson’
Mort2Dsmooth: no visible global function definition for ‘median’
Mort2Dsmooth_optimize: no visible global function definition for
  ‘median’
plot.Mort1Dsmooth: no visible global function definition for ‘matplot’
plot.Mort2Dsmooth: no visible global function definition for ‘quantile’
predict.Mort1Dsmooth: no visible global function definition for ‘glm’
predict.Mort1Dsmooth: no visible binding for global variable ‘poisson’
predict.Mort2Dsmooth: no visible global function definition for ‘glm’
predict.Mort2Dsmooth: no visible binding for global variable ‘poisson’
print.summary.Mort1Dsmooth: no visible global function definition for
  ‘quantile’
print.summary.Mort2Dsmooth: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  glm matplot median poisson quantile time
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
Package suggested but not available for checking: ‘fastR’
Running ‘testthat.R’ [76s/115s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library("checkmate")
  > library("testthat")
  > library("ParamHelpers")
  > library("mlr")
  'mlr' is in maintenance mode since July 2019. Future development
  efforts will go into its successor 'mlr3' (<https://mlr3.mlr-org.com>).
  > library("mlrCPO")
  > 
  > test_check("mosmafs")
  Loading required package: mosmafs
  Loading required package: ecr
  Loading required package: BBmisc
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  Loading required package: smoof
  
  Attaching package: 'ecr'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  
  Attaching package: 'mosmafs'
  
  The following objects are masked from 'package:ecr':
  
      getPopulations, getStatistics
  
  ── 1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232)  ─────────
  `slickEcr(...)` threw an error with unexpected message.
  Expected match: "Must be of type 'numeric', not 'factor'"
  Actual message: "Assertion on 'fidelity[[2]]' failed: Must be of type 'numeric', not 'character'."
  Backtrace:
    1. testthat::expect_error(...)
    6. mosmafs::slickEcr(...)
    7. mosmafs::initEcr(...)
    8. mosmafs:::checkFidelity(fidelity)
    9. checkmate::assertNumeric(fidelity[[2]], any.missing = FALSE)
   10. checkmate::makeAssertion(x, res, .var.name, add)
   11. checkmate:::mstop(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 458 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232) 
  
  Error: testthat unit tests failed
  Execution halted
getmouseDV: no visible global function definition for ‘tail’
interpltraj: no visible global function definition for ‘approx’
trim1: no visible global function definition for ‘tail’
Undefined global functions or variables:
  approx tail
Consider adding
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Package vignette with placeholder title ‘Vignette Title’:
  ‘mozzie.Rmd’
Non-standard file/directory found at top level:
  ‘mpa-Ex.R’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘mpa/R/zzz.R’:
  .First.lib calls:
    cat("\n mpa: CoWords Method")
    cat("\n ")
    cat("\n Universidad Nacional de Colombia")
    cat("\n ")
    cat("\n Elaborado por: Daniel Rodriguez <dhrodriguezt@unal.edu.co>")
    cat("\n                Campo Elias Pardo <cepardot@unal.edu.co>")
    cat("\n For help: ?mpa   \n\n")

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

diagram.mpa: no visible global function definition for ‘abline’
diagram.mpa: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline text
Consider adding
  importFrom("graphics", "abline", "text")
to your NAMESPACE file.
mpcv: no visible binding for global variable ‘median’
mpcv: no visible global function definition for ‘cov’
mpcv: no visible global function definition for ‘dist’
plot.mpcv: no visible binding for global variable ‘median’
plot.mpcv: no visible global function definition for ‘par’
plot.mpcv: no visible global function definition for ‘rect’
plot.mpcv: no visible global function definition for ‘lines’
plot.mpcv: no visible global function definition for ‘points’
plot.mpcv: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cov dist legend lines median par points rect
Consider adding
  importFrom("graphics", "legend", "lines", "par", "points", "rect")
  importFrom("stats", "cov", "dist", "median")
to your NAMESPACE file.
GetExampleData: no visible binding for global variable ‘MPINetData’
Getenvir: no visible binding for global variable ‘MPINetData’
getPSS: no visible global function definition for ‘lines’
performpcls: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  MPINetData binomial lines
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "binomial")
to your NAMESPACE file.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘KernSmooth’ ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of ‘imag’ to
  ‘imaginary’
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of ‘imag’ to
  ‘imaginary’
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
place: no visible global function definition for ‘points’
plot,mproc: no visible binding for global variable ‘rainbow’
plot,mproc: no visible global function definition for ‘plot.default’
plot,mproc: no visible global function definition for ‘axis’
plot,mproc: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis plot.default points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "plot.default", "points")
to your NAMESPACE file.
ppersp: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette
Consider adding
  importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
densityfn: no visible global function definition for ‘dnbinom’
densityfn: no visible global function definition for ‘dpois’
densityfn: no visible global function definition for ‘dgeom’
form.add: no visible global function definition for ‘formula’
mreg: no visible global function definition for ‘model.frame’
mreg: no visible global function definition for ‘model.response’
mreg: no visible global function definition for ‘model.matrix’
mreg: no visible global function definition for ‘model.offset’
mreg: no visible global function definition for ‘nlm’
paper: no visible global function definition for ‘model.matrix’
randfn: no visible global function definition for ‘rnbinom’
randfn: no visible global function definition for ‘rpois’
randfn: no visible global function definition for ‘rgeom’
randfn: no visible global function definition for ‘rbinom’
summary.mreg: no visible global function definition for ‘pnorm’
summary.mreg: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  dgeom dnbinom dpois formula model.frame model.matrix model.offset
  model.response nlm pnorm printCoefmat rbinom rgeom rnbinom rpois
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dpois", "formula",
             "model.frame", "model.matrix", "model.offset",
             "model.response", "nlm", "pnorm", "printCoefmat", "rbinom",
             "rgeom", "rnbinom", "rpois")
to your NAMESPACE file.
Found the following files/directories:
  ‘MRH_lung’
Packages in Depends field not imported from:
  ‘mvtnorm’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MRsurvival: no visible global function definition for ‘rmvnorm’
MRsurvival: no visible global function definition for ‘optim’
MRsurvival : <anonymous>: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  optim quantile rmvnorm
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
MRwarp: no visible global function definition for ‘dev.new’
MRwarp: no visible global function definition for ‘lines’
MRwarp: no visible global function definition for ‘points’
MRwarp: no visible global function definition for ‘hist’
Undefined global functions or variables:
  dev.new hist lines points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "lines", "points")
to your NAMESPACE file.
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
msap: no visible global function definition for ‘packageVersion’
msap: no visible global function definition for ‘read.csv’
msap: no visible global function definition for ‘write.csv’
msap: no visible global function definition for ‘sd’
msap: no visible global function definition for ‘wilcox.test’
msap: no visible global function definition for ‘dist’
msap: no visible global function definition for ‘rainbow’
msap: no visible global function definition for ‘png’
msap: no visible global function definition for ‘legend’
msap: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘cmdscale’
pcoa: no visible global function definition for ‘png’
pcoa: no visible global function definition for ‘par’
pcoa: no visible global function definition for ‘rainbow’
pcoa: no visible global function definition for ‘points’
pcoa: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  cmdscale dev.off dist legend packageVersion par png points rainbow
  read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "points")
  importFrom("stats", "cmdscale", "dist", "sd", "wilcox.test")
  importFrom("utils", "packageVersion", "read.csv", "write.csv")
to your NAMESPACE file.
cv.msda: no visible global function definition for ‘predict’
formatoutput: no visible global function definition for ‘new’
msda.prep: no visible global function definition for ‘cov’
plot.msda: no visible global function definition for ‘par’
plot.msda: no visible global function definition for ‘matplot’
plot.msda: no visible global function definition for ‘rainbow’
plot.msda: no visible global function definition for ‘approx’
plot.msda: no visible global function definition for ‘axis’
predict.msda: no visible binding for global variable ‘sd’
predict.msda: no visible global function definition for ‘predict’
zeromat: no visible global function definition for ‘new’
Undefined global functions or variables:
  approx axis cov matplot new par predict rainbow sd
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "matplot", "par")
  importFrom("methods", "new")
  importFrom("stats", "approx", "cov", "predict", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘test.txt’
MSIseq.classify: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
BS.var: no visible binding for global variable ‘var’
BS.var: no visible global function definition for ‘cov’
Dist.CIs: no visible global function definition for ‘qnorm’
MSM.CIs: no visible global function definition for ‘qnorm’
plot,msSurv-missing: no visible global function definition for ‘update’
summary,msSurv: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov qnorm quantile update var
Consider adding
  importFrom("stats", "cov", "qnorm", "quantile", "update", "var")
to your NAMESPACE file.
Running examples in ‘MST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MST
> ### Title: Multivariate Survival Trees
> ### Aliases: MST splitting.stat.MST1 splitting.stat.MST2
> ###   splitting.stat.MST3 splitting.stat.MST4
> ### Keywords: Trees Survival Multivariate Correlated
> 
> ### ** Examples
> 
> set.seed(186117)
> data <- rmultime(N = 200, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> test <- rmultime(N = 100, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> 
> #Construct Multivariate Survival Tree:
> fit <- MST(formula = Surv(time, status) ~ x1 + x2 + x3 + x4 | id, data, test,
+     method = "marginal", minsplit = 100, minevents = 20, selection.method = "test.sample")
Error in plot.window(...) : need finite 'ylim' values
Calls: MST -> plot -> plot.default -> localWindow -> plot.window
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
Execution halted
'library' or 'require' call to ‘MASS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Designer.sobol: no visible global function definition for ‘runif’
basicMonteCarlo: no visible global function definition for ‘runif’
lhs003: no visible global function definition for ‘runif’
plmm.mtk : GenereXplmm: no visible binding for global variable ‘poly’
plmm.mtk : calc.plm: no visible global function definition for ‘lm.fit’
plmm.mtk: no visible global function definition for ‘var’
plmm.mtk: no visible global function definition for ‘lm’
plmm.mtk: no visible global function definition for ‘formula’
plmm.mtk: no visible global function definition for ‘update’
plmm.mtk: no visible global function definition for ‘stepAIC’
plot.plmm: no visible global function definition for ‘par’
plot.plmm: no visible global function definition for ‘barplot’
plot.plmm: no visible global function definition for ‘segments’
plot.plmm: no visible global function definition for ‘abline’
plot.plmm: no visible global function definition for ‘title’
plot.plmm: no visible global function definition for ‘legend’
plot.regressionSI: no visible global function definition for ‘par’
plot.regressionSI: no visible global function definition for ‘title’
plot.regressionSI: no visible global function definition for ‘abline’
plot,mtkProcess: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘mtkMCDesigner.R’ ‘mtkRegressionTestAnalyser.R’ ‘mtkWWEvaluator.R’
Packages in Depends field not imported from:
  ‘DiceKriging’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CrossValidationMuFicokm: no visible global function definition for
  ‘covMatrix’
CrossValidationMuFicokmAll: no visible global function definition for
  ‘covMatrix’
MuFicokm: no visible global function definition for ‘km’
compute.beta.hat: no visible global function definition for ‘lm’
computeAuxVariables: no visible global function definition for
  ‘covMatrix’
kmCok: no visible global function definition for ‘new’
kmCok: no visible global function definition for ‘drop.response’
kmCok: no visible global function definition for ‘model.matrix’
kmCok: no visible global function definition for ‘covStruct.create’
kmCok: no visible global function definition for ‘validObject’
kmCok: no visible global function definition for ‘covParametersBounds’
kmCok: no visible binding for global variable ‘kmEstimate’
kmCok : cv: no visible global function definition for ‘leaveOneOut.km’
predict.kmCok: no visible global function definition for ‘model.matrix’
predict.kmCok: no visible global function definition for ‘covMat1Mat2’
predict.kmCok: no visible global function definition for ‘qnorm’
predict.kmCok: no visible global function definition for ‘qt’
predict.kmCok: no visible global function definition for ‘covMatrix’
summary.MuFicokm: no visible global function definition for
  ‘covparam2vect’
Undefined global functions or variables:
  covMat1Mat2 covMatrix covParametersBounds covStruct.create
  covparam2vect drop.response km kmEstimate leaveOneOut.km lm
  model.matrix new qnorm qt validObject
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "lm", "model.matrix", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error(s) in re-building vignettes:
  ...
--- re-building ‘muHVT.Rmd’ using rmarkdown
Warning in file(file, "rt") :
  cannot open URL 'https://raw.githubusercontent.com/SangeetM/dataset/master/Computers.csv': HTTP status was '500 Internal Server Error'
Quitting from lines 248-251 (muHVT.Rmd) 
Error: processing vignette 'muHVT.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/SangeetM/dataset/master/Computers.csv'
--- failed re-building ‘muHVT.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package vignette with placeholder title ‘Vignette Title’:
  ‘MullerPlot.Rmd’
multeq.diff: no visible global function definition for ‘cov’
multeq.diff: no visible global function definition for ‘pt’
multeq.diff: no visible global function definition for ‘qt’
multeq.rat: no visible global function definition for ‘cov’
multeq.rat: no visible global function definition for ‘pt’
multeq.rat: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cov pt qt
Consider adding
  importFrom("stats", "cov", "pt", "qt")
to your NAMESPACE file.
plotOptionValues: no visible global function definition for ‘persp’
Undefined global functions or variables:
  persp
Consider adding
  importFrom("graphics", "persp")
to your NAMESPACE file.
synthetic_multiband: no visible global function definition for ‘runif’
synthetic_multiband: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
calculate_direction: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
betas_plot: no visible global function definition for ‘cov2cor’
betas_plot: no visible global function definition for
  ‘colorRampPalette’
betas_plot: no visible global function definition for ‘pdf’
betas_plot: no visible global function definition for ‘dev.off’
mhplot: no visible global function definition for ‘read.table’
mhplot: no visible global function definition for ‘pdf’
mhplot: no visible global function definition for ‘points’
mhplot: no visible global function definition for ‘abline’
mhplot: no visible global function definition for ‘axis’
mhplot: no visible global function definition for ‘dev.off’
multi_meta: no visible global function definition for ‘write.table’
multi_meta: no visible global function definition for ‘read.table’
multi_meta: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘read.table’
qqplotter: no visible global function definition for ‘qchisq’
qqplotter: no visible global function definition for ‘ppoints’
qqplotter: no visible global function definition for ‘median’
qqplotter: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘pdf’
qqplotter: no visible global function definition for ‘abline’
qqplotter: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline axis colorRampPalette cov2cor dev.off median pchisq pdf points
  ppoints qchisq read.table write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "points")
  importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘Output_from_running_example.txt’
multinb.fit: no visible global function definition for ‘nlminb’
multinbmod: no visible global function definition for ‘is.empty.model’
multinbmod: no visible global function definition for ‘model.matrix’
multinbmod: no visible binding for global variable ‘contrasts’
multinbmod: no visible global function definition for ‘model.response’
multinbmod: no visible global function definition for ‘model.offset’
Undefined global functions or variables:
  contrasts is.empty.model model.matrix model.offset model.response
  nlminb
Consider adding
  importFrom("stats", "contrasts", "is.empty.model", "model.matrix",
             "model.offset", "model.response", "nlminb")
to your NAMESPACE file.
Package suggested but not available for checking: ‘rPorta’
Package in Depends field not imported from: ‘rgenoud’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onAttach: no visible global function definition for
  ‘packageDescription’
genoudRob: no visible global function definition for ‘genoud’
get.XYdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘model.matrix’
get.xy: no visible global function definition for ‘terms’
get.xynames: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘model.response’
get.ydata: no visible global function definition for ‘model.frame’
mt.dev: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘dt’
mt.mle: no visible global function definition for ‘optim’
multinomRob: no visible global function definition for ‘var’
plot.multinomRob: no visible global function definition for ‘par’
plot.multinomRob: no visible global function definition for ‘title’
rdirich: no visible global function definition for ‘rgamma’
residual.generator: no visible global function definition for ‘median’
rmultinomial: no visible global function definition for ‘runif’
rmultinomial: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  dt genoud median model.frame model.matrix model.response optim
  packageDescription par pt rbinom rgamma runif terms title var
Consider adding
  importFrom("graphics", "par", "title")
  importFrom("stats", "dt", "median", "model.frame", "model.matrix",
             "model.response", "optim", "pt", "rbinom", "rgamma",
             "runif", "terms", "var")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
multiPIM : expand.factors: no visible global function definition for
  ‘formula’
multiPIM : expand.factors: no visible global function definition for
  ‘model.matrix’
multiPIM : <anonymous>: no visible global function definition for ‘glm’
multiPIM : <anonymous>: no visible binding for global variable
  ‘binomial’
multiPIM : <anonymous>: no visible global function definition for
  ‘qlogis’
multiPIM : <anonymous>: no visible global function definition for
  ‘as.formula’
multiPIM : <anonymous>: no visible global function definition for ‘lm’
multiPIM: no visible global function definition for ‘glm’
multiPIM: no visible global function definition for ‘qlogis’
multiPIM: no visible binding for global variable ‘binomial’
multiPIM: no visible global function definition for ‘plogis’
multiPIM: no visible global function definition for ‘sd’
multiPIM: no visible global function definition for ‘lm’
summary.multiPIM: no visible binding for global variable ‘sd’
summary.multiPIM: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial formula glm lm model.matrix plogis pnorm qlogis
  sd
Consider adding
  importFrom("stats", "as.formula", "binomial", "formula", "glm", "lm",
             "model.matrix", "plogis", "pnorm", "qlogis", "sd")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Sensitivity_analysis.Rmd’
CCM_boot : <anonymous>: no visible global function definition for ‘sd’
SSR_check_signal: no visible global function definition for ‘cor’
SSR_check_signal: no visible global function definition for ‘cor.test’
SSR_check_signal: no visible global function definition for ‘lm’
SSR_pred_boot: no visible global function definition for ‘cor’
make_ccm_data: no visible global function definition for ‘rnorm’
make_ccm_data: no visible global function definition for ‘runif’
make_ccm_data: no visible global function definition for ‘rlnorm’
Undefined global functions or variables:
  cor cor.test lm rlnorm rnorm runif sd
Consider adding
  importFrom("stats", "cor", "cor.test", "lm", "rlnorm", "rnorm",
             "runif", "sd")
to your NAMESPACE file.
PrbMlt.default: no visible binding for global variable ‘na.omit’
PrbMlt.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  anova na.omit
Consider adding
  importFrom("stats", "anova", "na.omit")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘car’ ‘gplots’ ‘pdist’ ‘pls’ ‘rrcov’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘bitops’ ‘caTools’ ‘car’ ‘gplots’ ‘gtools’ ‘mvtnorm’ ‘pcaPP’ ‘pdist’
  ‘pls’ ‘robustbase’ ‘rrcov’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotFID: no visible global function definition for ‘points’
Undefined global functions or variables:
  points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
Found the following files/directories:
  ‘audio.wav’
prentice.test: 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').
mvb.simu: no visible global function definition for ‘runif’
plot.lps: no visible global function definition for ‘matplot’
unifit: no visible global function definition for ‘model.frame’
unifit: no visible global function definition for ‘model.matrix’
unifit: no visible global function definition for ‘model.response’
unilps: no visible global function definition for ‘model.frame’
unilps: no visible global function definition for ‘model.matrix’
unilps: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  matplot model.frame model.matrix model.response runif
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "runif")
to your NAMESPACE file.
conceptIndicesSkm: no visible global function definition for
  ‘txtProgressBar’
conceptIndicesSkm: no visible global function definition for
  ‘setTxtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘txtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘setTxtProgressBar’
mvcmb: no visible global function definition for ‘runif’
mvcmb: no visible global function definition for ‘str’
mvcsph: no visible global function definition for ‘pdf’
mvcsph: no visible global function definition for ‘heatmap’
mvcsph: no visible global function definition for ‘dev.off’
mvcsph: no visible global function definition for ‘hclust’
mvcsph: no visible global function definition for ‘dist’
mvcsph: no visible global function definition for ‘str’
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
mvnpermute: no visible global function definition for ‘lm’
mvnpermute: no visible global function definition for ‘coef’
mvnpermute: no visible global function definition for ‘resid’
Undefined global functions or variables:
  coef lm resid
Consider adding
  importFrom("stats", "coef", "lm", "resid")
to your NAMESPACE file.
mvorpb: no visible global function definition for ‘pnorm’
mvorpb: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
rtn: no visible global function definition for ‘runif’
rtn: no visible global function definition for ‘qnorm’
rtn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm runif
Consider adding
  importFrom("stats", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘RColorBrewer’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.matchedwake: no visible global function definition for
  ‘filled.contour’
plot.matchedwake: no visible binding for global variable ‘gray.colors’
plot.matchedwake: no visible global function definition for ‘axis’
plot.matchedwake: no visible global function definition for ‘rect’
slideWakeMatch: no visible binding for global variable ‘lm’
slideWakeMatch: no visible global function definition for ‘as.formula’
slideWakeMatch: no visible global function definition for ‘summary.glm’
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
mxkssd: no visible global function definition for ‘txtProgressBar’
mxkssd: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
abcpred_nmer: no visible global function definition for ‘write.table’
algpred: no visible global function definition for ‘read.table’
algpred: no visible global function definition for ‘write.table’
allermatch: no visible global function definition for ‘read.table’
allermatch: no visible global function definition for ‘write.table’
bcepred_nmer: no visible global function definition for ‘write.table’
bimas_nmer: no visible global function definition for ‘write.table’
filter.firstlayer: no visible global function definition for
  ‘read.table’
filter.firstlayer: no visible global function definition for
  ‘write.table’
iedb_arb_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_arb_mhcii_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhcii_nmer: no visible global function definition for
  ‘write.table’
netmhcNN_nmer: no visible global function definition for ‘write.table’
netmhcWT_nmer: no visible global function definition for ‘write.table’
propred_nmer: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
update_episode: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
abs_dif: no visible global function definition for ‘as.formula’
env_dif: no visible global function definition for ‘lm’
env_dif: no visible global function definition for ‘as.formula’
env_dif_logistic: no visible global function definition for
  ‘as.formula’
fam_env: no visible global function definition for ‘as.formula’
log_dif: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula lm
Consider adding
  importFrom("stats", "as.formula", "lm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘re2r’
Error(s) in re-building vignettes:
  ...
--- re-building ‘exploring-imputed-values.Rmd’ using rmarkdown
Quitting from lines 78-87 (exploring-imputed-values.Rmd) 
Error: processing vignette 'exploring-imputed-values.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘exploring-imputed-values.Rmd’

--- re-building ‘getting-started-w-naniar.Rmd’ using rmarkdown
Quitting from lines 284-292 (getting-started-w-naniar.Rmd) 
Error: processing vignette 'getting-started-w-naniar.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘getting-started-w-naniar.Rmd’

--- re-building ‘naniar-visualisation.Rmd’ using rmarkdown
--- finished re-building ‘naniar-visualisation.Rmd’

--- re-building ‘replace-with-na.Rmd’ using rmarkdown
Quitting from lines 43-52 (replace-with-na.Rmd) 
Error: processing vignette 'replace-with-na.Rmd' failed with diagnostics:
No common type for `y` <character> and `y` <double>.
--- failed re-building ‘replace-with-na.Rmd’

--- re-building ‘special-missing-values.Rmd’ using rmarkdown
--- finished re-building ‘special-missing-values.Rmd’

SUMMARY: processing the following files failed:
  ‘exploring-imputed-values.Rmd’ ‘getting-started-w-naniar.Rmd’
  ‘replace-with-na.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘NanoStringNorm_Example_Plots_All.pdf’
  ‘NanoStringNorm_Interactive_Plot’
NAPPA: no visible binding for global variable ‘sd’
NAPPA: no visible global function definition for ‘sd’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘coef’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘lm’
calibrate.sigmoid.curve: no visible global function definition for
  ‘nls’
calibrate.sigmoid.curve: no visible binding for global variable
  ‘weights’
calibrate.sigmoid.curve: no visible global function definition for
  ‘coef’
calibrate.sigmoid.curve: no visible global function definition for
  ‘rgb’
calibrate.sigmoid.curve: no visible global function definition for
  ‘box’
calibrate.sigmoid.curve: no visible global function definition for
  ‘axis’
calibrate.sigmoid.curve: no visible global function definition for
  ‘abline’
calibrate.sigmoid.curve: no visible global function definition for
  ‘lines’
calibrate.sigmoid.curve: no visible global function definition for
  ‘predict’
calibrate.sigmoid.curve: no visible global function definition for
  ‘smooth.spline’
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for ‘nls’
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable ‘weights’
calibrate.sigmoid.curve: no visible binding for global variable ‘coef’
calibrate.sigmoid.curve: no visible global function definition for ‘pf’
calibrate.sigmoid.curve: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (!requireNamespace("testthat", quietly=TRUE)) install.packages("testthat", dependencies=TRUE, repos="http://cran.rstudio.com/")
  > library(nbc4va)
  To view the 'nbc4va' package description see: 
  help(nbc4va) 
  
  To view the 'nbc4va' package documentation, see: 
  https://rrwen.github.io/nbc4va 
  
  To cite the original method used in the 'nbc4va' package see: 
  citation("nbc4va")
  > 
  > testthat::test_check("nbc4va")
  ── 1. Failure: (unknown) (@test_nbc4va.R#29)  ──────────────────────────────────
  `results <- nbc(train, test)` did not produce any warnings.
  
  ── 2. Failure: (unknown) (@test_nbc4va.R#32)  ──────────────────────────────────
  `resultsNoCauses <- nbc(train, noCauses, known = FALSE)` did not produce any warnings.
  
  ── 3. Failure: nbc() sets the out$test.known to correctly indicate whether or no
  `expect_equal(...)` did not produce any warnings.
  
  ── 4. Error: nbc() can handle incorrect column data types in the correct positio
  The train data IDs are not unique (duplicates found:)
  Backtrace:
   1. testthat::expect_warning(...)
   6. nbc4va:::internalCheckNBC(trainTypes, testTypes)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 68 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 4 ]
  1. Failure: (unknown) (@test_nbc4va.R#29) 
  2. Failure: (unknown) (@test_nbc4va.R#32) 
  3. Failure: nbc() sets the out$test.known to correctly indicate whether or not the test causes are known (@test_nbc4va.R#46) 
  4. Error: nbc() can handle incorrect column data types in the correct positions (@test_nbc4va.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
NB.estimator: no visible global function definition for ‘optimize’
NB.estimator: no visible global function definition for ‘uniroot’
NB.example.dataset: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  optimize uniroot write.table
Consider adding
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘sample_data.txt’
ncbit : FUN: no visible global function definition for ‘read.table’
ncbit : FUN: no visible global function definition for ‘head’
Undefined global functions or variables:
  head read.table
Consider adding
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
infoNcdfVars: no visible global function definition for ‘na.omit’
modifyNcdfDefAtts: no visible global function definition for ‘na.omit’
plotDatacube: no visible global function definition for ‘runif’
plotDatacube: no visible global function definition for
  ‘colorRampPalette’
plotDatacube: no visible global function definition for ‘dev.cur’
plotDatacube: no visible global function definition for ‘dev.new’
plotDatacube: no visible global function definition for ‘layout’
plotDatacube: no visible global function definition for ‘par’
plotDatacube: no visible global function definition for ‘points’
plotDatacube: no visible global function definition for ‘text’
plotDatacube: no visible global function definition for ‘plot.new’
plotDatacube: no visible global function definition for ‘mtext’
plotDatacube: no visible global function definition for ‘rgb’
plotDatacube: no visible global function definition for ‘legend’
transNcdfRotate: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colorRampPalette dev.cur dev.new layout legend mtext na.omit par
  plot.new points rgb runif text
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.cur", "dev.new",
             "rgb")
  importFrom("graphics", "layout", "legend", "mtext", "par", "plot.new",
             "points", "text")
  importFrom("stats", "na.omit", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘test.nc’
d0: no visible global function definition for ‘qnorm’
dncgamma: no visible global function definition for ‘dpois’
indncgamma: no visible global function definition for ‘pgamma’
indncgamma: no visible global function definition for ‘dpois’
inxncgamma: no visible global function definition for ‘qnorm’
inxncgamma: no visible global function definition for ‘pgamma’
inxncgamma: no visible global function definition for ‘dpois’
pncgamma: no visible global function definition for ‘pgamma’
pncgamma: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dpois pgamma qnorm
Consider adding
  importFrom("stats", "dpois", "pgamma", "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘testNet.dot’ ‘toy_epi_sim.net’
Found the following files/directories:
  ‘single_gene_ags.groups.tsv’
data.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
population: no visible global function definition for ‘weighted.mean’
population: no visible global function definition for ‘rpois’
population: no visible global function definition for ‘lm’
population: no visible global function definition for ‘coefficients’
population: no visible global function definition for ‘sd’
population: no visible global function definition for ‘par’
population: no visible global function definition for ‘lines’
Undefined global functions or variables:
  coefficients lines lm par rpois sd weighted.mean
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "coefficients", "lm", "rpois", "sd",
             "weighted.mean")
to your NAMESPACE file.
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’, ‘Rplots.ps’
Please remove them from your package.
netVal: no visible global function definition for ‘cutree’
netVal: no visible global function definition for ‘hclust’
netVal: no visible global function definition for ‘as.dist’
Undefined global functions or variables:
  as.dist cutree hclust
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘buildcmds’
EnvInd: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘fastshp’
Found the following files/directories:
  ‘map.png’ ‘maze.html’
simulate.sisnetwork: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
mlptrain : rect: no visible global function definition for ‘polygon’
mlptrain : drawnet: no visible global function definition for ‘title’
mlptrain : drawnet: no visible global function definition for ‘polygon’
mlptrain : drawnet: no visible global function definition for ‘text’
mlptrain : drawnet: no visible global function definition for ‘lines’
mlptrain: no visible global function definition for ‘runif’
mlptrain: no visible global function definition for ‘locator’
mlptrain: no visible global function definition for ‘polygon’
mlptrain: no visible global function definition for ‘text’
rbftrain : rect: no visible global function definition for ‘polygon’
rbftrain : drawnet: no visible global function definition for ‘title’
rbftrain : drawnet: no visible global function definition for ‘polygon’
rbftrain : drawnet: no visible global function definition for ‘text’
rbftrain : drawnet: no visible global function definition for ‘lines’
rbftrain : graph: no visible global function definition for ‘title’
rbftrain : graph: no visible global function definition for ‘polygon’
rbftrain : graph: no visible global function definition for ‘text’
rbftrain : graph: no visible global function definition for ‘lines’
rbftrain : graph: no visible global function definition for ‘points’
rbftrain: no visible global function definition for ‘runif’
rbftrain: no visible global function definition for ‘locator’
rbftrain: no visible global function definition for ‘polygon’
rbftrain: no visible global function definition for ‘text’
rbftrain: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans lines locator points polygon runif text title
Consider adding
  importFrom("graphics", "lines", "locator", "points", "polygon", "text",
             "title")
  importFrom("stats", "kmeans", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘neurobase.Rmd’ using rmarkdown
--- finished re-building ‘neurobase.Rmd’

--- re-building ‘nifti_basics.Rmd’ using rmarkdown
Quitting from lines 189-219 (nifti_basics.Rmd) 
Error: processing vignette 'nifti_basics.Rmd' failed with diagnostics:
Internal Server Error (HTTP 500).
--- failed re-building ‘nifti_basics.Rmd’

--- re-building ‘simple_io.Rmd’ using rmarkdown
trying URL ‘https://johnmuschelli.com/open_ms_data/cross_sectional/raw/patient01/T1W.nii.gz’
Content type 'application/gzip' length 21807043 bytes (20.8 MB)
==================================================
downloaded 20.8 MB

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

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘correlation_table.csv’ ‘mycorrplot.png’
balloon: no visible global function definition for ‘convolve’
physnoise: no visible global function definition for ‘sd’
physnoise: no visible global function definition for ‘rnorm’
rrice: no visible global function definition for ‘rnorm’
simTSrestingstate: no visible global function definition for ‘runif’
simTSrestingstate: no visible global function definition for ‘fft’
spatialnoise: no visible global function definition for ‘rnorm’
spatialnoise: no visible global function definition for ‘qgamma’
spatialnoise: no visible global function definition for ‘pnorm’
specifydesign: no visible global function definition for ‘convolve’
systemnoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘sd’
temporalnoise: no visible global function definition for ‘arima.sim’
Undefined global functions or variables:
  arima.sim convolve fft pnorm qgamma rnorm runif sd
Consider adding
  importFrom("stats", "arima.sim", "convolve", "fft", "pnorm", "qgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
nfca : nFCAmain: no visible global function definition for ‘hist’
nfca : nFCAmain: no visible global function definition for
  ‘flush.console’
nfca : nFCAmain: no visible global function definition for ‘qnorm’
nfca : nFCAmain: no visible global function definition for ‘read.csv’
nfca : nFCAmain: no visible global function definition for ‘cor’
nfca : nFCAmain: no visible global function definition for ‘as.dist’
nfca : nFCAmain: no visible global function definition for ‘cophenetic’
nfca : nFCAmain: no visible global function definition for ‘hclust’
nfca : thresholdTEST: no visible global function definition for
  ‘read.csv’
nfca : gScript: no visible global function definition for ‘read.csv’
nfca : gScript0: no visible global function definition for ‘read.csv’
nfca : gMatrix: no visible global function definition for ‘read.csv’
nfca: no visible global function definition for ‘cor’
Undefined global functions or variables:
  as.dist cophenetic cor flush.console hclust hist qnorm read.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cophenetic", "cor", "hclust", "qnorm")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘Hgraph.dot’ ‘Igraph.dot’
Package suggested but not available for checking: ‘NFPdata’
Package vignette with placeholder title ‘Vignette Title’:
  ‘nitrcbot.Rmd’
nlmeODE: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Pwr.lme: no visible global function definition for ‘anova’
Pwr.lme: no visible global function definition for ‘qf’
Pwr.lme: no visible global function definition for ‘pf’
logLik1.lme: no visible global function definition for ‘coef’
logLik1.lme: no visible global function definition for ‘model.matrix’
logLik1.lme: no visible global function definition for ‘predict’
logLik1.lme: no visible global function definition for ‘formula’
runScript: no visible binding for global variable ‘example’
sigmaTolme: no visible global function definition for ‘vcov’
simulateY.lme: no visible global function definition for ‘runif’
simulateY.lme: no visible global function definition for ‘fitted’
simulateY.lme: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  anova coef example fitted formula model.matrix pf predict qf rnorm
  runif vcov
Consider adding
  importFrom("stats", "anova", "coef", "fitted", "formula",
             "model.matrix", "pf", "predict", "qf", "rnorm", "runif",
             "vcov")
  importFrom("utils", "example")
to your NAMESPACE file.
Missing or unexported object: ‘cleanNLP::cnlp_get_token’
Running examples in ‘nlrx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nldoc
> ### Title: Create NetLogo documentation
> ### Aliases: nldoc
> 
> ### ** Examples
> 
> 
> # List model files (.nls subfiles are also supported)
> modelfiles <- c("https://raw.githubusercontent.com/nldoc/nldoc_pg/master/WSP.nlogo",
+                 "https://raw.githubusercontent.com/nldoc/nldoc_pg/master/WSP.nls")
> 
> # Define output directory:
> outdir <- tempdir()  # adjust path to your needs
> 
> # Create documentation:
> nldoc(modelfiles = modelfiles,
+       infotab=TRUE,
+       gui=TRUE,
+       bs=TRUE,
+       outpath = outdir,
+       output_format = "html",
+       number_sections = TRUE,
+       theme = "cosmo",
+       date = date(),
+       toc = TRUE)
Warning in file(con, "r") :
  cannot open URL 'https://raw.githubusercontent.com/nldoc/nldoc_pg/master/WSP.nlogo': HTTP status was '500 Internal Server Error'
Error in file(con, "r") : 
  cannot open the connection to 'https://raw.githubusercontent.com/nldoc/nldoc_pg/master/WSP.nlogo'
Calls: nldoc -> nldoc_read_nlogo -> readLines -> file
Execution halted
Package in Depends field not imported from: ‘proto’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘stats:::nlsModel’ ‘stats:::nlsModel.plinear’
  See the note in ?`:::` about the use of this operator.
nls2: no visible global function definition for ‘nls.control’
nls2: no visible global function definition for ‘as.formula’
nls2: no visible global function definition for ‘coef’
nls2: no visible global function definition for ‘runif’
nls2 : <anonymous>: no visible global function definition for
  ‘deviance’
Undefined global functions or variables:
  as.formula coef deviance nls.control runif
Consider adding
  importFrom("stats", "as.formula", "coef", "deviance", "nls.control",
             "runif")
to your NAMESPACE file.
nnmf_als: no visible global function definition for ‘rnorm’
nnmf_mm: no visible global function definition for ‘rnorm’
nnmf_prob: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
makeRules: no visible global function definition for ‘sd’
makeRules: no visible global function definition for ‘rnorm’
nodeHarvest: no visible global function definition for ‘capture.output’
nodeHarvest: no visible global function definition for ‘lm’
nodeHarvest: no visible global function definition for ‘coef’
plot.nodeHarvest: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  capture.output coef lm rgb rnorm sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "coef", "lm", "rnorm", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘rms’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘pwt’ ‘rms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
additive: no visible global function definition for ‘lp’
ar.dual.dea: no visible global function definition for ‘lp’
cost.dea: no visible global function definition for ‘lp’
ddf: no visible global function definition for ‘lp’
dea: no visible global function definition for ‘lp’
direc.dea: no visible global function definition for ‘lp’
dual.dea: no visible global function definition for ‘lp’
effdea.b.f: no visible global function definition for ‘convhulln’
effdea.b.f: no visible global function definition for ‘lp’
faremalm2: no visible binding for global variable ‘Lag’
faremalm2: no visible global function definition for ‘na.omit’
int.dea: no visible global function definition for ‘lp’
lp2: no visible global function definition for ‘lp’
revenue.dea: no visible global function definition for ‘lp’
sbm.tone: no visible global function definition for ‘lp’
sbm.vrs: no visible global function definition for ‘lp’
Undefined global functions or variables:
  Lag convhulln lp na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘histogram’ ‘optimx’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dnormgam: no visible global function definition for ‘qgamma’
dnormgam: no visible global function definition for ‘fft’
dnormgam: no visible global function definition for ‘dgamma’
dnormgam: no visible global function definition for ‘approx’
normgam.fit : mkdfftNormalGammaOptim : <anonymous>: no visible global
  function definition for ‘dnorm’
normgam.fit : estimation_param_normexp_RMA : max.density: no visible
  global function definition for ‘density’
normgam.fit: no visible global function definition for ‘sd’
normgam.fit: no visible global function definition for ‘median’
normgam.fit: no visible global function definition for ‘IQR’
normgam.fit: no visible global function definition for ‘optimx’
normgam.fit: no visible global function definition for ‘coef’
normgam.signal: no visible global function definition for ‘approx’
normgam.signal: no visible global function definition for ‘hist’
Undefined global functions or variables:
  IQR approx coef density dgamma dnorm fft hist median optimx qgamma sd
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "IQR", "approx", "coef", "density", "dgamma",
             "dnorm", "fft", "median", "qgamma", "sd")
to your NAMESPACE file.
ajb.norm.test: no visible global function definition for ‘rnorm’
frosini.norm.test: no visible global function definition for ‘var’
frosini.norm.test: no visible global function definition for ‘pnorm’
frosini.norm.test: no visible global function definition for ‘rnorm’
geary.norm.test: no visible global function definition for ‘rnorm’
hegazy1.norm.test: no visible global function definition for ‘var’
hegazy1.norm.test: no visible global function definition for ‘qnorm’
hegazy1.norm.test: no visible global function definition for ‘rnorm’
hegazy2.norm.test: no visible global function definition for ‘var’
hegazy2.norm.test: no visible global function definition for ‘qnorm’
hegazy2.norm.test: no visible global function definition for ‘rnorm’
jb.norm.test: no visible global function definition for ‘rnorm’
kurtosis.norm.test: no visible global function definition for ‘rnorm’
skewness.norm.test: no visible global function definition for ‘rnorm’
spiegelhalter.norm.test: no visible global function definition for
  ‘rnorm’
wb.norm.test: no visible global function definition for ‘qnorm’
wb.norm.test: no visible global function definition for ‘var’
wb.norm.test: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
normality.test1: no visible global function definition for ‘cov.wt’
normality.test1: no visible global function definition for ‘cor’
normality.test1: no visible global function definition for ‘pnorm’
normality.test1: no visible global function definition for ‘pchisq’
normality.test2: no visible global function definition for ‘cov.wt’
normality.test2: no visible global function definition for ‘cor’
normality.test2: no visible global function definition for ‘acf’
normality.test2: no visible global function definition for ‘pnorm’
normality.test2: no visible global function definition for ‘pchisq’
whitenoise.test: no visible global function definition for ‘acf’
whitenoise.test: no visible global function definition for ‘spec.pgram’
whitenoise.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  acf cor cov.wt pchisq pnorm spec.pgram
Consider adding
  importFrom("stats", "acf", "cor", "cov.wt", "pchisq", "pnorm",
             "spec.pgram")
to your NAMESPACE file.
.newReportId : <anonymous>: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘smcure’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NPHMC: no visible global function definition for ‘integrate’
NPHMC: no visible global function definition for ‘qnorm’
NPHMC: no visible global function definition for ‘pnorm’
NPHMC: no visible global function definition for ‘lines’
NPHMC: no visible global function definition for ‘smcure’
NPHMC: no visible global function definition for ‘coxph’
Undefined global functions or variables:
  coxph integrate lines pnorm qnorm smcure
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "integrate", "pnorm", "qnorm")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘tmp.R’
File ‘NPsimex/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("NPsimex 0.2-1 loaded")

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

lambda.select: no visible global function definition for ‘bw.nrd0’
lambda.select: no visible global function definition for ‘bw.nrd’
lambda.select: no visible global function definition for ‘bw.ucv’
lambda.select: no visible global function definition for ‘bw.bcv’
lambda.select: no visible global function definition for ‘bw.SJ’
plot.NPsimex: no visible global function definition for ‘plot.default’
simex.H.density : simex1.est: no visible global function definition for
  ‘lm’
simex.density : simex1.est: no visible global function definition for
  ‘lm’
span.H.select: no visible global function definition for ‘density’
span.H.select : conden : <anonymous>: no visible global function
  definition for ‘dnorm’
span.select: no visible global function definition for ‘density’
span.select : conden : <anonymous>: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm lm plot.default
Consider adding
  importFrom("graphics", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "lm")
to your NAMESPACE file.
nps.test: no visible global function definition for ‘qnorm’
nps.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
npst: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
  mclapply
Package in Depends field not imported from: ‘mco’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boundedPolyMutation: no visible global function definition for ‘runif’
boundedSBXover: no visible global function definition for ‘runif’
nsga2R : <anonymous>: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘nsrr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nsrr_version
> ### Title: NSRR Gem version online
> ### Aliases: nsrr_version nsrr_gem_version nsrr_api_version
> 
> ### ** Examples
> 
> nsrr_version()
[1] "0.1.3"
> nsrr_gem_version()
Error in nsrr_gem_version() : Internal Server Error (HTTP 500).
Calls: nsrr_gem_version -> <Anonymous>
Execution halted
.mcmc.bar: no visible global function definition for ‘rnorm’
.mcmc.bar: no visible global function definition for ‘runif’
.mcmc.comb: no visible global function definition for ‘rnorm’
.mcmc.comb: no visible global function definition for ‘runif’
.mcmc.rd: no visible global function definition for ‘rnorm’
.mcmc.rd: no visible global function definition for ‘runif’
.mcmc.trans: no visible global function definition for ‘rnorm’
.mcmc.trans: no visible global function definition for ‘runif’
.simulate.bar: no visible global function definition for ‘rlnorm’
.simulate.bar: no visible global function definition for ‘rbeta’
.simulate.bar: no visible global function definition for ‘rbinom’
.simulate.comb: no visible global function definition for ‘rlnorm’
.simulate.comb: no visible global function definition for ‘rbeta’
.simulate.comb: no visible global function definition for ‘rbinom’
.simulate.rd: no visible global function definition for ‘rlnorm’
.simulate.rd: no visible global function definition for ‘rbinom’
.simulate.trans: no visible global function definition for ‘rlnorm’
.simulate.trans: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbeta rbinom rlnorm rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rlnorm", "rnorm", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
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.
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of ‘env’ to ‘envir’
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of ‘env’ to ‘envir’
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘objectSignals’
A package should be listed in only one of these fields.
Color: no visible global function definition for ‘new’
NegativeInteger: no visible global function definition for ‘new’
NonnegativeInteger: no visible global function definition for ‘new’
NonpositiveInteger: no visible global function definition for ‘new’
PositiveInteger: no visible global function definition for ‘new’
setMultipleEnum: no visible global function definition for ‘setClass’
setMultipleEnum: no visible global function definition for ‘prototype’
setNumericWithRange: no visible global function definition for
  ‘setClass’
setNumericWithRange: no visible global function definition for
  ‘prototype’
setPropertySet: no visible binding for global variable ‘extends’
setPropertySet: no visible global function definition for ‘setRefClass’
setSingleEnum: no visible global function definition for ‘setClass’
setSingleEnum: no visible global function definition for ‘prototype’
as.list,PropertySet: no visible global function definition for ‘as’
initialize,SingleEnum: no visible global function definition for
  ‘callNextMethod’
initialize,SingleEnum: no visible global function definition for ‘head’
Undefined global functions or variables:
  as callNextMethod extends head new prototype setClass setRefClass
Consider adding
  importFrom("methods", "as", "callNextMethod", "extends", "new",
             "prototype", "setClass", "setRefClass")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
Signal.gen: 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').
obliclus: no visible global function definition for ‘rnorm’
obliclus: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘ROCR’ ‘e1071’ ‘mda’ ‘pls’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
log_wrapper: no visible global function definition for ‘glm’
log_wrapper: no visible global function definition for ‘binomial’
log_wrapper: no visible global function definition for ‘coef’
log_wrapper: no visible global function definition for ‘anova’
obliqueRF.default: no visible binding for global variable ‘predict’
obliqueRF.default: no visible global function definition for
  ‘prediction’
obliqueRF.default: no visible global function definition for
  ‘performance’
pls_wrapper: no visible global function definition for ‘kernelpls.fit’
pls_wrapper: no visible global function definition for ‘coef’
ridge_slow_wrapper: no visible global function definition for
  ‘gen.ridge’
ridge_slow_wrapper: no visible global function definition for ‘predict’
ridge_svd_wrapper: no visible global function definition for
  ‘gen.ridge’
rnd_wrapper: no visible global function definition for ‘rnorm’
svm_wrapper: no visible global function definition for ‘svm’
svm_wrapper: no visible global function definition for ‘predict’
Undefined global functions or variables:
  anova binomial coef gen.ridge glm kernelpls.fit performance predict
  prediction rnorm svm
Consider adding
  importFrom("stats", "anova", "binomial", "coef", "glm", "predict",
             "rnorm")
to your NAMESPACE file.
IBMD: no visible global function definition for ‘runif’
IBMD: no visible global function definition for ‘quantile’
RAI: no visible global function definition for ‘runif’
RAI: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile runif
Consider adding
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
obsSensCCC: no visible global function definition for ‘coef’
obsSensCCC: no visible global function definition for ‘confint’
obsSensCCN: no visible global function definition for ‘coef’
obsSensCCN: no visible global function definition for ‘confint’
obsSensCNN: no visible global function definition for ‘coef’
obsSensCNN: no visible global function definition for ‘confint’
obsSensCNN: no visible global function definition for ‘sd’
obsSensCNN: no visible global function definition for ‘model.matrix’
obsSensNNN: no visible global function definition for ‘coef’
obsSensNNN: no visible global function definition for ‘confint’
obsSensNNN: no visible global function definition for ‘sd’
obsSensNNN: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  coef confint model.matrix sd
Consider adding
  importFrom("stats", "coef", "confint", "model.matrix", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import ‘sf::st_make_valid’ by ‘lwgeom::st_make_valid’ when loading ‘oceanis’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/oceanis.Rcheck/00install.out’ for details.
Running examples in ‘oceanis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coordonnees_etiquettes
> ### Title: Data table of labels
> ### Aliases: coordonnees_etiquettes
> ### Keywords: documentation
> 
> ### ** Examples
> 
> data("donnees_monoloc")
> data("depm")
> 
> etiquettes <- coordonnees_etiquettes(fondMaille = depm,
+ listeCode = c("06","13","31","33","44","67","69","59","75"))
> etiquettes$LIBELLE <- c("Nice","Marseille","Toulouse","Bordeaux","Nantes",
+ "Lille","Strasbourg","Lyon","Paris")
> etiquettes[etiquettes$CODE=="75","TAILLE"] <- 1.3
> 
> # Ronds proportionnels sur une analyse en classes
> fond_ronds <- plot_classes_ronds(data = donnees_monoloc, fondMaille = depm,
+ idData = "COD_DEP", varVolume = "POP_2015", varRatio = "VAR_AN_MOY", nbClasses = 4,
+ titreLegRonds = "POP_2015", titreLegClasses = "VAR_AN_MOY",
+ xLegClasses = 1150000, yLegClasses = 6600000, etiquettes = etiquettes)
Warning in CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create: crs not found
Error in CPL_transform(x, crs, aoi, pipeline, reverse) : 
  crs not found: is it missing?
Calls: plot_classes_ronds ... st_transform -> st_transform.sfc -> structure -> CPL_transform
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘integration_shiny.Rmd’ using rmarkdown
--- finished re-building ‘integration_shiny.Rmd’

--- re-building ‘oceanis.Rmd’ using rmarkdown
Quitting from lines 384-506 (oceanis.Rmd) 
Error: processing vignette 'oceanis.Rmd' failed with diagnostics:
crs not found: is it missing?
--- failed re-building ‘oceanis.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: setEvents
> ### Title: Setting Events
> ### Aliases: setEvents
> 
> ### ** Examples
> 
> masses <- 1
> dampers <- as.matrix(1.5)
> springs <- as.matrix(4)
> odenet <- ODEnetwork(masses, dampers, springs)
> eventdat <- data.frame(  var = c("x.1", "x.1")
+                        , time = c(1, 3)
+                        , value = c(1, 3)
+                        )
> odenet <- setState(odenet, 0, 0)
> odenet <- setEvents(odenet, eventdat)
Error: Assertion failed. One of the following must apply:
 * checkDataFrame(events): May only contain the following types:
 * {factor,numeric,numeric}, but element 1 has type 'character'
 * checkDataFrame(events): Must have exactly 4 cols, but has 3 cols
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ODEnetwork.Rmd’ using rmarkdown
Quitting from lines 168-175 (ODEnetwork.Rmd) 
Error: processing vignette 'ODEnetwork.Rmd' failed with diagnostics:
Assertion failed. One of the following must apply:
 * checkDataFrame(events): May only contain the following types:
 * {factor,numeric,numeric}, but element 1 has type 'character'
 * checkDataFrame(events): Must have exactly 4 cols, but has 3 cols
--- failed re-building ‘ODEnetwork.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following hidden files and directories:
  .Rapp.history
  data/.Rapp.history
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RCurl’ ‘maps’
A package should be listed in only one of these fields.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘OIdata/R/mapvar.R’:
  data(state.fips)
See section ‘Good practice’ in ‘?data’.
avgokmts: no visible global function definition for ‘aggregate’
downloadstn: no visible global function definition for ‘read.csv’
nearstn: no visible binding for global variable ‘okstations’
nearstn: no visible binding for global variable ‘Commissioned’
nearstn: no visible binding for global variable ‘Decommissioned’
okcurobs: no visible global function definition for ‘read.csv’
okmts: no visible binding for global variable ‘okstations’
okmts: no visible binding for global variable ‘TIME’
retrievemts: no visible global function definition for ‘read.csv’
totalprecip: no visible binding for global variable ‘TIME’
totalprecip: no visible global function definition for ‘aggregate’
vincenty: no visible global function definition for ‘runif’
Undefined global functions or variables:
  Commissioned Decommissioned TIME aggregate okstations read.csv runif
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
OLScurve: no visible global function definition for ‘as.formula’
OLScurve: no visible global function definition for ‘na.omit’
OLScurve: no visible global function definition for ‘lm’
OLScurve: no visible global function definition for ‘predict’
OLScurve: no visible global function definition for ‘residuals’
OLScurve: no visible global function definition for ‘model.frame’
OLScurve: no visible global function definition for ‘model.matrix’
plot.OLScurve : plotOLScurve: no visible global function definition for
  ‘reshape’
print.OLScurve: no visible global function definition for ‘na.omit’
print.OLScurve: no visible global function definition for ‘model.frame’
print.OLScurve: no visible global function definition for
  ‘model.matrix’
print.OLScurve: no visible global function definition for ‘cov’
print.OLScurve: no visible global function definition for ‘cor’
print.OLScurve: no visible global function definition for ‘sd’
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for ‘devAskNewPage’
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for ‘reshape’
subjplot.OLScurve : plotOLScurve : mypanel: no visible global function
  definition for ‘gray’
subjplot.OLScurve: no visible global function definition for
  ‘devAskNewPage’
Undefined global functions or variables:
  as.formula cor cov devAskNewPage gray lm model.frame model.matrix
  na.omit predict reshape residuals sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "gray")
  importFrom("stats", "as.formula", "cor", "cov", "lm", "model.frame",
             "model.matrix", "na.omit", "predict", "reshape",
             "residuals", "sd")
to your NAMESPACE file.
fhcor: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor
Consider adding
  importFrom("stats", "cor")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Omu_vignette.Rmd’
Found an obsolete/platform-specific call in the following function:
  ‘comp.freq’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
Undefined global functions or variables:
  optim par x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par")
  importFrom("stats", "optim")
to your NAMESPACE file.
generate.data: no visible global function definition for ‘rbinom’
least.common.ancestor: no visible global function definition for
  ‘na.omit’
oncotree.fit : estimate.error.rates: no visible global function
  definition for ‘optim’
plot.boottree: no visible global function definition for ‘par’
plot.boottree: no visible global function definition for
  ‘dev.interactive’
plot.boottree: no visible global function definition for ‘mtext’
plot.oncotree: no visible global function definition for ‘par’
plot.oncotree: no visible global function definition for ‘xinch’
plot.oncotree: no visible global function definition for ‘yinch’
plot.oncotree: no visible global function definition for ‘lines’
plot.oncotree: no visible global function definition for ‘rect’
plot.oncotree: no visible global function definition for ‘strwidth’
plot.oncotree: no visible global function definition for ‘strheight’
plot.oncotree: no visible global function definition for ‘text’
Undefined global functions or variables:
  dev.interactive lines mtext na.omit optim par rbinom rect strheight
  strwidth text xinch yinch
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "lines", "mtext", "par", "rect", "strheight",
             "strwidth", "text", "xinch", "yinch")
  importFrom("stats", "na.omit", "optim", "rbinom")
to your NAMESPACE file.
ci.prop: no visible global function definition for ‘qf’
ci.prop: no visible global function definition for ‘qnorm’
ePCP: no visible global function definition for ‘qnorm’
sevennum: no visible global function definition for ‘na.omit’
sevennum: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘opencage.Rmd’
Running ‘testthat.R’ [26s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OpenLand)
  > 
  > test_check("OpenLand")
  ── 1. Error: Behavior of summary_map (@test_generalfunctions.R#53)  ────────────
  Assigned data `c(as.numeric(names(value_map)[i]), value_map[[i]])` must be compatible with row subscript `i`.
  ✖ 1 row must be assigned.
  ✖ Assigned data has 2 rows.
  ℹ Only vectors of size 1 are recycled.
  Backtrace:
    1. testthat::expect_silent(...)
    9. OpenLand::summary_map(...)
   11. tibble:::`[<-.tbl_df`(`*tmp*`, i, c(1:2), value = c(1, 1983))
   12. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   13. tibble:::vectbl_recycle_rhs(...)
   14. base::tryCatch(...)
   15. base:::tryCatchList(expr, classes, parentenv, handlers)
   16. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   17. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 112 | SKIPPED: 0 | WARNINGS: 24 | FAILED: 1 ]
  1. Error: Behavior of summary_map (@test_generalfunctions.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘openNLPmodels.en’
Df2SpLinesDf: no visible global function definition for ‘slot’
PlotTraj: no visible global function definition for ‘par’
PlotTraj: no visible global function definition for ‘grid’
PlotTraj: no visible global function definition for ‘box’
PlotTrajFreq: no visible global function definition for ‘par’
PlotTrajFreq: no visible global function definition for ‘grid’
PlotTrajFreq: no visible global function definition for
  ‘colorRampPalette’
PlotTrajFreq: no visible global function definition for ‘legend’
PlotTrajFreq: no visible binding for global variable ‘title’
PlotTrajFreq: no visible global function definition for ‘dev.off’
ReadFiles: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  box colorRampPalette dev.off grid legend par read.table slot title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "box", "grid", "legend", "par", "title")
  importFrom("methods", "slot")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running ‘testthat.R’ [2s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(opentripplanner)
  > 
  > test_check("opentripplanner")
  trying URL 'https://github.com/ropensci/opentripplanner/releases/download/0.1/isle-of-wight-demo.zip'
  ── 1. Error: (unknown) (@test_02_without_OTP.R#23)  ────────────────────────────
  cannot open URL 'https://github.com/ropensci/opentripplanner/releases/download/0.1/isle-of-wight-demo.zip'
  Backtrace:
   1. opentripplanner::otp_dl_demo(path_data)
   2. utils::download.file(...)
  
  trying URL 'https://github.com/ropensci/opentripplanner/releases/download/0.1/centroids.gpkg'
  ── 2. Error: (unknown) (@test_03_with_OTP.R#12)  ───────────────────────────────
  cannot open URL 'https://github.com/ropensci/opentripplanner/releases/download/0.1/centroids.gpkg'
  Backtrace:
   1. utils::download.file(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 24 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
  1. Error: (unknown) (@test_02_without_OTP.R#23) 
  2. Error: (unknown) (@test_03_with_OTP.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [18s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(openxlsx)
  > 
  > test_check("openxlsx")
  ── 1. Error: read.xlsx from different sources (@test-read_sources.R#14)  ───────
  cannot open URL 'https://github.com/awalker89/openxlsx/raw/master/inst/readTest.xlsx'
  Backtrace:
   1. openxlsx::read.xlsx(xlsxFile)
   2. openxlsx:::read.xlsx.default(xlsxFile)
   3. openxlsx:::getFile(xlsxFile)
   4. utils::download.file(...)
  
  ── 2. Error: loadWorkbook from different sources (@test-read_sources.R#42)  ────
  cannot open URL 'https://github.com/awalker89/openxlsx/raw/master/inst/readTest.xlsx'
  Backtrace:
   1. openxlsx::loadWorkbook(xlsxFile)
   2. openxlsx:::getFile(file)
   3. utils::download.file(...)
  
  ── 3. Error: getDateOrigin from different sources (@test-read_sources.R#62)  ───
  cannot open URL 'https://github.com/awalker89/openxlsx/raw/master/inst/readTest.xlsx'
  Backtrace:
   1. openxlsx::getDateOrigin(xlsxFile)
   2. openxlsx:::getFile(xlsxFile)
   3. utils::download.file(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 984 | SKIPPED: 3 | WARNINGS: 3 | FAILED: 3 ]
  1. Error: read.xlsx from different sources (@test-read_sources.R#14) 
  2. Error: loadWorkbook from different sources (@test-read_sources.R#42) 
  3. Error: getDateOrigin from different sources (@test-read_sources.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
nlsolve: no visible global function definition for ‘optim’
nlsolve: no visible global function definition for ‘runif’
optAUC: no visible global function definition for ‘var’
Undefined global functions or variables:
  optim runif var
Consider adding
  importFrom("stats", "optim", "runif", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
avg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
print.optimbase: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘UserGuide.Rmd’
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
getMinimumArborescence: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for ‘par’
getMinimumSpanningTree: no visible global function definition for
  ‘capture.output’
getShortestPathTree: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output par
Consider adding
  importFrom("graphics", "par")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Agrestiind.CI: no visible global function definition for ‘qnorm’
BPexact.CI: no visible global function definition for ‘uniroot’
BPmidp.CI: no visible global function definition for ‘uniroot’
Cornfieldexact.CI: no visible global function definition for ‘uniroot’
Cornfieldmidp.CI: no visible global function definition for ‘uniroot’
Gart.CI: no visible global function definition for ‘qnorm’
Invsinh.CI: no visible global function definition for ‘qnorm’
Woolf.CI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm uniroot
Consider adding
  importFrom("stats", "qnorm", "uniroot")
to your NAMESPACE file.
BTLboost: no visible global function definition for ‘as.formula’
design: no visible global function definition for ‘as.formula’
wide2long: no visible global function definition for ‘reshape’
Undefined global functions or variables:
  as.formula reshape
Consider adding
  importFrom("stats", "as.formula", "reshape")
to your NAMESPACE file.
'library' or 'require' call to ‘psych’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following files/directories:
  ‘orddom_csv.txt’ ‘orddom_csv_tab.txt’ ‘tmp_r.txt’
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of ‘nr’ to ‘nrow’
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of ‘nc’ to ‘ncol’
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
genRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
ORICC1: no visible binding for global variable ‘sd’
ORICC1: no visible global function definition for ‘write.table’
ORICC1: no visible global function definition for ‘postscript’
ORICC1: no visible global function definition for ‘jpeg’
ORICC1: no visible global function definition for ‘points’
ORICC1: no visible global function definition for ‘dev.off’
ORICC1: no visible global function definition for ‘par’
ORICC2: no visible binding for global variable ‘sd’
ORICC2: no visible global function definition for ‘write.table’
ORICC2: no visible global function definition for ‘postscript’
ORICC2: no visible global function definition for ‘jpeg’
ORICC2: no visible global function definition for ‘points’
ORICC2: no visible global function definition for ‘dev.off’
ORICC2: no visible global function definition for ‘par’
Undefined global functions or variables:
  dev.off jpeg par points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
boat3d: no visible global function definition for ‘rgl.cur’
boat3d: no visible global function definition for ‘open3d’
boat3d: no visible global function definition for ‘clear3d’
boat3d: no visible global function definition for ‘bg3d’
boat3d: no visible global function definition for ‘rgl.set’
boat3d: no visible global function definition for ‘triangles3d’
boat3d: no visible global function definition for ‘quads3d’
boat3d: no visible global function definition for ‘decorate3d’
boat3d: no visible global function definition for ‘scatterplot3d’
orientlm: no visible global function definition for ‘model.matrix’
orientlm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  bg3d clear3d decorate3d lm model.matrix open3d quads3d rgl.cur
  rgl.set scatterplot3d triangles3d
Consider adding
  importFrom("stats", "lm", "model.matrix")
to your NAMESPACE file.
File ‘OriGen/libs/OriGen.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mdr.c: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘dcemriS4’
Packages in Depends field not imported from:
  ‘Rcpp’ ‘genefilter’ ‘gtools’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of ‘ties’ to ‘ties.method’
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
plot.SplineBasis: no visible global function definition for ‘matplot’
plot,SplineBasis-matrix: no visible global function definition for
  ‘matplot’
plot,SplineBasis-missing: no visible global function definition for
  ‘matplot’
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
'library' or 'require' call to ‘polynom’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘polynom’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
chebyshev.c.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.s.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
gegenbauer.polynomials: no visible global function definition for
  ‘polynomial’
ghermite.h.polynomials: no visible global function definition for
  ‘polynomial’
glaguerre.polynomials: no visible global function definition for
  ‘polynomial’
hermite.h.polynomials: no visible global function definition for
  ‘polynomial’
hermite.he.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.g.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.p.polynomials: no visible global function definition for
  ‘polynomial’
legendre.polynomials: no visible global function definition for
  ‘polynomial’
monic.polynomials: no visible global function definition for
  ‘polynomial’
orthogonal.polynomials: no visible global function definition for
  ‘polynomial’
orthonormal.polynomials: no visible global function definition for
  ‘polynomial’
polynomial.derivatives: no visible global function definition for
  ‘deriv’
polynomial.integrals: no visible global function definition for
  ‘integral’
polynomial.values: no visible global function definition for ‘predict’
schebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
schebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
slegendre.polynomials: no visible global function definition for
  ‘polynomial’
Undefined global functions or variables:
  deriv integral polynomial predict
Consider adding
  importFrom("stats", "deriv", "predict")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘igraph’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
as_igraph : <anonymous>: no visible global function definition for
  ‘distHaversine’
as_igraph: no visible global function definition for ‘graph.edgelist’
as_igraph: no visible global function definition for ‘E’
as_igraph: no visible global function definition for ‘E<-’
as_sp_lines: no visible global function definition for ‘Lines’
as_sp_points: no visible global function definition for
  ‘SpatialPointsDataFrame’
as_sp_polygons: no visible global function definition for ‘Polygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygonsDataFrame’
make_SLDF: no visible global function definition for ‘SpatialLines’
make_SLDF: no visible global function definition for
  ‘SpatialLinesDataFrame’
osm_crs: no visible global function definition for ‘CRS’
plot.osmar: no visible global function definition for ‘gray’
plot_nodes: no visible global function definition for ‘points’
plot_ways: no visible global function definition for ‘lines’
ways_nodes2Line: no visible global function definition for ‘Line’
ways_nodes2Polygon: no visible global function definition for ‘Polygon’
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "points")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘OTclust.Rmd’
odm: no visible binding for global variable ‘sd’
odm : <anonymous>: no visible global function definition for ‘sd’
odm : <anonymous>: no visible global function definition for ‘quantile’
odm: no visible global function definition for ‘prcomp’
quant.const: no visible global function definition for ‘quantile’
quant.const.D: no visible global function definition for ‘reshape’
quant.const.D: no visible global function definition for ‘quantile’
quant.linear.D: no visible global function definition for ‘reshape’
quant.nonlin : FrankModel: no visible global function definition for
  ‘qt’
quant.nonlin : FrankModel: no visible global function definition for
  ‘pt’
quant.nonlin: no visible global function definition for ‘predict’
quant.nonlin.D: no visible global function definition for ‘reshape’
quant.nonlin.D: no visible global function definition for ‘predict’
quant.nonpar.D: no visible global function definition for ‘reshape’
rgrubbs.test: no visible global function definition for ‘sd’
plot,OutlierDM-missing: no visible binding for global variable ‘pch’
summary,OutlierDM: no visible global function definition for ‘head’
Undefined global functions or variables:
  head pch prcomp predict pt qt quantile reshape sd
Consider adding
  importFrom("stats", "prcomp", "predict", "pt", "qt", "quantile",
             "reshape", "sd")
  importFrom("utils", "head")
to your NAMESPACE file.
Found the following files/directories:
  ‘result.txt’
loadCSVtoP2distance: no visible global function definition for
  ‘read.table’
p2distance : calcularDistancia: no visible binding for global variable
  ‘sd’
p2distance : ordenarVariables: no visible global function definition
  for ‘cor’
p2distance : calculoFactoresPonderacion: no visible global function
  definition for ‘lm’
p2distance: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
p3state: no visible global function definition for ‘survfit’
p3state: no visible global function definition for ‘terms’
p3state: no visible global function definition for ‘as.formula’
p3state: no visible global function definition for ‘coxph’
p3state: no visible binding for global variable ‘na.exclude’
plot.p3state: no visible global function definition for ‘matplot’
plot.p3state: no visible global function definition for ‘devAskNewPage’
plot.p3state: no visible global function definition for ‘persp’
plot.p3state: no visible global function definition for ‘colours’
plot.p3state: no visible global function definition for
  ‘filled.contour’
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
pacbpred : thetaFunc: no visible global function definition for ‘lsfit’
pacbpred : thetaFunc: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘var’
pacbpred: no visible global function definition for ‘runif’
pacbpred: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Missing or unexported objects:
  ‘devtools::use_build_ignore’ ‘devtools::use_travis’
Non-standard files/directories found at top level:
  ‘DESCRIPTION_EX’ ‘divers’ ‘main.R’ ‘testsDev’
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  ‘EXP’ to ‘EXPR’
[,ClassW: warning in return(x@u1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@u2): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@w1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in x@u1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@u2 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@w1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
Running ‘testthat.R’ [8s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(padr)
  > 
  > test_check("padr")
  ── 1. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R
  fill_by_prevalent(x_df, y4)$y4[2] not equal to "A".
  names for target but not for current
  
  ── 2. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R
  fill_by_prevalent(x_df, y3)$y3[2] not equal to 10.
  names for target but not for current
  
  ── 3. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R
  fill_by_prevalent(x_df, y3, y4)$y4[2] not equal to "A".
  names for target but not for current
  
  ── 4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R
  fill_by_prevalent(x_df, y3, y4)$y3[2] not equal to 10.
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 602 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 4 ]
  1. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R#42) 
  2. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R#43) 
  3. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R#44) 
  4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
paf: no visible global function definition for ‘as.formula’
paf: no visible global function definition for ‘model.response’
paf: no visible global function definition for ‘model.frame’
paf: no visible global function definition for ‘model.matrix’
plot.paf: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
CalGIF: no visible binding for global variable ‘PAGIData’
CalGIF2: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible global function definition for ‘p.adjust’
PAGI.Main: no visible global function definition for ‘pt’
getclass.labels: no visible binding for global variable ‘ExampleData’
getdataset: no visible binding for global variable ‘ExampleData’
Undefined global functions or variables:
  ExampleData PAGIData p.adjust pt
Consider adding
  importFrom("stats", "p.adjust", "pt")
to your NAMESPACE file.
paired.Loc: no visible global function definition for ‘qt’
paired.Loc: no visible global function definition for ‘median’
paired.Loc: no visible global function definition for ‘qsignrank’
paired.Loc: no visible global function definition for ‘qnorm’
paired.Scale: no visible global function definition for ‘var’
paired.Scale: no visible global function definition for ‘cor’
paired.Scale: no visible global function definition for ‘qt’
paired.Scale: no visible global function definition for ‘median’
paired.Scale: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  cor median qnorm qsignrank qt var
Consider adding
  importFrom("stats", "cor", "median", "qnorm", "qsignrank", "qt", "var")
to your NAMESPACE file.
pairsD3: no visible global function definition for ‘gray.colors’
Undefined global functions or variables:
  gray.colors
Consider adding
  importFrom("grDevices", "gray.colors")
to your NAMESPACE file.
Found the following files/directories:
  ‘GDPgrowthRESULTS.csv’
Package which this enhances but not available for checking: ‘CorShrink’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘lattice’ ‘vegan’
  Please remove these calls from your code.
Found the following files/directories:
  ‘Dispersion.pdf’
GOpredict: no visible global function definition for ‘fisher.test’
KEGGpredict: no visible global function definition for ‘fisher.test’
ProteinCluster: no visible global function definition for ‘ecdf’
ProteinCluster: no visible global function definition for ‘as.hclust’
ProteinCluster: no visible global function definition for
  ‘as.dendrogram’
ProteinCluster : addE: no visible global function definition for
  ‘is.leaf’
SignificantSubcluster: no visible global function definition for
  ‘order.dendrogram’
SignificantSubcluster: no visible global function definition for
  ‘fisher.test’
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
Consider adding
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
Paneldata.formula: no visible global function definition for
  ‘model.frame’
Paneldata.formula: no visible global function definition for
  ‘model.matrix’
Paneldata.formula: no visible global function definition for
  ‘model.response’
summary.Paneldata: no visible global function definition for ‘coef’
summary.Paneldata: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
Running ‘testthat.R’ [7s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PANICr)
  > 
  > test_check("PANICr")
  ── 1. Failure: Panic 10 demeaned consistency (@test_panic_io.R#25)  ────────────
  panic10(test1, nfac = 10L, k1 = 7, criteria = "IC1", demean = TRUE) not equal to `test_10_dm`.
  Component "MP.tests": Component "pool_test": Modes: character, numeric
  Component "MP.tests": Component "pool_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "pool_test": target is character, current is factor
  Component "MP.tests": Component "mp_test": Modes: character, numeric
  Component "MP.tests": Component "mp_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "mp_test": target is character, current is factor
  
  ── 2. Failure: Panic 10 non-demeaned consistency (@test_panic_io.R#40)  ────────
  panic10(test1, nfac = 10L, k1 = 7, criteria = "IC1", demean = FALSE) not equal to `test_10_ndm`.
  Component "MP.tests": Component "mp_test": Modes: character, numeric
  Component "MP.tests": Component "mp_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "mp_test": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Panic 10 demeaned consistency (@test_panic_io.R#25) 
  2. Failure: Panic 10 non-demeaned consistency (@test_panic_io.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Warning: no function found corresponding to methods exports from ‘parallelize.dynamic’ for: ‘initialize’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to ‘package’ 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:
  ‘methods’ ‘parallel’ ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
parallelSVM.default: no visible binding for global variable ‘na.omit’
parallelSVM.formula: no visible binding for global variable ‘na.omit’
predict.parallelSVM: no visible binding for global variable ‘predict’
Undefined global functions or variables:
  na.omit predict
Consider adding
  importFrom("stats", "na.omit", "predict")
to your NAMESPACE file.
Found the following files/directories:
  ‘example.csv’ ‘example.tsv’ ‘example.xlsx’
.formula.make: no visible global function definition for ‘formula’
regress: no visible global function definition for ‘lm’
regress: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  formula lm model.matrix
Consider adding
  importFrom("stats", "formula", "lm", "model.matrix")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-parcoords-.Rmd’
adalasso: no visible global function definition for ‘predict’
lm.ridge.univariate: no visible global function definition for ‘sd’
mylars: no visible global function definition for ‘predict’
mylars: no visible binding for global variable ‘var’
performance.pcor: no visible global function definition for
  ‘ggm.test.edges’
performance.pcor: no visible global function definition for ‘var’
ridge.cv: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef ggm.test.edges predict sd var
Consider adding
  importFrom("stats", "coef", "predict", "sd", "var")
to your NAMESPACE file.
File ‘parmigene/libs/parmigene.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘nnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitOR: no visible global function definition for ‘multinom’
fitOR: no visible global function definition for ‘formula’
fitOR: no visible global function definition for ‘coef’
fitOR: no visible global function definition for ‘optim’
reportOR: no visible global function definition for ‘qnorm’
reportOR: no visible global function definition for ‘pchisq’
reportOR: no visible global function definition for ‘coef’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
partitionMap: no visible global function definition for ‘predict’
partitionMap: no visible global function definition for ‘rnorm’
partitionMap: no visible binding for global variable ‘sd’
partitionMap: no visible global function definition for ‘sd’
partitionMap: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  predict quantile rnorm sd
Consider adding
  importFrom("stats", "predict", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Warning: no function found corresponding to methods exports from ‘partsm’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
parviol: no visible global function definition for ‘plot.new’
parviol: no visible global function definition for ‘plot.window’
parviol: no visible global function definition for ‘title’
parviol: no visible global function definition for ‘lines’
parviol: no visible global function definition for ‘text’
parviol: no visible global function definition for ‘rgb’
selecto: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot.new plot.window rgb text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot.new", "plot.window", "text",
             "title")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘passport.Rmd’ using rmarkdown
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.3.0     ✔ purrr   0.3.3
✔ tibble  3.0.0     ✔ dplyr   0.8.5
✔ tidyr   1.0.2     ✔ stringr 1.4.0
✔ readr   1.3.1     ✔ forcats 0.5.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 79-83 (passport.Rmd) 
Error: processing vignette 'passport.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘passport.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘ape’ ‘caper’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
conch: no visible global function definition for ‘read.tree’
conch: no visible global function definition for ‘reorder’
conch: no visible global function definition for ‘read.nexus’
conch: no visible global function definition for ‘.compressTipLabel’
conch: no visible global function definition for ‘drop.tip’
conch: no visible global function definition for ‘extract.clade’
conch: no visible global function definition for ‘which.edge’
conch: no visible global function definition for ‘write.tree’
pastis_main: no visible global function definition for ‘combn’
read_input: no visible global function definition for ‘read.tree’
read_input: no visible global function definition for ‘reorder’
read_input: no visible global function definition for ‘read.csv’
read_input: no visible global function definition for ‘read.dna’
Undefined global functions or variables:
  .compressTipLabel combn drop.tip extract.clade read.csv read.dna
  read.nexus read.tree reorder which.edge write.tree
Consider adding
  importFrom("stats", "reorder")
  importFrom("utils", "combn", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘pastis_data_1’ ‘pastis_data_2’ ‘pastis_data_3’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘e1071’
  Please remove these calls from your code.
SweaveAll: no visible global function definition for ‘file_test’
texi2dvi: no visible global function definition for ‘file_test’
Undefined global functions or variables:
  file_test
Consider adding
  importFrom("utils", "file_test")
to your NAMESPACE file.
Found the following files/directories:
  ‘Minimal-concordance.tex’ ‘Minimal.Rnw’ ‘Minimal.pdf’
  ‘Minimal.synctex.gz’ ‘Minimal.tex’ ‘figure’
Package vignette with placeholder title ‘Vignette Title’:
  ‘pathlibr.Rmd’
Packages in Depends field not imported from:
  ‘plspm’ ‘tester’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘patternplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: imagebar_s
> ### Title: Plot a stacked bar chart with bars filled with png and jpeg
> ###   images.
> ### Aliases: imagebar_s
> 
> ### ** Examples
> 
> library(patternplot)
> library(jpeg)
> library(ggplot2)
> 
> childcare<-readJPEG(system.file("img", "childcare.jpg", package="patternplot"))
> food<-readJPEG(system.file("img", "food.jpg", package="patternplot"))
> housing <-readJPEG(system.file("img", "housing.jpg", package="patternplot"))
> 
> data <- read.csv(system.file("extdata", "monthlyexp.csv", package="patternplot"))
> x<-data$Location
> y<-data$Amount
> group<-data$Type
> pattern.type<-list(childcare, food, housing)
> 
> imagebar_s(data,x, y, group, xlab='', ylab='Monthly Expenses, Dollar',
+ pattern.type=pattern.type, label.size=3.5, frame.size=1, frame.color='black',
+ legend.type='h', legend.h=6, legend.y.pos=0.49, legend.pixel=20, legend.w=0.2,
+  legend.x.pos=1.1)+scale_y_continuous(limits = c(0, 6800))
Error: geom_text requires the following missing aesthetics: label
Backtrace:
    █
 1. ├─(function (x, ...) ...
 2. └─ggplot2:::print.ggplot(x)
 3.   ├─ggplot2::ggplot_build(x)
 4.   └─ggplot2:::ggplot_build.ggplot(x)
 5.     └─ggplot2:::by_layer(function(l, d) l$compute_geom_1(d))
 6.       └─ggplot2:::f(l = layers[[i]], d = data[[i]])
 7.         └─l$compute_geom_1(d)
 8.           └─ggplot2:::f(..., self = self)
 9.             └─ggplot2:::check_required_aesthetics(...)
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘patternplot-intro.Rmd’ using docco_linear
Quitting from lines 271-281 (patternplot-intro.Rmd) 
Error: processing vignette 'patternplot-intro.Rmd' failed with diagnostics:
geom_text requires the following missing aesthetics: label
--- failed re-building ‘patternplot-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
add_noise: no visible global function definition for ‘rnorm’
estimate_risk_dream6 : <anonymous>: no visible global function
  definition for ‘var’
generate_sample: no visible global function definition for ‘rnorm’
generate_sample: no visible global function definition for ‘runif’
sample_function: no visible global function definition for ‘runif’
sample_function : <anonymous>: no visible global function definition
  for ‘var’
sample_function_multi_mod_weight: no visible global function definition
  for ‘runif’
sample_function_multi_mod_weight : <anonymous>: no visible global
  function definition for ‘var’
sample_function_single_mod: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  rnorm runif var
Consider adding
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘PAWL’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘foreach’ ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘foreach’ ‘ggplot2’ ‘methods’ ‘mvtnorm’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dotplot.pbo: no visible global function definition for ‘reorder’
pbo: no visible global function definition for ‘%dopar%’
pbo: no visible global function definition for ‘foreach’
pbo: no visible global function definition for ‘lm’
xyplot.pbo: no visible global function definition for ‘ecdf’
xyplot.pbo: no visible global function definition for ‘doubleYScale’
xyplot.pbo: no visible global function definition for ‘reorder’
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
a_get_native: no visible global function definition for ‘par’
a_get_relative: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘dist’
brackets: no visible global function definition for ‘lines’
Undefined global functions or variables:
  dist lines par
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "dist")
to your NAMESPACE file.
draw.pcaBootPlot: no visible global function definition for ‘grid’
draw.pcaBootPlot: no visible global function definition for ‘points’
draw.pcaBootPlot: no visible global function definition for ‘symbols’
draw.pcaBootPlot: no visible global function definition for ‘legend’
pcaBootPlot: no visible global function definition for ‘prcomp’
pcaBootPlot: no visible global function definition for ‘cor’
pcaBootPlot: no visible global function definition for ‘quantile’
pcaBootPlot: no visible global function definition for ‘pdf’
pcaBootPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  cor dev.off grid legend pdf points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
PCDReg.wf: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Found the following files/directories:
  ‘AbsolutePlot_Absolute Risk.pdf’ ‘ContrastPlot_OR.pdf’
Package suggested but not available for checking: ‘FFTrees’
PdofCSGt.bootstrap5: no visible global function definition for ‘rnorm’
PdofCSGt.bootstrap5: no visible global function definition for ‘rt’
PdofCSt.T1or2: no visible global function definition for ‘combn’
PofCSGt: no visible global function definition for ‘combn’
PofCSLt.bootstrap5: no visible global function definition for ‘rnorm’
PofCSLt.bootstrap5: no visible global function definition for ‘rt’
PofCSt: no visible global function definition for ‘pnorm’
tindep: no visible binding for global variable ‘var’
tindep: no visible global function definition for ‘pt’
Undefined global functions or variables:
  combn pnorm pt rnorm rt var
Consider adding
  importFrom("stats", "pnorm", "pt", "rnorm", "rt", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
pdist: no visible global function definition for ‘dist’
pdist: no visible global function definition for ‘new’
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
band.chol.cv: no visible global function definition for ‘cov’
pdsoft.cv: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘peakPick-vignette.Rmd’
peacf: no visible global function definition for ‘is.ts’
peacf: no visible global function definition for ‘cycle’
peacf: no visible global function definition for ‘ts.intersect’
peacf: no visible global function definition for ‘lag’
peacf: no visible global function definition for ‘ts’
peacf: no visible global function definition for ‘pchisq’
peacf.plot: no visible global function definition for ‘segments’
peacf.plot: no visible global function definition for ‘title’
pear: no visible global function definition for ‘cycle’
pear: no visible global function definition for ‘pchisq’
peboxplot: no visible global function definition for ‘cycle’
peboxplot: no visible global function definition for ‘boxplot’
peboxplot: no visible global function definition for ‘title’
peplot: no visible global function definition for ‘par’
peplot: no visible global function definition for ‘cycle’
peplot: no visible global function definition for ‘identify’
peplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq segments title ts
  ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
The following files should probably not be installed:
  ‘addendum.tex’, ‘slplot.tex’, ‘table1.tex’, ‘table3.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
PearsonICA: no visible global function definition for ‘rnorm’
PearsonICAdemo: no visible global function definition for ‘rnorm’
PearsonICAdemo: no visible global function definition for ‘dev.new’
PearsonICAdemo: no visible global function definition for ‘par’
PearsonICAdemo: no visible global function definition for ‘axis’
PearsonICAdemo: no visible global function definition for ‘title’
PearsonICAdemo: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis dev.new lines par rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AssoTestProc: no visible global function definition for ‘rbinom’
AssoTestProc: no visible global function definition for ‘princomp’
AssoTestProc: no visible global function definition for ‘loadings’
AssoTestProc: no visible global function definition for ‘lm’
CNVtypeAnay: no visible global function definition for ‘cov’
ClusProc: no visible global function definition for ‘princomp’
ClusProc: no visible global function definition for ‘prcomp’
ClusProc0: no visible global function definition for ‘kmeans’
ClusProc0: no visible global function definition for ‘cov’
Inde: no visible global function definition for ‘lm’
Inde: no visible global function definition for ‘var’
STE: no visible global function definition for ‘pchisq’
STIM: no visible global function definition for ‘cor’
STIM: no visible global function definition for ‘pchisq’
plot.clust: no visible global function definition for ‘princomp’
plot.clust: no visible global function definition for ‘loadings’
plot.clust: no visible global function definition for ‘qplot’
plot.clust: no visible global function definition for ‘geom_histogram’
plot.clust: no visible global function definition for ‘aes_string’
plot.clust: no visible global function definition for ‘barplot’
plot.clust: no visible global function definition for ‘title’
plot.clust: no visible global function definition for ‘mtext’
plot.clust: no visible global function definition for ‘text’
Undefined global functions or variables:
  aes_string barplot cor cov geom_histogram kmeans lm loadings mtext
  pchisq prcomp princomp qplot rbinom text title var
Consider adding
  importFrom("graphics", "barplot", "mtext", "text", "title")
  importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq",
             "prcomp", "princomp", "rbinom", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
blup: no visible global function definition for ‘model.matrix’
blup: no visible global function definition for ‘model.frame’
blup: no visible global function definition for ‘read.table’
calcG: no visible global function definition for ‘as’
gblup: no visible global function definition for ‘model.matrix’
gblup: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  as model.frame model.matrix read.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "model.frame", "model.matrix")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘A.txt’ ‘Ainv.txt’
PEMM_fun : find.lambda: no visible global function definition for
  ‘optimize’
PEMM_fun: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘CoxBoost’ ‘codetools’ ‘locfit’ ‘penalized’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
complexity.LASSO: no visible global function definition for ‘profL1’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘locfit’
complexity.mincv.CoxBoost: no visible global function definition for
  ‘cv.CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘locfit’
extract: no visible global function definition for ‘findGlobals’
fit.CoxBoost: no visible global function definition for ‘CoxBoost’
fit.LASSO: no visible global function definition for ‘penalized’
Undefined global functions or variables:
  CoxBoost cv.CoxBoost findGlobals locfit penalized profL1
Found the following files/directories:
  ‘PARMA21del1_ident’
performance.curves.plot: no visible global function definition for
  ‘postscript’
performance.curves.plot: no visible global function definition for
  ‘axis’
performance.curves.plot: no visible global function definition for
  ‘lines’
performance.curves.plot: no visible global function definition for
  ‘legend’
performance.curves.plot: no visible global function definition for
  ‘grid’
performance.curves.plot: no visible global function definition for
  ‘dev.off’
precision.recall.curves.plot: no visible global function definition for
  ‘postscript’
precision.recall.curves.plot: no visible global function definition for
  ‘axis’
precision.recall.curves.plot: no visible global function definition for
  ‘lines’
precision.recall.curves.plot: no visible global function definition for
  ‘legend’
precision.recall.curves.plot: no visible global function definition for
  ‘grid’
precision.recall.curves.plot: no visible global function definition for
  ‘dev.off’
Undefined global functions or variables:
  axis dev.off grid legend lines postscript
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "grid", "legend", "lines")
to your NAMESPACE file.
Package suggested but not available for checking: ‘dendextendRcpp’
permalgorithm: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘permus_per_dist_4’ ‘permus_per_shape_bin_4_0’
  ‘permus_per_shape_bin_4_1’ ‘permus_per_shape_bin_4_2’
  ‘permus_per_shape_bin_4_3’
ksample.pclt: no visible global function definition for ‘pchisq’
pCI: no visible global function definition for ‘qbeta’
permKS.formula: no visible global function definition for ‘terms’
permTREND.default: no visible global function definition for ‘cor’
permTREND.formula: no visible global function definition for ‘terms’
permTS.formula: no visible global function definition for ‘terms’
trend.pclt: no visible global function definition for ‘pnorm’
twosample.pclt: no visible global function definition for ‘pnorm’
twosample.pclt: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor pchisq pnorm qbeta terms
Consider adding
  importFrom("stats", "cor", "pchisq", "pnorm", "qbeta", "terms")
to your NAMESPACE file.
hasMethod: no visible global function definition for ‘getS3method’
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
Found the following files/directories:
  ‘neural_network-s0000r1000.html’ ‘neural_network-s1000r1000.html’
  ‘neural_network-s2000r1000.html’ ‘neural_network-s3000r1000.html’
Found the following files/directories:
  ‘Myfile.txt’
pGLS: no visible global function definition for ‘model.response’
pGLS: no visible global function definition for ‘model.matrix’
pGLS: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.matrix model.response pt
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
Found the following files/directories:
  ‘animation.gif’
PharmPow_crossover: no visible global function definition for
  ‘read.table’
PharmPow_crossover: no visible global function definition for
  ‘write.csv’
PharmPow_crossover: no visible global function definition for ‘pdf’
PharmPow_crossover: no visible global function definition for ‘dev.off’
PharmPow_parallel: no visible global function definition for
  ‘read.table’
PharmPow_parallel: no visible global function definition for
  ‘write.csv’
PharmPow_parallel: no visible global function definition for ‘pdf’
PharmPow_parallel: no visible global function definition for ‘dev.off’
fig_PharmPow_crossover: no visible global function definition for
  ‘read.csv’
fig_PharmPow_parallel: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  dev.off pdf read.csv read.table write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "read.csv", "read.table", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘test.pdf’
fox: no visible binding for global variable ‘sd’
fox: no visible global function definition for ‘cor’
fox: no visible global function definition for ‘interaction.plot’
fox: no visible global function definition for ‘reorder’
kang: no visible global function definition for ‘var’
kang: no visible binding for global variable ‘sd’
kang: no visible global function definition for ‘cor’
kang: no visible global function definition for ‘interaction.plot’
kang: no visible global function definition for ‘reorder’
nahu: no visible global function definition for ‘interaction.plot’
nahu: no visible global function definition for ‘reorder’
thsu: no visible global function definition for ‘median’
thsu: no visible binding for global variable ‘sd’
thsu: no visible global function definition for ‘cor’
thsu: no visible global function definition for ‘interaction.plot’
thsu: no visible global function definition for ‘reorder’
Undefined global functions or variables:
  cor interaction.plot median reorder sd var
Consider adding
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
pheno.ddm: no visible global function definition for ‘new’
pheno.flm.fit: no visible binding for global variable ‘na.exclude’
pheno.flm.fit: no visible global function definition for ‘terms’
pheno.flm.fit: no visible global function definition for ‘residuals’
pheno.flm.fit: no visible global function definition for ‘qt’
pheno.lad.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  na.exclude new qt residuals terms
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.exclude", "qt", "residuals", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
Running ‘testthat.R’ [5s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(photobiology)
  Loading required package: tibble
  News at https://www.r4photobiology.info/
  > library(photobiologyInOut)
  > 
  > test_check("photobiology")
  Read 25 items
  Read 12 items
  Read 7 items
  Read 7 items
  Read 7 items
  ── 1. Failure: colorSpec (@test-foreign.R#18)  ─────────────────────────────────
  signif(...) not equal to 38468.75.
  1/1 mismatches
  [1] 0 - 38469 == -38469
  
  ── 2. Error: colorSpec (@test-foreign.R#25)  ───────────────────────────────────
  non-numeric argument to mathematical function
  Backtrace:
   1. testthat::expect_equal(...)
   2. testthat::quasi_label(enquo(object), label, arg = "object")
   3. rlang::eval_bare(expr, quo_get_env(quo))
  
  Read 7 items
  Read 7 items
  Read 7 items
  Read 7 items
  Read 4 items
  Read 151 records
  Read 4 items
  Read 18 items
  Read 4 items
  Read 18 items
  Read 3 items
  Read 16 items
  Read 3 items
  Read 16 items
  Read 3 items
  Read 16 items
  Read 3 items
  Read 16 items
  Read 3 items
  Read 16 items
  Read 4 items
  Read 18 items
  Read 3 items
  Read 16 items
  Read 3 items
  Read 16 items
  Read 1 item
  Read 4 items
  Read 1 item
  Read 4 items
  Read 1 record
  Read 1 record
  Read 1 record
  Read 1 item
  Read 1 record
  Read 5 items
  Read 8 items
  Read 8 items
  Read 5 items
  Read 8 items
  Read 8 items
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 437 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: colorSpec (@test-foreign.R#18) 
  2. Error: colorSpec (@test-foreign.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Package vignette with placeholder title ‘Vignette Title’:
  ‘photosynthesis-introduction.Rmd’
Running examples in ‘phuse-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extract_fns
> ### Title: Extract File Names from Script Metadata
> ### Aliases: extract_fns
> 
> ### ** Examples
> 
>   a <- "https://github.com/phuse-org/phuse-scripts/raw/master"
>   b <- "development/R/scripts"
>   c <- "Draw_Dist2_R.yml"
>   f1 <- paste(a,b,c, sep = '/')
>   f2 <- read_yml(f1)
No encoding supplied: defaulting to UTF-8.
Warning in file(con, "rb") :
  cannot open URL 'https://github.com/phuse-org/phuse-scripts/raw/master/development/R/scripts/Draw_Dist2_R.yml': HTTP status was '504 Gateway Timeout'
Error in file(con, "rb") : 
  cannot open the connection to 'https://github.com/phuse-org/phuse-scripts/raw/master/development/R/scripts/Draw_Dist2_R.yml'
Calls: read_yml -> yaml.load -> paste -> readChar -> file
Execution halted
Package suggested but not available for checking: ‘OutbreakTools’
Found the following files/directories:
  ‘output_values’
Unknown packages ‘surface’, ‘bayou’ in Rd xrefs
Found the following files/directories:
  ‘subj_slp_sum.csv’ ‘wa_ps_V811043_sum.csv’
incident: no visible global function definition for ‘splinefun’
incident: no visible global function definition for ‘integrate’
phytoprod: no visible global function definition for ‘approx’
phytoprod: no visible global function definition for ‘splinefun’
phytoprod: no visible global function definition for ‘integrate’
reflectance: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx integrate splinefun
Consider adding
  importFrom("stats", "approx", "integrate", "splinefun")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  ‘src/pijavski.cpp’
Running examples in ‘pins-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pin
> ### Title: Pin Resource
> ### Aliases: pin
> 
> ### ** Examples
> 
> library(pins)
> 
> # define local board
> board_register_local(cache = tempfile())
> 
> # cache the mtcars dataset
> pin(mtcars)
> 
> # cache computation over mtcars
> mtcars[mtcars$mpg > 30,] %>%
+   pin(name = "mtefficient")
> 
> # retrieve cached pin
> pin_get("mtefficient")
# A tibble: 4 x 11
    mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb
  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1  32.4     4  78.7    66  4.08  2.2   19.5     1     1     4     1
2  30.4     4  75.7    52  4.93  1.62  18.5     1     1     4     2
3  33.9     4  71.1    65  4.22  1.84  19.9     1     1     4     1
4  30.4     4  95.1   113  3.77  1.51  16.9     1     1     5     2
> 
> # url to remote resource
> resource <- file.path("https://raw.githubusercontent.com/facebook/prophet",
+                       "master/examples/example_retail_sales.csv")
> 
> # cache remote resource
> pin(resource, name = "example_retail_sales")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [raw.githubusercontent.com] Operation timed out after 5000 milliseconds with 0 bytes received
Calls: pin ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
plot.pred.int: no visible global function definition for ‘plot.default’
plot.pred.int: no visible global function definition for ‘axis’
plot.pred.int: no visible global function definition for ‘box’
plot.pred.int : cidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : negcidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : pi.col.fun: no visible global function definition for
  ‘gray’
plot.pred.int: no visible global function definition for ‘segments’
plot.pred.int: no visible global function definition for ‘points’
plot.pred.int: no visible global function definition for ‘abline’
pred.int: no visible binding for global variable ‘sd’
prop.test.mult: no visible global function definition for ‘qnorm’
sim.basic: no visible global function definition for ‘rbinom’
sim.basic: no visible global function definition for ‘rnorm’
t.test.mult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ggsubplot’
Running ‘test-async.R’ [14s/23s]
  Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  ── 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  ───────────────────
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RGtk2’ ‘gWidgetsRGtk2’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘cairoDevice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
PKmod: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Running examples in ‘PK-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nca
> ### Title: Estimation of various PK parameters
> ### Aliases: nca nca.ssd nca.batch nca.complete
> ### Keywords: htest
> 
> ### ** Examples
> 
> #### serial sampling designs
> ## example for a serial sampling data design from Wolfsegger and Jaki (2009)
> conc <- c(0, 0, 0, 2.01, 2.85, 2.43, 0.85, 1.00, 0.91, 0.46, 0.35, 0.63, 0.39, 0.32, 
+           0.45, 0.11, 0.18, 0.19, 0.08, 0.09, 0.06)
> time <- c(rep(0,3), rep(5/60,3), rep(3,3), rep(6,3), rep(9,3), rep(16,3), rep(24,3))
> 
> # Direct call of the function
> # CAUTION: this might take a few minutes
> # Note: 1E4 bootstrap replications were used in the example given 
> # in Wolfsegger and Jaki (2009)
> set.seed(34534)
> nca.ssd(conc=conc, time=time, n.tail=4, dose=200, method=c("z","boott"), 
+          conf.level=0.95, nsample=500)
Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
Calls: nca.ssd ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<-
Execution halted
PKadjust: no visible binding for global variable ‘jpeg’
PKadjust: no visible binding for global variable ‘bmp’
PKadjust: no visible binding for global variable ‘png’
PKadjust: no visible binding for global variable ‘tiff’
PKadjust: no visible binding for global variable ‘dev.new’
PKadjust: no visible global function definition for ‘dev.off’
PKfigure: no visible global function definition for ‘dev.cur’
PKfigure: no visible global function definition for ‘dev.off’
PKoutput: no visible global function definition for ‘heatmap’
PKoutput: no visible global function definition for
  ‘packageDescription’
PKshow: no visible global function definition for ‘browseURL’
addList1: no visible global function definition for ‘formula’
addList1.old: no visible global function definition for ‘formula’
addList2: no visible global function definition for ‘formula’
generate.plot: no visible global function definition for ‘dev.off’
writeHTML: no visible global function definition for
  ‘packageDescription’
writeLst: no visible global function definition for
  ‘packageDescription’
writeLst.tab: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for ‘quantile’
initialize,nonmem: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘Indometh_Bolus_Linear_CoreOutput.txt’
  ‘Indometh_Bolus_Log_CoreOutput.txt’
  ‘Indometh_Infusion_Linear_CoreOutput.txt’
  ‘Indometh_Infusion_Log_CoreOutput.txt’ ‘Output’
  ‘Theoph_Linear_CoreOutput.txt’ ‘Theoph_Log_CoreOutput.txt’
Package suggested but not available for checking: ‘BradleyTerryScalable’
Running examples in ‘pla-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AgarDiffusionAssay
> ### Title: Antibiotic agar diffusion assay using a rectangular tray
> ### Aliases: AgarDiffusionAssay
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(AgarDiffusionAssay); Agar <- AgarDiffusionAssay
> Agar <- read.table(paste(system.file(package = "pla"),
+                    "vignettes/PhEur/data/AntibioticAgarDiffusionAssay.txt",
+                    sep = "/"), header = TRUE)
> select   <- c("Row", "Column", "Sample", "Dilution", "Response")
> PHframe  <- data2assayFrame(Agar[, select])
Warning in data2assayFrame(Agar[, select]) : NAs introduced by coercion
> plaModel <- pla(Agar, design = "lsd",
+                 assayTitle = "PhEur: Antibiotic agar diffusion assay")
Warning in data2assayFrame(data[, select], dr = dilutionRatio, design = design) :
  NAs introduced by coercion
Error in if ((indexOfReference == 1) & (indexOfReference != iOR)) indexOfReference <- iOR : 
  argument is of length zero
Calls: pla
Execution halted
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
bwfw.hmm: no visible global function definition for ‘dnorm’
bwfw1.hmm: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Formula’ ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nrmlepln: no visible global function definition for ‘pchisq’
nrmlerasch: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Running ‘testthat.R’ [181s/219s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("plotly")
  Loading required package: ggplot2
  
  Attaching package: 'plotly'
  
  The following object is masked from 'package:ggplot2':
  
      last_plot
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:graphics':
  
      layout
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  OGR: Unsupported geometry type
  ── 1. Error: (unknown) (@test-cookbook-lines.R#192)  ───────────────────────────
  arguments imply differing number of rows: 0, 2
  Backtrace:
   1. base::data.frame(cond = levels(df$cond), xval = c(10, 11.5))
  
  ── 2. Failure: paths with the same color but different groups stay together (@te
  info$data[[1]]$name not identical to "positive".
  1/1 mismatches
  x[1]: "negative"
  y[1]: "positive"
  
  ── 3. Failure: paths with the same color but different groups stay together (@te
  info$data[[2]]$name not identical to "negative".
  1/1 mismatches
  x[1]: "positive"
  y[1]: "negative"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1395 | SKIPPED: 48 | WARNINGS: 63 | FAILED: 3 ]
  1. Error: (unknown) (@test-cookbook-lines.R#192) 
  2. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#51) 
  3. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
plotAuto: no visible global function definition for ‘window’
plotAuto: no visible global function definition for ‘title’
plotAuto: no visible global function definition for ‘axis’
plotAuto: no visible global function definition for ‘box’
plotCumu: no visible global function definition for ‘title’
plotCumu: no visible global function definition for ‘axis’
plotCumu: no visible global function definition for ‘box’
plotDens : panel.dens: no visible global function definition for ‘var’
plotDens : panel.dens: no visible global function definition for
  ‘quantile’
plotDens : panel.dens: no visible global function definition for
  ‘median’
plotDens: no visible global function definition for ‘tail’
plotQuant: no visible global function definition for ‘par’
plotQuant: no visible binding for global variable ‘quantile’
plotQuant: no visible global function definition for ‘lines’
plotQuant: no visible global function definition for ‘bxp’
plotQuant: no visible global function definition for ‘matplot’
plotQuant: no visible global function definition for ‘axis’
plotQuant: no visible global function definition for ‘box’
plotQuant: no visible global function definition for ‘title’
plotSplom: no visible global function definition for ‘pairs’
plotTrace : panel.trace: no visible global function definition for
  ‘var’
plotTrace : panel.trace: no visible global function definition for
  ‘median’
plotTrace: no visible global function definition for ‘tail’
Undefined global functions or variables:
  axis box bxp lines matplot median pairs par quantile tail title var
  window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
generateEnvelope: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
llla.bi: no visible global function definition for ‘as.formula’
llla.bi: no visible global function definition for ‘glm’
llla.bi: no visible global function definition for ‘binomial’
llla.bi: no visible binding for global variable ‘logit’
llla.bi: no visible global function definition for ‘vcov’
llla.bi: no visible global function definition for ‘coef’
llla.mc: no visible global function definition for ‘model.matrix’
llla.mc: no visible global function definition for ‘as.formula’
llla.mc: no visible global function definition for ‘coxph’
llla.mc: no visible global function definition for ‘vcov’
llla.mc: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘as.formula’
llla.mle: no visible global function definition for ‘glm’
llla.mle: no visible global function definition for ‘poisson’
llla.mle: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘vcov’
mclgen: no visible global function definition for ‘reshape’
simRasch.1D: no visible global function definition for ‘rnorm’
simRasch.1D: no visible global function definition for ‘runif’
vcov.sandwich.glm: no visible global function definition for
  ‘model.matrix’
vcov.sandwich.glm: no visible global function definition for ‘weights’
vcov.sandwich.glm: no visible global function definition for
  ‘residuals’
vcov.sandwich.glm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
print.densityEHpi: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
.MCM: no visible global function definition for ‘runif’
.MCM: no visible global function definition for ‘rmultinom’
.MCM: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘optimize’
.MCM : f: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘alarm’
.igpark: no visible global function definition for ‘kmeans’
.loglik: no visible global function definition for ‘mahalanobis’
.plot.gpcm: no visible global function definition for ‘lines’
.plot.gpcm: no visible global function definition for ‘legend’
.rwgpar: no visible global function definition for ‘rexp’
.weights: no visible global function definition for ‘mahalanobis’
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize rexp rmultinom runif
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
dbm: no visible global function definition for ‘optim’
dbm: no visible global function definition for ‘new’
destat: no visible global function definition for ‘weighted.mean’
local.knn: no visible global function definition for ‘sd’
local.knn: no visible global function definition for ‘optim’
mdpref: no visible global function definition for ‘sd’
mdpref: no visible global function definition for ‘text’
mdpref: no visible global function definition for ‘lines’
phicom: no visible global function definition for ‘optim’
phicom: no visible global function definition for ‘new’
pl: no visible global function definition for ‘optim’
pl: no visible global function definition for ‘new’
rol: no visible global function definition for ‘nlm’
rol: no visible global function definition for ‘new’
wdbm: no visible global function definition for ‘optim’
wdbm: no visible global function definition for ‘new’
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for ‘pnorm’
pnmtrem1: no visible global function definition for ‘dnorm’
pnmtrem1: no visible global function definition for ‘ginv’
pnmtrem1 : fun: no visible global function definition for ‘pnorm’
pnmtrem1 : derf: no visible global function definition for ‘dnorm’
pnmtrem1 : derf: no visible global function definition for ‘pnorm’
pnmtrem1 : fun: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘rgenoud’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
smooth: no visible global function definition for ‘genoud’
Undefined global functions or variables:
  genoud
bipoilogMLE: no visible global function definition for ‘optim’
bipoilogMLE: no visible global function definition for ‘write.table’
poilogMLE: no visible global function definition for ‘optim’
rbipoilog : sim: no visible global function definition for ‘rnorm’
rbipoilog : sim: no visible global function definition for ‘rpois’
rpoilog : sim: no visible global function definition for ‘rnorm’
rpoilog : sim: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/poio.Rcheck/00install.out’ for details.
approxMargMLE: no visible global function definition for ‘optim’
approxMargMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
approxMargMLECI: no visible global function definition for ‘uniroot’
margMLE: no visible global function definition for ‘optim’
margMLECI: no visible global function definition for ‘optim’
margMLECI : unNormLikeMinusVal: no visible global function definition
  for ‘qchisq’
margMLECI: no visible global function definition for ‘uniroot’
profMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
profMLECI: no visible global function definition for ‘uniroot’
rtbinom: no visible global function definition for ‘rbinom’
rtpois: no visible global function definition for ‘rpois’
waldCI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘combinat’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for ‘quantile’
PS.FDR: no visible global function definition for ‘quantile’
Permu.Ind: no visible global function definition for ‘permn’
Permu.Ind: no visible global function definition for ‘hcube’
Trans.Data: no visible global function definition for ‘write.table’
Trans.Data: no visible global function definition for ‘predict’
Trans.Data: no visible global function definition for ‘lm’
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘pow.txt’
rpoistweedie: no visible global function definition for ‘runif’
testOmegaPT: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘scatterplot3d’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for ‘layout’
plot.poLCA: no visible global function definition for ‘par’
poLCA: no visible global function definition for ‘model.frame’
poLCA: no visible global function definition for ‘model.response’
poLCA: no visible global function definition for ‘model.matrix’
poLCA: no visible global function definition for ‘runif’
poLCA: no visible global function definition for ‘ginv’
poLCA: no visible global function definition for ‘flush.console’
poLCA.makeplot.dich: no visible global function definition for
  ‘scatterplot3d’
poLCA.makeplot.poly: no visible global function definition for
  ‘scatterplot3d’
poLCA.se: no visible global function definition for ‘ginv’
poLCA.simdata: no visible global function definition for ‘runif’
poLCA.simdata: no visible global function definition for ‘rnorm’
poLCA.table: no visible global function definition for ‘model.frame’
print.poLCA: no visible global function definition for ‘pt’
print.poLCA: no visible global function definition for ‘flush.console’
rmulti: no visible global function definition for ‘runif’
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following files/directories:
  ‘Table.Output.html’
Package suggested but not available for checking: ‘pollimetrydata’
Running examples in ‘pollimetry-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bodysize
> ### Title: Converts the intertegular distance (IT) and co-variates to body
> ###   size in dry weight (mg) for bees or hoverflies.
> ### Aliases: bodysize
> 
> ### ** Examples
> 
> example=cbind.data.frame(IT=c(1.3,2.3),
+                          Sex=c("Female","Male"), 
+                          Subfamily=c("Syrphinae","Eristalinae"),
+                          Region=c("Australasia","Europe"),
+                          Species=c("Sphaerophoria_macrogaster","Myathropa_florea"))
> bodysize(x=example,taxa="hov",type="taxo")
Loading required namespace: pollimetrydata
Failed with error:  ‘there is no package called ‘pollimetrydata’’
Downloading data from: https://github.com/liamkendall/pollimetrydata/raw/master/data/hov_tax_mod.rdata 

Error in download_data_intern(url = url, sha1 = sha1, temp_file = temp_file) : 
  Gateway Timeout (HTTP 504).
Calls: bodysize ... <Anonymous> -> download_data_intern -> stop_for_status
Execution halted
qPolyaAeppliSingle: no visible global function definition for ‘qgamma’
rPolyaAeppli: no visible global function definition for ‘rpois’
rPolyaAeppli: no visible global function definition for ‘rgeom’
Undefined global functions or variables:
  qgamma rgeom rpois
Consider adding
  importFrom("stats", "qgamma", "rgeom", "rpois")
to your NAMESPACE file.
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
Package vignette with placeholder title ‘Vignette Title’:
  ‘polynomials.Rmd’
Found the following files/directories:
  ‘AbsorbedDrugMetabolites’ ‘CorrelationResults’
  ‘EndogenousMetabolites’ ‘HeatMap’ ‘PKresults’
  ‘SecondAbsorbedMetabolites’ ‘preprocessed-data’
Found the following files/directories:
  ‘SPAGfreqExample2.txt’ ‘SpagInputExample.txt’ ‘SpagOutExample.txt’
  ‘SpagTemp.txt’ ‘TetrasatExample.txt’ ‘atetraexample.txt’
  ‘atetratest.txt’ ‘exampleGMoutput.txt’ ‘forPOPDIST.txt’
  ‘genodiveExample.txt’ ‘readGMtest.txt’ ‘strtemp.txt’ ‘structtest.txt’
  ‘testGenoDive2.txt’ ‘testGenoDive3.txt’ ‘testPOPDIST.txt’
  ‘tetrasattest.txt’
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
'library' or 'require' call to ‘matrixcalc’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘matrixcalc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for ‘pnorm’
print.pom: no visible global function definition for ‘pnorm’
siteocc : get.mod.matrix: no visible binding for global variable
  ‘na.pass’
siteocc : get.mod.matrix: no visible global function definition for
  ‘formula’
siteocc : get.mod.matrix: no visible global function definition for
  ‘model.matrix’
siteocc: no visible global function definition for ‘nlminb’
siteocc: no visible global function definition for
  ‘is.positive.definite’
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘PopED_output_summary_D_cont_opt_1.txt’ ‘PopED_output_summary_RS.txt’
  ‘PopED_output_summary_mfea_opt_1.txt’ ‘test.csv’
Package suggested but not available for checking: ‘WhopGenome’
asymmetricIntervals: no visible global function definition for ‘stack’
bonferroniIntervals: no visible global function definition for ‘stack’
bonferroniIntervals: no visible global function definition for ‘lm’
bonferroniIntervals: no visible global function definition for
  ‘predict’
bootstrapIntervals: no visible global function definition for ‘stack’
component1a: no visible global function definition for ‘pnorm’
component1b: no visible global function definition for ‘pnorm’
component2: no visible global function definition for ‘dgamma’
eqnForMin: no visible global function definition for ‘pnorm’
eqnForMin: no visible global function definition for ‘integrate’
integrand : <anonymous>: no visible global function definition for
  ‘pnorm’
integrand: no visible global function definition for ‘dnorm’
integrate2: no visible global function definition for ‘integrate’
integrate2a: no visible global function definition for ‘integrate’
integrate2b: no visible global function definition for ‘integrate’
integrate4a: no visible global function definition for ‘integrate’
integrate4b: no visible global function definition for ‘integrate’
optimalCScalar2: no visible global function definition for ‘uniroot’
optimalLambda: no visible global function definition for ‘optimise’
optimalLambdaC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dgamma dnorm integrate lm optimise pnorm predict stack uniroot
Consider adding
  importFrom("stats", "dgamma", "dnorm", "integrate", "lm", "optimise",
             "pnorm", "predict", "uniroot")
  importFrom("utils", "stack")
to your NAMESPACE file.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘portfolioSim/R/AllClasses.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

contributionSummaryDf,simResult : <anonymous>: no visible global
  function definition for ‘aggregate’
getSimTrades,stiFromSignal-orderable-portfolio-simData-logical: no
  visible binding for global variable ‘shares’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.freq’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.errors’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.type’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.summary.interface’
loadIn,simResultSinglePeriod-character-missing: no visible binding for
  global variable ‘x’
plot,simResult-missing: no visible global function definition for
  ‘xyplot’
runSim,portfolioSim-logical: no visible binding for global variable
  ‘id’
runSim,portfolioSim-logical: no visible global function definition for
  ‘updateSummary’
securityPerfSummaryDf,simResult: no visible global function definition
  for ‘aggregate’
summary,simResult: no visible global function definition for ‘sd’
summary,simResult: no visible global function definition for ‘head’
summary,simResult: no visible global function definition for ‘tail’
Undefined global functions or variables:
  aggregate head id master.errors master.freq master.summary.interface
  master.type sd shares tail updateSummary x xyplot
Consider adding
  importFrom("stats", "aggregate", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
fnfam: no visible global function definition for ‘qnorm’
fx: no visible global function definition for ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘pnorm’
normplot : <local> : replot: no visible global function definition for
  ‘dnorm’
normplot : <local> : replot: no visible global function definition for
  ‘points’
normplot : <local> : replot: no visible global function definition for
  ‘lines’
normplot : <local> : regen: no visible global function definition for
  ‘rnorm’
normplot : <local> : regen: no visible global function definition for
  ‘rexp’
nsibs: no visible global function definition for ‘qnorm’
ntdt: no visible global function definition for ‘uniroot’
plotNtdt: no visible global function definition for ‘lines’
plotNtdt: no visible global function definition for ‘legend’
ptdt: no visible global function definition for ‘optimize’
ptdt: no visible global function definition for ‘uniroot’
ptdt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm legend lines optimize pnorm points qnorm rexp rnorm uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Found the following files/directories:
  ‘Quad1.RData’ ‘Sp Env Data.RData’ ‘Sp PPM Data.RData’
  ‘SpEnvData.RData’ ‘Test.RData’ ‘TestPPM.RData’ ‘TestSP.RData’
pps1: no visible global function definition for ‘runif’
ppss: no visible global function definition for ‘runif’
ppswr: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LDA.Tree : Find.proj: no visible binding for global variable ‘var’
LDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
LDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘var’
PDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.Tree : Find.proj: no visible binding for global variable ‘var’
PP.Tree : Find.proj: no visible binding for global variable ‘median’
PP.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.optimize.Huber: no visible binding for global variable ‘sd’
PP.optimize.anneal: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible global function definition for ‘hist’
PP.optimize.plot: no visible global function definition for ‘text’
PP.optimize.plot: no visible global function definition for ‘par’
PP.optimize.plot: no visible global function definition for ‘colors’
PP.optimize.plot: no visible global function definition for ‘pairs’
PP.optimize.random: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  IQR colors hist median pairs par sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
TT.test : <anonymous>: no visible global function definition for
  ‘t.test’
TT.test: no visible binding for global variable ‘sd’
TT.test: no visible global function definition for ‘setNames’
kirjelda : combo: no visible binding for global variable ‘sd’
kor.tabel: no visible binding for global variable ‘cor.test’
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
PKG_CXXFLAGS set in ‘src/Makevars.win’ without any corresponding files
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.
Non-standard file/directory found at top level:
  ‘DESCRIPTION.bck’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘predmixcor/R/firstlib.r’:
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for ‘dbinom’
abs_cor: no visible global function definition for ‘cor’
gen.alpha.IGamma: no visible global function definition for ‘qgamma’
gendata.mix: no visible global function definition for ‘runif’
gendata.mix: no visible global function definition for ‘rbeta’
mh1.unif: no visible global function definition for ‘runif’
train_predict_mix: no visible global function definition for ‘dbinom’
training: no visible global function definition for ‘runif’
training: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
basisplot: no visible global function definition for ‘abline’
basisplot: no visible global function definition for ‘text’
basisplot: no visible global function definition for ‘par’
plot.prinsimp: no visible global function definition for ‘screeplot’
plot.simpart: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘strwidth’
simpart.formula: no visible global function definition for ‘terms’
simpart.formula: no visible global function definition for
  ‘model.matrix’
varperc: no visible global function definition for ‘lines’
varperc: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘points’
varsimp: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines model.matrix par points screeplot strwidth terms text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "points", "strwidth",
             "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘priorcd.Rmd’
Found the following files/directories:
  ‘network.html’ ‘network_files’
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.
.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.
GPois: no visible global function definition for ‘dnorm’
GPois: no visible binding for global variable ‘poisson’
GPois: no visible global function definition for ‘predict’
GPois: no visible global function definition for ‘fitted’
GPois: no visible global function definition for ‘residuals’
GPois: no visible global function definition for ‘smooth.spline’
ProDenICA: no visible global function definition for ‘rnorm’
d.gaussmix: no visible global function definition for ‘dnorm’
djordan: no visible global function definition for ‘dt’
djordan: no visible global function definition for ‘dunif’
mixmat: no visible global function definition for ‘rnorm’
mixmat: no visible global function definition for ‘runif’
r.gaussmix: no visible global function definition for ‘rmultinom’
r.gaussmix: no visible global function definition for ‘rnorm’
rjordan: no visible global function definition for ‘rt’
rjordan: no visible global function definition for ‘runif’
rmix.dexp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm dt dunif fitted poisson predict residuals rmultinom rnorm rt
  runif smooth.spline
Consider adding
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘qtbase’
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.
Running ‘run-all.R’ [7s/19s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ProjectTemplate")
  Loading required package: ProjectTemplate
  ── 1. Failure: Custom configuration is added to config (@test-add_config.R#12)  
  `load.project()` generated warnings:
  * 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
  
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  
  You are a coding rockstar!
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] TRUE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 852 | SKIPPED: 4 | WARNINGS: 281 | FAILED: 1 ]
  1. Failure: Custom configuration is added to config (@test-add_config.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Running examples in ‘PROSPER-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gen_diploid
> ### Title: Diploid genetics: recombination of alleles
> ### Aliases: gen_diploid
> 
> ### ** Examples
> 
> # generate a 'dfgenotype' data.frame:
> struc_preparation(Rmx=10, n_loci=2, epis=0, dom=1)
struc_preparation starts...Error in matrix(ncol = n_loci, as.numeric(unlist(strsplit(as.character(dfgenotype[,  : 
  invalid 'ncol' value (too large or NA)
Calls: struc_preparation -> sel_resist -> data.frame -> matrix
Execution halted
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.
'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: ‘rdt’
Package vignette with placeholder title ‘Vignette Title’:
  ‘TargetDecoyFDR_Example.Rmd’
Package in Depends field not imported from: ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mahalanobisComposite: no visible global function definition for
  ‘princomp’
prepareComposite: no visible global function definition for ‘cov’
winsorizor : f: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov princomp quantile
Consider adding
  importFrom("stats", "cov", "princomp", "quantile")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘PSF_vignette.Rmd’
candidate.overlap: no visible global function definition for
  ‘write.table’
fisher: no visible global function definition for ‘fisher.test’
fisher.iteration: no visible global function definition for
  ‘download.file’
fisher.iteration: no visible global function definition for
  ‘read.table’
pSI.list: no visible global function definition for ‘write.table’
specificity.index: no visible global function definition for ‘png’
specificity.index: no visible global function definition for ‘par’
specificity.index: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off download.file fisher.test par png read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par")
  importFrom("stats", "fisher.test")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘gene_count_1.csv’
'library' or 'require' call to ‘numDeriv’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for ‘grad’
test.problem: no visible global function definition for ‘new’
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for ‘new’
show,test.result: no visible global function definition for ‘show’
show,test.result: no visible global function definition for ‘sd’
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pspearman: no visible global function definition for ‘pt’
spearman.test: no visible global function definition for
  ‘complete.cases’
spearman.test: no visible global function definition for ‘cor’
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘orig’
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘barebones_correlation.Rmd’ using rmarkdown
--- finished re-building ‘barebones_correlation.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 97-103 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
invalid 'row.names' length
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘multilevel’ ‘nlme’
A package should be listed in only one of these fields.
Non-standard file/directory found at top level:
  ‘README.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘multilevel’ ‘nlme’
  Please remove these calls from your code.
Package vignette with placeholder title ‘Vignette Title’:
  ‘ptstem.Rmd’
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.
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.
CandidateBio.getBio : <anonymous>: no visible global function
  definition for ‘na.omit’
Committee.getCommittee : <anonymous>: no visible global function
  definition for ‘na.omit’
getAllBios: no visible global function definition for ‘txtProgressBar’
getAllBios: no visible global function definition for
  ‘setTxtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘txtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘setTxtProgressBar’
getAllVotes: no visible global function definition for ‘txtProgressBar’
getAllVotes: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
.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').
Package vignette with placeholder title ‘Vignette Title’:
  ‘qaig-introduction.Rmd’
Found the following files/directories:
  ‘exampleplot_1_blockdist_1.png’ ‘exampleplot_1_blockdist_2.png’
  ‘exampleplot_1_blockdist_3.png’ ‘exampleplot_1_bootdist.png’
  ‘exampleplot_1_dist.png’ ‘exampleplot_1_histogramtest_EMD.png’
  ‘exampleplot_1_roc_dynamic.png’ ‘exampleplot_1_slidedist_1.png’
  ‘exampleplot_1_slidedist_2.png’ ‘exampleplot_1_slidedist_3.png’
  ‘exampleplot_1_trimmeddist.png’ ‘exampleplot_blockdist_1.png’
  ‘exampleplot_blockdist_2.png’ ‘exampleplot_blockdist_3.png’
  ‘exampleplot_bootdist.png’ ‘exampleplot_dist.png’
  ‘exampleplot_lim_dyn.png’ ‘exampleplot_lim_sig.png’
  ‘exampleplot_lim_sta.png’ ‘exampleplot_noc.png’
  ‘exampleplot_roc_dyn.png’ ‘exampleplot_roc_sta.png’
  ‘exampleplot_slidedist_1.png’ ‘exampleplot_slidedist_2.png’
  ‘exampleplot_slidedist_3.png’ ‘exampleplot_trimmeddist.png’
  ‘myworkflow_result.xml’ ‘test_2_roc_dynamic.png’ ‘test_4_dist.png’
  ‘test_5_blockdist_1.png’ ‘test_5_blockdist_2.png’
  ‘test_5_blockdist_3.png’ ‘test_6_slidedist_1.png’
  ‘test_6_slidedist_2.png’ ‘test_6_slidedist_3.png’
  ‘test_7_trimmeddist.png’ ‘test_8_bootdist.png’ ‘test_emd_1d.png’
  ‘test_emd_2d.png’ ‘test_jsd_1d.png’ ‘test_jsd_2d.png’
  ‘test_kld_1d.png’ ‘test_kld_2d.png’ ‘test_ms_1d.png’ ‘test_ms_2d.png’
  ‘test_rms_1d.png’ ‘test_rms_2d.png’
csQCAbinTest: no visible global function definition for ‘p.adjust’
fsQCApermTest: no visible global function definition for ‘p.adjust’
mvQCAbinTest: no visible global function definition for ‘p.adjust’
p.threshold.adjust: no visible global function definition for
  ‘p.adjust’
plot.fsQCApt: no visible global function definition for ‘dev.cur’
plot.fsQCApt: no visible global function definition for ‘dev.new’
plot.fsQCApt: no visible global function definition for ‘par’
plot.fsQCApt: no visible global function definition for ‘density’
plot.fsQCApt: no visible global function definition for ‘axis’
plot.fsQCApt: no visible global function definition for ‘polygon’
plot.fsQCApt: no visible global function definition for ‘points’
plot.fsQCApt: no visible global function definition for ‘hist’
summary.csQCAbt: no visible global function definition for
  ‘printCoefmat’
summary.fsQCApt: no visible global function definition for
  ‘printCoefmat’
summary.mvQCAbt: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "points", "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
Found the following files/directories:
  ‘EWAS_QC_graph_effectsize.png’ ‘EWAS_QC_graph_precision.png’
  ‘EWAS_QC_legend.txt’ ‘sample1.txt.gz’ ‘sample2.txt.gz’
  ‘sample_map.txt.gz’ ‘sample_output.graph_M.png’
  ‘sample_output.graph_QQ.png’ ‘sample_output.graph_p.png’
  ‘sample_output.graph_volcano.png’ ‘sample_output.histo.png’
  ‘sample_output.txt’ ‘sample_output1.graph_M.png’
  ‘sample_output1.graph_QQ.png’ ‘sample_output1.graph_p.png’
  ‘sample_output1.graph_volcano.png’ ‘sample_output1.histo.png’
  ‘sample_output2.graph_M.png’ ‘sample_output2.graph_QQ.png’
  ‘sample_output2.graph_p.png’ ‘sample_output2.graph_volcano.png’
  ‘sample_output2.histo.png’ ‘translation_table.txt’
Found the following files/directories:
  ‘sample_QQ.png’ ‘sample_QQ1.png’ ‘sample_QQ2.png’ ‘sample_QQ3.png’
  ‘sample_distribution.png’ ‘sample_graph_p-correlation.png’
  ‘sample_histogram.png’ ‘sample_histogram1.png’
  ‘sample_histogram2.png’ ‘sample_histogram3.png’
  ‘sample_plots_graph_M.png’ ‘sample_plots_graph_QQ.png’
  ‘sample_precision.png’ ‘sample_regional_association.png’
  ‘sample_skewness_kurtosis.png’
Error(s) in re-building vignettes:
  ...
--- re-building ‘orthography_processing.Rmd’ using rmarkdown
--- finished re-building ‘orthography_processing.Rmd’

--- re-building ‘recoding_nominal_data.Rmd’ using rmarkdown
Quitting from lines 49-60 (recoding_nominal_data.Rmd) 
Error: processing vignette 'recoding_nominal_data.Rmd' failed with diagnostics:
factor level [3] is duplicated
--- failed re-building ‘recoding_nominal_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.matrix’
chooseMDoubleBootstrap: no visible global function definition for
  ‘as.formula’
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.frame’
chooseMDoubleBootstrap: no visible global function definition for ‘lm’
chooseMDoubleBootstrap: no visible global function definition for
  ‘coef’
chooseMDoubleBootstrap: no visible global function definition for
  ‘quantile’
chooseMDoubleBootstrap: no visible global function definition for
  ‘qnorm’
getModel: no visible global function definition for ‘lm’
getModel: no visible global function definition for ‘model.matrix’
getModel: no visible global function definition for ‘as.formula’
getModel: no visible global function definition for ‘model.frame’
getModel: no visible global function definition for ‘model.response’
getModel: no visible global function definition for ‘coef’
getModel: no visible global function definition for ‘qnorm’
qLearn: no visible global function definition for ‘model.matrix’
qLearn: no visible global function definition for ‘as.formula’
qLearn: no visible global function definition for ‘model.frame’
qLearn: no visible global function definition for ‘coef’
qLearn: no visible global function definition for ‘lm’
qLearn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
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.
Found the following files/directories:
  ‘datInSFexample6_1pxCube.csv’ ‘datInSFexample6_1pxCubeA0.csv ’
  ‘datInSFexample6_1pxCubeA1.csv ’ ‘datInSFexample6_1pxCubeData.csv ’
  ‘datInSFexample6_1pxCubeVariable.csv’
  ‘datInSFexample6_1pxCubeVariableDomain.csv’
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qtbase.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘qtl2’
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘qtlnet.Rnw’ using Sweave
Loading required package: qtl
Loading required package: igraph

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

Loading required package: sem
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

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

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

    normalize, path, union

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, which.max, which.min


Attaching package: ‘graph’

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

    degree, edges, intersection

Loading required package: pcalg

Error: processing vignette 'qtlnet.Rnw' failed with diagnostics:
 chunk 2 
Error in igraph::graph.data.frame(edges, TRUE, vertices = vertices) : 
  Some vertex names in edge list are not listed in vertex data frame

--- failed re-building ‘qtlnet.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘qtbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' call to ‘Rmpfr’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
adjacencyMatrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
quadp: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
alphaf: no visible global function definition for ‘pchisq’
alphaf: no visible global function definition for ‘dbinom’
conout: no visible global function definition for ‘sd’
ibgaout: no visible global function definition for ‘qnorm’
ibgaout: no visible global function definition for ‘pnorm’
plot.qualint: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘rnorm’
powerval: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘pnorm’
print.expplot: no visible global function definition for ‘gray’
print.expplot: no visible binding for global variable ‘coef’
print.outplot: no visible global function definition for ‘gray’
print.outplot: no visible binding for global variable ‘coef’
qualint: no visible global function definition for ‘qnorm’
qualval: no visible global function definition for ‘qnorm’
surout: no visible global function definition for ‘tail’
surout: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef dbinom gray pchisq pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘Judge.pdf’
Found the following files/directories:
  ‘Example’
File ‘QUIC/libs/QUIC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘chk1_1.dat’ ‘chk1_1.mem’ ‘chk1_1.noisy’
mutualCoherence : .setOneMutualP: no visible global function definition
  for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
conf2d.default: no visible global function definition for ‘polygon’
conf2d_int: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘R2DGC.Rmd’
'library' or 'require' call to ‘rgdal’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘matrixStats’ ‘rgdal’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘ndvi.rgf’
Found the following files/directories:
  ‘output.html’
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
‘gs+qpdf’ made some significant size reductions:
     compacted ‘R2OpenBUGS.pdf’ from 911Kb to 639Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
Found the following files/directories:
  ‘test.html’ ‘test.swf’
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package vignette with placeholder title ‘Vignette Title’:
  ‘r511-intro.Rmd’
getsonde: no visible global function definition for ‘read.table’
plotsonde: no visible global function definition for ‘par’
plotwind: no visible global function definition for ‘mtext’
plotwind: no visible global function definition for ‘abline’
skewt.axis: no visible global function definition for ‘par’
skewt.axis: no visible global function definition for ‘axis’
skewt.axis: no visible global function definition for ‘mtext’
skewt.axis: no visible global function definition for ‘segments’
skewt.axis: no visible global function definition for ‘text’
skewt.axis: no visible global function definition for ‘lines’
skewt.lines: no visible global function definition for ‘lines’
skewt.points: no visible global function definition for ‘points’
station.symbol: no visible global function definition for ‘sd’
station.symbol: no visible global function definition for ‘par’
station.symbol: no visible global function definition for ‘lines’
station.symbol: no visible global function definition for ‘polygon’
station.symbol: no visible global function definition for ‘text’
station.symbol: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline axis lines mtext par points polygon read.table sd segments
  text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘SondeFile.txt’
Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(radjust)
  > test_check("radjust")
  ── 1. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_adaptive` not equivalent to eo$mice_rv_adaptive.
  Component "results_table": Component "name": target is character, current is factor
  
  ── 2. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_non_adpt_sel` not equivalent to eo$mice_rv_non_adpt_sel.
  Component "results_table": Component "name": target is character, current is factor
  
  ── 3. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_non_adpt` not equivalent to eo$mice_rv_non_adpt.
  Component "results_table": Component "name": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#9) 
  2. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#10) 
  3. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Found the following files/directories:
  ‘blcs.dot’ ‘ex1.dot’ ‘ex1bridge1.dot’ ‘ex1bridge2.dot’
  ‘ex1bridge3.dot’ ‘ex1effect1.dot’ ‘ex1effect2.dot’ ‘gcmlinear.dot’
  ‘latent.dot’ ‘lcs.dot’ ‘mimic.dot’
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘randomGLM/R/randomGLM.R’:
  assign(".randomGLMparallelCluster", cluster, pos = ".GlobalEnv")
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.
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.
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.
'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.
freq: no visible global function definition for ‘xtabs’
freq: no visible binding for global variable ‘na.pass’
freq: no visible global function definition for ‘melt’
freq: no visible global function definition for ‘complete.cases’
freq: no visible global function definition for ‘tail’
kurtosis: no visible global function definition for ‘na.omit’
label: no visible global function definition for ‘tail’
name: no visible global function definition for ‘tail’
nvalid : <anonymous>: no visible global function definition for
  ‘na.omit’
rp.desc: no visible global function definition for ‘melt.data.frame’
rp.desc: no visible global function definition for ‘cast’
rp.desc: no visible global function definition for ‘na.omit’
rp.desc : <anonymous>: no visible global function definition for ‘tail’
rp.desc : <anonymous>: no visible global function definition for ‘head’
rp.freq: no visible global function definition for ‘xtabs’
rp.freq: no visible binding for global variable ‘na.pass’
rp.freq: no visible global function definition for ‘melt’
rp.freq: no visible global function definition for ‘complete.cases’
rp.freq: no visible global function definition for ‘tail’
rp.label: no visible global function definition for ‘tail’
rp.name: no visible global function definition for ‘tail’
rp.outlier : lundcrit: no visible global function definition for ‘qf’
rp.outlier: no visible global function definition for ‘lm’
rp.outlier: no visible global function definition for ‘rstandard’
rp.valid : <anonymous>: no visible global function definition for
  ‘na.omit’
skewness: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  cast complete.cases head lm melt melt.data.frame na.omit na.pass qf
  rstandard tail xtabs
Consider adding
  importFrom("stats", "complete.cases", "lm", "na.omit", "na.pass", "qf",
             "rstandard", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
fnRAP: no visible global function definition for ‘chisq.test’
fnRAP: no visible global function definition for ‘combn’
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
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.
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.
rateratio.test: no visible global function definition for
  ‘complete.cases’
rateratio.test: no visible global function definition for ‘pbinom’
rateratio.test : p.L: no visible global function definition for ‘qbeta’
rateratio.test : p.U: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
concordance: no visible global function definition for ‘quantile’
concordance : Normal: no visible global function definition for ‘qnorm’
concordance : Normal: no visible global function definition for ‘pnorm’
concordance : MC: no visible global function definition for ‘rmultinom’
concordance : MC: no visible global function definition for ‘quantile’
concordance: no visible global function definition for ‘qnorm’
concordance: no visible global function definition for ‘pnorm’
concordance : Chisq: no visible global function definition for ‘qchisq’
concordance : Chisq: no visible global function definition for ‘pchisq’
concordance : Normal2: no visible global function definition for
  ‘qnorm’
concordance : Normal2: no visible global function definition for
  ‘pnorm’
concordance : MC2: no visible global function definition for
  ‘rmultinom’
concordance : MC2: no visible global function definition for ‘quantile’
wlin.conc: no visible global function definition for ‘quantile’
wlin.conc : MC: no visible global function definition for ‘rmultinom’
wlin.conc : MC: no visible global function definition for ‘quantile’
wquad.conc: no visible global function definition for ‘quantile’
wquad.conc : MC: no visible global function definition for ‘rmultinom’
wquad.conc : MC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  pchisq pnorm qchisq qnorm quantile rmultinom
Consider adding
  importFrom("stats", "pchisq", "pnorm", "qchisq", "qnorm", "quantile",
             "rmultinom")
to your NAMESPACE file.
.GCD: no visible global function definition for ‘as.polynomial’
.LCM: no visible global function definition for ‘as.polynomial’
.is_zero_polynomial: no visible global function definition for ‘coef’
.poly2expr: no visible global function definition for ‘coef’
integral.rationalfun: no visible global function definition for ‘coef’
integraterf.transcendent: no visible global function definition for
  ‘coef’
rationalfun: no visible global function definition for ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘is.polynomial’
rfun: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘is.polynomial’
simplify: no visible global function definition for ‘coef’
simplify: no visible global function definition for ‘polynomial’
Undefined global functions or variables:
  as.polynomial coef is.polynomial polynomial
Consider adding
  importFrom("stats", "coef")
to your NAMESPACE file.
.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.
GetHistoricTradeData: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘RBitmoji.Rmd’
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
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.
find_available_versions: no visible global function definition for
  ‘contrib.url’
find_available_versions: no visible global function definition for
  ‘available.packages’
install_version: no visible global function definition for
  ‘contrib.url’
install_version: no visible global function definition for
  ‘available.packages’
install_version: no visible global function definition for
  ‘install_url’
load_available_packages: no visible global function definition for
  ‘contrib.url’
validate_installed_package: no visible global function definition for
  ‘installed.packages’
Undefined global functions or variables:
  available.packages contrib.url install_url installed.packages
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "installed.packages")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘rcane.Rmd’
Found the following files/directories:
  ‘rcanvec.cache’
RC.read.table: no visible global function definition for ‘type.convert’
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
Found the following files/directories:
  ‘temp.RData’
.onAttach: no visible global function definition for
  ‘packageDescription’
rselect.list: no visible global function definition for ‘select.list’
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
Found the following files/directories:
  ‘data.csv’
get_ClinicalCodes: no visible global function definition for ‘read.csv’
get_ClinicalCodes : <anonymous>: no visible global function definition
  for ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘file1.arp’ ‘file2.arp’ ‘test.txt’ ‘test2.txt’
cmaOptimDP: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  flush.console
Consider adding
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following files/directories:
  ‘outcmaesdisp.dat’
enterTableMHTest : onOK: no visible global function definition for
  ‘na.omit’
startStop: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Namespace with empty importFrom: ‘tcltk’
'library' or 'require' calls to packages already attached by Depends:
  ‘depthTools’ ‘tcltk’
  Please remove these calls from your code.
computeMBD : OnOutput: no visible global function definition for
  ‘tkbutton’
computeMBD: no visible global function definition for ‘tkbutton’
computeMBD : OnPlot: no visible global function definition for
  ‘tkcanvas’
computeMBD : OnPlot: no visible global function definition for
  ‘tkbutton’
computeTmean: no visible global function definition for ‘tkcanvas’
computeTmean: no visible global function definition for ‘tkbutton’
computeTmean : onOK: no visible global function definition for ‘par’
plotCentralCurves: no visible global function definition for ‘tkcanvas’
plotCentralCurves: no visible global function definition for ‘tkbutton’
plotCentralCurves : onOK: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
managedata: no visible binding for global variable ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘ENmisc’ ‘Hmisc’ ‘Rcmdr’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onAttach: no visible global function definition for ‘getRcmdr’
.onAttach: no visible global function definition for ‘closeCommander’
.onAttach: no visible global function definition for ‘Commander’
mosaicMenuItem: no visible global function definition for
  ‘mosaicSelectDialog’
mosaicMenuItem: no visible global function definition for ‘Message’
Undefined global functions or variables:
  Commander Message closeCommander getRcmdr mosaicSelectDialog
BOXWP: no visible binding for global variable ‘top’
BOXWP: no visible binding for global variable ‘buttonsFrame’
HIST: no visible binding for global variable ‘top’
HIST: no visible binding for global variable ‘buttonsFrame’
QQN: no visible binding for global variable ‘top’
QQN: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  buttonsFrame top
Namespaces with empty importFrom:
  ‘stats’ ‘tcltk’
fncLRpROC: no visible global function definition for ‘palette’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘rgb’
fncPairedpROC: no visible global function definition for ‘palette’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncUnpairedpROC: no visible global function definition for ‘palette’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncvpROC: no visible global function definition for ‘palette’
fncvpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncvpROC : onOK : convert: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
SampleSizes: no visible global function definition for ‘xtabs’
SampleSizes: no visible global function definition for ‘weighted.mean’
SampleSizes: no visible global function definition for ‘reshape’
stage1Sample.fn: no visible global function definition for ‘runif’
stage2Sample.fn: no visible global function definition for ‘runif’
strata.options : onOK: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to ‘SLC’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘SLC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.steeptestDij : onOK: no visible binding for global variable
  ‘replications’
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  ‘replications’
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ROpenOffice’
brewer.pal: no visible global function definition for ‘rgb’
display.brewer.all: no visible global function definition for ‘par’
display.brewer.all: no visible global function definition for ‘rect’
display.brewer.all: no visible global function definition for ‘text’
display.brewer.pal: no visible global function definition for ‘image’
Undefined global functions or variables:
  image par rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
addLine: no visible global function definition for ‘abline’
ellipse: no visible global function definition for ‘approx’
ellipse: no visible global function definition for ‘tail’
Undefined global functions or variables:
  abline approx tail
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Gauss: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘rcreds.Rmd’
Packages in Depends field not imported from:
  ‘MASS’ ‘Matrix’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CUR: no visible global function definition for ‘runif’
CUR: no visible global function definition for ‘new’
plotLeverage,CURobj: no visible global function definition for ‘points’
plotLeverage,CURobj: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline new points runif
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("methods", "new")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
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.
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RDieHarder.Rcheck/00install.out’ for details.
mve_single_cvxr: no visible global function definition for ‘Semidef’
Undefined global functions or variables:
  Semidef
Error(s) in re-building vignettes:
  ...
--- re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’ using rmarkdown
Loading required package: rJava
Loading required package: Rdroolsjars

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'purrr'

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.thoughtworks.xstream.core.util.Fields (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rdroolsjars/java/xstream-1.4.9.jar) to field java.util.TreeMap.comparator
WARNING: Please consider reporting this to the maintainers of com.thoughtworks.xstream.core.util.Fields
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Quitting from lines 183-187 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
Assigned data `paste(seq(as.numeric(lowerRange), as.numeric(upperRange)), collapse = ",")` must be compatible with existing data.
ℹ Error occurred for column `Indices`.
✖ No common type for `value` <character> and `x` <double>.
--- failed re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘synchronicity’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘a.desc’ ‘b.desc’ ‘barrnumleft.desc’ ‘barrsense.desc’ ‘c.desc’
  ‘m.desc’ ‘u.desc’ ‘x’ ‘x.desc’
ip2coordinates: no visible global function definition for ‘URLencode’
street2coordinates: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Found the following files/directories:
  ‘example.pdf’
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(readroper)
  readroper package loaded.
  > 
  > test_check("readroper")
  ── 1. Error: First row of multicard dataset matches (@test-readroper.R#4)  ─────
  Must subset rows with a valid subscript vector.
  ℹ Logical subscripts must match the size of the indexed input.
  ✖ The input has size 1976 but the subscript `card_v` has size 2.
  Backtrace:
    1. readroper::read_rpr(...)
   16. vctrs:::stop_indicator_size(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: First row of multicard dataset matches (@test-readroper.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Non-standard file/directory found at top level:
  ‘devel’
'library' or 'require' calls to packages already attached by Depends:
  ‘leaps’ ‘mgcv’
  Please remove these calls from your code.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of ‘env’ to ‘envir’
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of ‘env’ to ‘envir’
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
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.
Running ‘test-all.R’ [4s/10s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > # Modeled after the R6 testing structure: https://github.com/wch/R6/blob/master/tests/testthat.R
  > library(testthat)
  > library(REDCapR)
  > 
  > testthat::test_check("REDCapR")
  ── 1. Failure: validate_no_logical -concern dataset (@test-validate.R#36)  ─────
  ds$field_index not equal to 2.
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 135 | SKIPPED: 79 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: validate_no_logical -concern dataset (@test-validate.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
AutoCorrelationLRtest: no visible global function definition for
  ‘logLik’
AutoCorrelationLRtest: no visible global function definition for
  ‘pchisq’
REEMtree: no visible global function definition for ‘terms’
REEMtree: no visible binding for global variable ‘SubsetVector’
REEMtree: no visible global function definition for ‘predict’
REEMtree: no visible global function definition for ‘logLik’
fitted.REEMtree: no visible global function definition for ‘fitted’
predict.REEMtree: no visible global function definition for ‘predict’
residuals.REEMtree: no visible global function definition for
  ‘residuals’
Undefined global functions or variables:
  SubsetVector fitted logLik pchisq predict residuals terms
Consider adding
  importFrom("stats", "fitted", "logLik", "pchisq", "predict",
             "residuals", "terms")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'fitted.REEMtree':
  ‘fitted.REEMtree’

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

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

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

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
cook.outliers: no visible global function definition for ‘lm’
cook.outliers: no visible global function definition for
  ‘cooks.distance’
nonparRI: no visible global function definition for ‘quantile’
plot.interval: no visible global function definition for ‘par’
plot.interval: no visible global function definition for ‘plot.new’
plot.interval: no visible global function definition for ‘plot.window’
plot.interval: no visible global function definition for ‘segments’
plot.interval: no visible global function definition for ‘axis’
plot.interval: no visible global function definition for ‘title’
plot.interval: no visible global function definition for ‘legend’
plot.interval: no visible global function definition for ‘box’
plot.interval: no visible global function definition for ‘text’
robust: no visible global function definition for ‘qt’
singleRefLimit: no visible global function definition for ‘qnorm’
singleRefLimit: no visible global function definition for
  ‘shapiro.test’
singleRefLimit: no visible global function definition for ‘ks.test’
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
cluster.reg: no visible global function definition for ‘rnorm’
cluster.reg: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
Non-standard files/directories found at top level:
  ‘prebuild.sh’ ‘regtest-Ex.R’
binregtest: no visible global function definition for ‘str’
binregtest: no visible binding for global variable ‘str’
binregtest: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif str
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
'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
print.summary.rem: no visible global function definition for
  ‘printCoefmat’
print.summary.rem: no visible global function definition for ‘pnorm’
print.summary.rem: no visible binding for global variable ‘quantile’
print.summary.rem: no visible global function definition for ‘pchisq’
print.summary.rem.dyad: no visible global function definition for
  ‘printCoefmat’
print.summary.rem.dyad: no visible global function definition for
  ‘pnorm’
print.summary.rem.dyad: no visible global function definition for
  ‘pchisq’
rem: no visible global function definition for ‘rnorm’
rem: no visible global function definition for ‘dnorm’
rem: no visible global function definition for ‘runif’
rem: no visible global function definition for ‘rchisq’
rem: no visible global function definition for ‘cov’
rem.dyad: no visible global function definition for ‘rnorm’
rem.dyad: no visible global function definition for ‘optim’
rem.dyad: no visible global function definition for ‘rchisq’
rem.dyad: no visible global function definition for ‘quantile’
rem.dyad: no visible global function definition for ‘sd’
rem.dyad: no visible global function definition for ‘var’
rem.dyad.lprior: no visible global function definition for ‘dnorm’
rem.dyad.lprior: no visible global function definition for ‘dt’
Undefined global functions or variables:
  cov dnorm dt optim pchisq pnorm printCoefmat quantile rchisq rnorm
  runif sd var
Consider adding
  importFrom("stats", "cov", "dnorm", "dt", "optim", "pchisq", "pnorm",
             "printCoefmat", "quantile", "rchisq", "rnorm", "runif",
             "sd", "var")
to your NAMESPACE file.
duane: no visible global function definition for ‘optim’
duane.plot: no visible global function definition for ‘lines’
duane.plot: no visible global function definition for ‘legend’
duane.plot: no visible global function definition for ‘title’
littlewood.verall: no visible global function definition for ‘optim’
littlewood.verall.plot: no visible global function definition for
  ‘lines’
littlewood.verall.plot: no visible global function definition for
  ‘legend’
littlewood.verall.plot: no visible global function definition for
  ‘title’
moranda.geometric: no visible global function definition for ‘optimize’
moranda.geometric.plot: no visible global function definition for
  ‘lines’
moranda.geometric.plot: no visible global function definition for
  ‘legend’
moranda.geometric.plot: no visible global function definition for
  ‘title’
musa.okumoto: no visible global function definition for ‘optimize’
musa.okumoto.plot: no visible global function definition for ‘lines’
musa.okumoto.plot: no visible global function definition for ‘legend’
musa.okumoto.plot: no visible global function definition for ‘title’
rel.plot: no visible global function definition for ‘lines’
rel.plot: no visible global function definition for ‘segments’
rel.plot: no visible global function definition for ‘legend’
rel.plot: no visible global function definition for ‘title’
total.plot: no visible global function definition for ‘lines’
total.plot: no visible global function definition for ‘legend’
total.plot: no visible global function definition for ‘title’
Undefined global functions or variables:
  legend lines optim optimize segments title
Consider adding
  importFrom("graphics", "legend", "lines", "segments", "title")
  importFrom("stats", "optim", "optimize")
to your NAMESPACE file.
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.
Running examples in ‘rematch2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: re_exec
> ### Title: Extract Data From First Regular Expression Match Into a Data
> ###   Frame
> ### Aliases: re_exec $.rematch_records $.rematch_allrecords
> 
> ### ** Examples
> 
> name_rex <- paste0(
+   "(?<first>[[:upper:]][[:lower:]]+) ",
+   "(?<last>[[:upper:]][[:lower:]]+)"
+ )
> notables <- c(
+   "  Ben Franklin and Jefferson Davis",
+   "\tMillard Fillmore"
+ )
> # Match first occurrence
> pos <- re_exec(notables, name_rex)
> pos
Error: Input must be a vector, not a `rematch_records` object.
Backtrace:
     █
  1. ├─(function (x, ...) ...
  2. ├─tibble:::print.tbl(x)
  3. │ ├─cli::cat_line(format(x, ..., n = n, width = width, n_extra = n_extra))
  4. │ │ └─base::paste0(..., collapse = "\n")
  5. │ ├─base::format(x, ..., n = n, width = width, n_extra = n_extra)
  6. │ └─tibble:::format.tbl(x, ..., n = n, width = width, n_extra = n_extra)
  7. │   └─tibble::trunc_mat(x, n = n, width = width, n_extra = n_extra)
  8. │     ├─base::as.data.frame(head(x, n))
  9. │     ├─utils::head(x, n)
 10. │     └─utils:::head.data.frame(x, n)
 11. │       ├─base::do.call("[", args)
 12. │       ├─x[1:2, , drop = FALSE]
 13. │       └─tibble:::`[.tbl_df`(x, 1:2, , drop = FALSE)
 14. │         └─tibble:::tbl_subset_row(xo, i = i, i_arg)
 15. │           └─base::lapply(unclass(x), vec_slice, i = i)
 16. │             └─vctrs:::FUN(X[[i]
Execution halted
RearrangeData: no visible global function definition for ‘rainbow’
RearrangeData: no visible global function definition for ‘hclust’
RearrangeData: no visible global function definition for
  ‘as.dendrogram’
RearrangeData: no visible global function definition for ‘heatmap’
RearrangeData: no visible global function definition for ‘pdf’
RearrangeData: no visible global function definition for
  ‘colorRampPalette’
RearrangeData: no visible global function definition for ‘legend’
RearrangeData: no visible global function definition for ‘dev.off’
RearrangeJoseph: no visible global function definition for
  ‘write.table’
RearrangeJoseph: no visible global function definition for
  ‘as.dendrogram’
RearrangeJoseph: no visible global function definition for
  ‘order.dendrogram’
colorDendClass : colLab: no visible global function definition for
  ‘is.leaf’
colorDendClass: no visible global function definition for ‘dendrapply’
testData1: no visible global function definition for ‘runif’
testData1: no visible global function definition for ‘image’
testData2: no visible global function definition for ‘runif’
testData2: no visible global function definition for ‘image’
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf rainbow runif write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘A.txt’ ‘minI.txt’ ‘minJ.txt’
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.
Found the following files/directories:
  ‘PackageCites.bib’
delete: no visible global function definition for ‘menu’
doc_temp: no visible global function definition for ‘menu’
html5: no visible global function definition for ‘na.omit’
install_pandoc: no visible global function definition for
  ‘download.file’
new_report: no visible global function definition for ‘tail’
new_report: no visible global function definition for ‘head’
new_report: no visible global function definition for ‘menu’
presentation: no visible global function definition for ‘head’
presentation: no visible global function definition for ‘tail’
presentation: no visible global function definition for ‘menu’
repo2github: no visible global function definition for ‘download.file’
repo2github: no visible global function definition for ‘unzip’
reveal.js: no visible global function definition for ‘na.omit’
update_bib: no visible global function definition for ‘tail’
update_bib: no visible global function definition for ‘menu’
Undefined global functions or variables:
  download.file head menu na.omit tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "tail", "unzip")
to your NAMESPACE file.
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.
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.
Found the following files/directories:
  ‘P.csv’ ‘correct_alpha.csv’ ‘correct_beta.csv’ ‘correct_gamma.csv’
  ‘correct_lambda.csv’ ‘correct_perm_list.csv’ ‘correct_psi.csv’
PKG_CFLAGS set in ‘src/Makevars’ without any corresponding files
Found the following files/directories:
  ‘forest.out’
Package vignette with placeholder title ‘Vignette Title’:
  ‘rERR.Rmd’
.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').
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(reshape2)
  > 
  > test_check("reshape2")
  ── 1. Failure: labels are correct when missing combinations dropped/kept (@test-
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 4 - 16 == -12
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 126 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: labels are correct when missing combinations dropped/kept (@test-cast.r#126) 
  
  Error: testthat unit tests failed
  Execution halted
Non-standard file/directory found at top level:
  ‘load.r’
Packages in Depends field not imported from:
  ‘gWidgets’ ‘gWidgetsRGtk2’ ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
reshapeGUI: no visible global function definition for ‘gwindow’
reshapeGUI: no visible global function definition for ‘gnotebook’
reshapeGUI: no visible global function definition for ‘size<-’
reshapeGUI: no visible global function definition for ‘ggroup’
reshapeGUI: no visible global function definition for ‘gtable’
reshapeGUI: no visible global function definition for ‘addSpring’
reshapeGUI: no visible global function definition for ‘gbutton’
reshapeGUI: no visible global function definition for ‘glabel’
reshapeGUI: no visible global function definition for ‘gedit’
reshapeGUI: no visible global function definition for ‘gcheckbox’
reshapeGUI: no visible global function definition for ‘gdf’
reshapeGUI: no visible global function definition for ‘visible<-’
reshapeGUI: no visible global function definition for
  ‘addHandlerClicked’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘gmessage’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘svalue’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘svalue<-’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘delete’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘add’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘gdf’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘visible<-’
reshapeGUI: no visible global function definition for
  ‘addHandlerChanged’
updateMeltCodeBox: no visible global function definition for ‘svalue<-’
Undefined global functions or variables:
  add addHandlerChanged addHandlerClicked addSpring delete gbutton
  gcheckbox gdf gedit ggroup glabel gmessage gnotebook gtable gwindow
  size<- svalue svalue<- visible<-
GUI_template : onHelp: no visible global function definition for ‘help’
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘retimes’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
dexgauss: no visible global function definition for ‘pnorm’
loglik: no visible global function definition for ‘pnorm’
mexgauss: no visible global function definition for ‘sd’
rexgauss: no visible global function definition for ‘rnorm’
rexgauss: no visible global function definition for ‘rexp’
timefit: no visible global function definition for ‘optim’
timefit: no visible global function definition for ‘sd’
timefit: no visible global function definition for ‘par’
timefit: no visible global function definition for ‘hist’
timefit: no visible global function definition for ‘density’
timefit: no visible global function definition for ‘curve’
timefit: no visible global function definition for ‘new’
plot,timefit: no visible global function definition for ‘density’
plot,timefit: no visible global function definition for ‘par’
plot,timefit: no visible global function definition for ‘curve’
Undefined global functions or variables:
  curve density hist new optim par pnorm rexp rnorm sd
Consider adding
  importFrom("graphics", "curve", "hist", "par")
  importFrom("methods", "new")
  importFrom("stats", "density", "optim", "pnorm", "rexp", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [14s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("retistruct")
  Loading required package: retistruct
  ── 1. Error: IDT format is read correctly (@test-format-idt.R#9)  ──────────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(r)
  
  ── 2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8)  ───────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  ── 3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45)  
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  ── 4. Error: Serialisation works with a particular example (@test-reconstruct.R#
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a, error = message)
  
  ── 5. Error: No regression on Issue #21 (@test-regressions.R#5)  ───────────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 138 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 5 ]
  1. Error: IDT format is read correctly (@test-format-idt.R#9) 
  2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8) 
  3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45) 
  4. Error: Serialisation works with a particular example (@test-reconstruct.R#98) 
  5. Error: No regression on Issue #21 (@test-regressions.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
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.
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.
fs_author_ids : <anonymous>: no visible global function definition for
  ‘select.list’
fs_download : <anonymous>: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘XML’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
quoteFXTsData : function.fx: no visible global function definition for
  ‘xmlValue’
quoteFundTsData : function.fund: no visible global function definition
  for ‘xmlValue’
quoteStockTsData : function.stock: no visible global function
  definition for ‘xmlSize’
quoteStockTsData : function.stock: no visible global function
  definition for ‘xmlValue’
quoteTsData: no visible global function definition for ‘xmlRoot’
quoteTsData: no visible global function definition for ‘htmlTreeParse’
quoteTsData: no visible global function definition for
  ‘xmlErrorCumulator’
quoteTsData: no visible global function definition for ‘xmlSize’
toXts: no visible global function definition for ‘as.xts’
Undefined global functions or variables:
  as.xts htmlTreeParse xmlErrorCumulator xmlRoot xmlSize xmlValue
Found the following files/directories:
  ‘Test.txt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RFmerge-RainfallExample-minimal.Rmd’ using rmarkdown

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 7.0.0
Loading required package: sp
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 3.0.4, released 2020/01/28
 Path to GDAL shared files: 
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 7.0.0, March 1st, 2020, [PJ_VERSION: 700]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
(C) 2019 M. Zambrano-Bigiarini and Oscar M. Baez-Villanueva (GPL >=3 license)
Type 'citation('RFmerge')' to see how to cite this package
Quitting from lines 268-274 (RFmerge-RainfallExample-minimal.Rmd) 
Error: processing vignette 'RFmerge-RainfallExample-minimal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘RFmerge-RainfallExample-minimal.Rmd’

SUMMARY: processing the following file failed:
  ‘RFmerge-RainfallExample-minimal.Rmd’

Error: Vignette re-building failed.
Execution halted
.testLTS: no visible binding for global variable ‘stackloss’
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
Found the following files/directories:
  ‘interactions.dot’
Package vignette with placeholder title ‘Vignette Title’:
  ‘rfVarImpOOB-vignette.Rmd’
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.
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.
Running examples in ‘rGEDI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clipLevel1BGeo
> ### Title: Clip GEDI Full Waveform Geolocations by Coordinates
> ### Aliases: clipLevel1BGeo
> 
> ### ** Examples
> 
> # Specifying the path to GEDI level1B data (zip file)
> level1B_fp_zip <- system.file("extdata",
+                   "GEDI01_B_2019108080338_O01964_T05337_02_003_01_sub.zip",
+                   package="rGEDI")
> 
> # Unzipping GEDI level1B data
> level1Bpath <- unzip(level1B_fp_zip,exdir = dirname(level1B_fp_zip))
Error in unzip(level1B_fp_zip, exdir = dirname(level1B_fp_zip)) : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rGEDI/extdata/GEDI01_B_2019108080338_O01964_T05337_02_003_01_sub.h5': Read-only file system
Execution halted
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rgeolocate.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rggobi.Rcheck/00install.out’ for details.
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
prepare_Rd: replacing previous import ‘sf::st_make_valid’ by ‘lwgeom::st_make_valid’ when loading ‘tmap’
Found the following files/directories:
  ‘MD_display.csv’ ‘kola.c_COUNTRY_Cu.csv’
  ‘kola.c_COUNTRY_Cu_fences.txt’ ‘ogrady.mvalloc_mvalloc.csv’
  ‘sind.mat2open_NGR_summary.csv’ ‘sind.save_PC-loadings.csv’
  ‘sind.save_PC-scores.csv’ ‘test.save.mvalloc_mvalloc.csv’
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_new_custom_connection’,
    ‘Rf_EncodeInteger’, ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.quick_fetch: no visible global function definition for ‘POST’
.quick_fetch: no visible global function definition for ‘add_headers’
.quick_fetch: no visible global function definition for
  ‘stop_for_status’
.quick_fetch: no visible global function definition for ‘content’
fetch_healthdata: no visible binding for global variable ‘resources’
fetch_healthdata : <anonymous>: no visible binding for global variable
  ‘filters’
Undefined global functions or variables:
  POST add_headers content filters resources stop_for_status
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ECL: no visible global function definition for ‘new’
ECLDataset: no visible global function definition for ‘new’
ECLDedUp: no visible global function definition for ‘new’
ECLDistribute: no visible global function definition for ‘new’
ECLIterate: no visible global function definition for ‘new’
ECLJoin: no visible global function definition for ‘new’
ECLOutput: no visible global function definition for ‘new’
ECLProject: no visible global function definition for ‘new’
ECLRecord: no visible global function definition for ‘new’
ECLRollUp: no visible global function definition for ‘new’
ECLSort: no visible global function definition for ‘new’
ECLTOPN: no visible global function definition for ‘new’
ECLTable: no visible global function definition for ‘new’
ECLTransform: no visible global function definition for ‘new’
eclDirectCall: no visible global function definition for ‘postForm’
parseResults: no visible global function definition for ‘xmlRoot’
parseResults: no visible global function definition for ‘xmlTreeParse’
parseResults: no visible global function definition for ‘getNodeSet’
parseResults: no visible global function definition for ‘xmlGetAttr’
parseResults: no visible global function definition for ‘xmlValue’
parseResults: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  getNodeSet new postForm write.table xmlGetAttr xmlRoot xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
FusedQDA : <anonymous>: no visible global function definition for ‘cov’
RidgeFused: no visible binding for global variable ‘cov2cor’
RidgeFusedCV : <anonymous>: no visible global function definition for
  ‘cov’
SSRidgeFused : <anonymous>: no visible global function definition for
  ‘cov’
Undefined global functions or variables:
  cov cov2cor
Consider adding
  importFrom("stats", "cov", "cov2cor")
to your NAMESPACE file.
ridit.raw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
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.
plot.ijzip: no visible global function definition for ‘axis’
read.ijzip: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  axis unzip
Consider adding
  importFrom("graphics", "axis")
  importFrom("utils", "unzip")
to your NAMESPACE file.
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘mtcars.txt’
desmat.sanitize: no visible global function definition for ‘aggregate’
dispdist: no visible global function definition for ‘quantile’
dispdist: no visible global function definition for ‘hist’
dispdist: no visible global function definition for ‘lines’
estate: no visible global function definition for ‘weighted.mean’
estate: no visible global function definition for ‘lm’
genperms: no visible global function definition for ‘combn’
genprobexact: no visible global function definition for ‘ave’
invert.ci: no visible global function definition for ‘quantile’
invert.ci: no visible global function definition for ‘uniroot’
omni.ate: no visible global function definition for ‘hist’
omni.ate: no visible global function definition for ‘lines’
omni.ate: no visible global function definition for ‘quantile’
resresplot: no visible global function definition for ‘lm’
resresplot: no visible global function definition for ‘symbols’
resresplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline aggregate ave combn hist lines lm quantile symbols uniroot
  weighted.mean
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "symbols")
  importFrom("stats", "aggregate", "ave", "lm", "quantile", "uniroot",
             "weighted.mean")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(riskclustr)
  > 
  > test_check("riskclustr")
  ── 1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_message(...)
    6. riskclustr::optimal_kmeans_d(...)
    7. base::lapply(...)
    8. riskclustr:::FUN(X[[i]], ...)
    9. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   12. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   13. tibble:::tbl_subset_row(xo, i = i, i_arg)
   14. tibble:::vectbl_as_row_index(i, x, i_arg)
   15. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   22. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ── 2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_equal(...)
    4. riskclustr::optimal_kmeans_d(...)
    5. base::lapply(...)
    6. riskclustr:::FUN(X[[i]], ...)
    7. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   10. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   11. tibble:::tbl_subset_row(xo, i = i, i_arg)
   12. tibble:::vectbl_as_row_index(i, x, i_arg)
   13. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   20. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 26 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_kmeans_d.R#49) 
  2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_kmeans_d.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘calculate_d.Rmd’ using rmarkdown
--- finished re-building ‘calculate_d.Rmd’

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

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

--- re-building ‘factor_pvalue.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 ‘factor_pvalue.Rmd’

--- re-building ‘optimal_d.Rmd’ using rmarkdown
Quitting from lines 36-46 (optimal_d.Rmd) 
Error: processing vignette 'optimal_d.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘optimal_d.Rmd’

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

Error: Vignette re-building failed.
Execution halted
KM.plot: no visible global function definition for ‘lines’
SchoenSmooth: no visible global function definition for ‘lm’
llCoxReg: no visible binding for global variable ‘time’
risksetAUC: no visible global function definition for ‘abline’
risksetROC: no visible global function definition for ‘abline’
weightedKM: no visible binding for global variable ‘time’
Undefined global functions or variables:
  abline lines lm time
Consider adding
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Alg2: no visible global function definition for ‘uniroot’
Alg3: no visible global function definition for ‘optim’
NVCopula: no visible global function definition for ‘rnorm’
NVCopula: no visible global function definition for ‘rgamma’
NVCopula: no visible global function definition for ‘var’
NVCopula: no visible global function definition for ‘cov’
NVCopula: no visible global function definition for ‘qnorm’
NVCopulaMT: no visible global function definition for ‘rnorm’
NVCopulaMT: no visible global function definition for ‘rgamma’
NVCopulaMT: no visible global function definition for ‘var’
NVCopulaMT: no visible global function definition for ‘cov’
NVCopulaMT: no visible global function definition for ‘qnorm’
R2X: no visible global function definition for ‘write.table’
ReturnCopula: no visible global function definition for ‘qt’
ReturnCopula: no visible global function definition for ‘pt’
SISCopula: no visible global function definition for ‘runif’
SISCopula: no visible global function definition for ‘qnorm’
SISCopula: no visible global function definition for ‘rnorm’
SISCopula: no visible global function definition for ‘qgamma’
SISCopula: no visible global function definition for ‘var’
SISCopula: no visible global function definition for ‘cov’
SISCopulaMT: no visible global function definition for ‘runif’
SISCopulaMT: no visible global function definition for ‘qnorm’
SISCopulaMT: no visible global function definition for ‘rnorm’
SISCopulaMT: no visible global function definition for ‘qgamma’
SISCopulaMT: no visible global function definition for ‘var’
SISCopulaMT: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optim pt qgamma qnorm qt rgamma rnorm runif uniroot var
  write.table
Consider adding
  importFrom("stats", "cov", "optim", "pt", "qgamma", "qnorm", "qt",
             "rgamma", "rnorm", "runif", "uniroot", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
Packages in Depends field not imported from:
  ‘compiler’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NumConv: no visible global function definition for ‘pchip’
NumConv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘pchip’
NumDeconv : error_function: no visible global function definition for
  ‘pchip’
NumDeconv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘optim’
RivivcA: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmpfun lm optim pchip
Consider adding
  importFrom("stats", "lm", "optim")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘getsp.class’ ‘getsp.java’ ‘install-sh’ ‘jri’ ‘version’
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)
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘Barplot’ ‘Boxplot’ ‘BubblePlot’ ‘CircularFV’ ‘DataTable’
  ‘Dendrogram’ ‘DensityPlot’ ‘Heatmap’ ‘HivePlot’ ‘Network’ ‘Piechart’
  ‘Scatter3d’ ‘ScatterPlot’ ‘Surface3d’ ‘SymHeatmap’ ‘WordCloud’
Running examples in ‘rJST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_parameter
> ### Title: Get parameter from (reversed) JST results
> ### Aliases: get_parameter
> 
> ### ** Examples
> 
> data <- quanteda::dfm(quanteda::data_corpus_irishbudget2010)
Error: 'data_corpus_irishbudget2010' is not an exported object from 'namespace:quanteda'
Execution halted
'library' or 'require' call to ‘rJava’ which was already attached by Depends.
  Please remove these calls from your code.
Package vignette with placeholder title ‘Vignette Title’:
  ‘rKIN_Introduction.Rmd’
cv.coef: no visible global function definition for ‘sd’
normalize.softmax: no visible global function definition for ‘plogis’
plot.rknnSupport: no visible global function definition for ‘dotchart’
predicted: no visible global function definition for ‘influence’
predicted: no visible global function definition for ‘fitted’
predicted: no visible global function definition for ‘resid’
pressresid: no visible global function definition for ‘influence’
pressresid: no visible global function definition for ‘resid’
Undefined global functions or variables:
  dotchart fitted influence plogis resid sd
Consider adding
  importFrom("graphics", "dotchart")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
':::' 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.
Found the following Makefile(s) without a final LF:
  src/Makevars.in
Some ‘make’ programs ignore lines not ending in LF.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rlo.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘file.out’
Package in Depends field not imported from: ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘EMSRb_internal’ ‘EM_internal’ ‘PD_internal’
EMSRb_internal: no visible global function definition for ‘qnorm’
EM_internal: no visible global function definition for ‘dnorm’
EM_internal: no visible global function definition for ‘pnorm’
PD_internal: no visible global function definition for ‘qtnorm’
PD_internal: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm pnorm qnorm qtnorm sd
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
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.
Running examples in ‘RmarineHeatWaves-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: detect
> ### Title: Detect heatwaves and cold-spells.
> ### Aliases: detect
> 
> ### ** Examples
> 
> ts_dat <- make_whole(sst_WA)
> res <- detect(ts_dat, climatology_start = "1983-01-01",
+               climatology_end = "2012-12-31")
Error: Assigned data `zoo::na.approx(tDat[59:61, no_NA], maxgap = 1, na.rm = TRUE)` must be compatible with existing data.
ℹ Error occurred for column `doy`.
✖ Can't cast <double[,31]> to <double>.
Can not decrease dimensions.
Backtrace:
    █
 1. └─RmarineHeatWaves::detect(...)
 2.   ├─base::`[<-`(...)
 3.   └─tibble:::`[<-.tbl_df`(...)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::tbl_subassign_row(xj, i, value, value_arg)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
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').
.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.
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
rms.pval: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘rmtl.Rmd’
dWishartSpike: no visible global function definition for ‘dnorm’
pWishartSpike: no visible global function definition for ‘pnorm’
qWishartSpike: no visible global function definition for ‘qnorm’
rWishartSpike: no visible global function definition for ‘qnorm’
rmp: no visible global function definition for ‘runif’
rtw: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘DESeq’ ‘seqinr’ ‘topGO’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘rnaturalearthhires’
well19937.validate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Nnls.trimW : fun1: no visible global function definition for ‘runif’
initM: no visible global function definition for ‘runif’
rnmf: no visible global function definition for ‘txtProgressBar’
rnmf: no visible global function definition for ‘setTxtProgressBar’
see: no visible global function definition for ‘heat.colors’
see: no visible global function definition for ‘colorRampPalette’
see: no visible global function definition for ‘grey’
see: no visible global function definition for ‘par’
see: no visible global function definition for ‘image’
see: no visible global function definition for ‘mtext’
simtum: no visible global function definition for ‘runif’
simtum: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'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.
RobRSVD: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
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.
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.
Packages in Depends field not imported from:
  ‘penalized’ ‘splines’ ‘survival’ ‘survivalROC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot.ROC: no visible global function definition for ‘qnorm’
boot.ROC: no visible global function definition for ‘penalized’
boot.ROC: no visible global function definition for ‘coefficients’
boot.ROC: no visible global function definition for ‘sd’
boot.ROC: no visible global function definition for ‘optL1’
boot.ROCt: no visible global function definition for ‘qnorm’
boot.ROCt: no visible global function definition for ‘penalized’
boot.ROCt: no visible global function definition for ‘Surv’
boot.ROCt: no visible global function definition for ‘coefficients’
boot.ROCt: no visible global function definition for ‘sd’
boot.ROCt: no visible global function definition for ‘survivalROC’
boot.ROCt: no visible global function definition for ‘optL1’
Undefined global functions or variables:
  Surv coefficients optL1 penalized qnorm sd survivalROC
Consider adding
  importFrom("stats", "coefficients", "qnorm", "sd")
to your NAMESPACE file.
Running examples in ‘ROCt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EUt2
> ### Title: Optimal Cut-Off Estimation Of A Prognostic Marker (The Two
> ###   Groups Are observed).
> ### Aliases: EUt2
> ### Keywords: utility
> 
> ### ** Examples
> 
> 
> # import and attach the data example
> 
> data(csl)
> csl <- csl[order(csl$id, csl$time),]
> csl$ordre <-0
> for (i in unique(csl$id)) {csl$ordre[csl$id==i] <- 1:sum(csl$id==i)}
> 
> csl$ttt[csl$treat==0]<-"A"
> csl$ttt[csl$treat==1]<-"B"
> 
> csl0 <- csl[csl$ordre==1,]
> csl0<-csl0[,c(1,4,5,14,9)]
> 
> # the expected utility function for a prognostic up to 8 years
> 
> EUt.obj <- EUt2(csl0$eventT, csl0$dc, csl0$prot.base, treatment= csl0$ttt,
+  pro.time=8, u.A0=0.75*0.95, u.A1=0, u.B0=0.75, u.B1=0)
Warning in EUt2(csl0$eventT, csl0$dc, csl0$prot.base, treatment = csl0$ttt,  :
  NAs introduced by coercion
Warning in max(tab.res$utility, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(tab.res$utility, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(event[who2]) :
  no non-missing arguments to max; returning -Inf
Error in rep(1:nstrat, x$strata) : invalid 'times' argument
Calls: EUt2 -> meanALL -> summary -> summary.survfit -> survmean
Execution halted
NPROCwoGS: no visible global function definition for ‘quantile’
NPROCwoGS : rdirichlet: no visible global function definition for
  ‘rgamma’
NPROCwoGS: no visible global function definition for ‘rbinom’
NPROCwoGS: no visible global function definition for ‘rbeta’
NPROCwoGS: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  quantile rbeta rbinom rgamma
Consider adding
  importFrom("stats", "quantile", "rbeta", "rbinom", "rgamma")
to your NAMESPACE file.
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.
ROSE.eval: no visible global function definition for ‘methods’
ROSE.eval: no visible binding for global variable ‘model.frame’
ROSE.eval: no visible binding for global variable ‘predict’
adj.formula: no visible global function definition for ‘terms’
adj.formula: no visible global function definition for ‘as.formula’
omnibus.balancing: no visible binding for global variable ‘model.frame’
ou.sampl: no visible global function definition for ‘rbinom’
over.sampl: no visible global function definition for ‘rbinom’
roc.curve: no visible global function definition for ‘lines’
roc.curve: no visible global function definition for ‘abline’
rose.real: no visible binding for global variable ‘sd’
rose.real: no visible global function definition for ‘sd’
rose.real: no visible global function definition for ‘rnorm’
rose.sampl: no visible global function definition for ‘rbinom’
under.sampl: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  abline as.formula lines methods model.frame predict rbinom rnorm sd
  terms
Consider adding
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
bestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
mfix : m4m: no visible global function definition for ‘median’
rrfa: no visible global function definition for ‘predict’
rrfb: no visible global function definition for ‘predict’
rrfc1: no visible global function definition for ‘predict’
rrfc2: no visible global function definition for ‘predict’
rrfc3: no visible global function definition for ‘predict’
rrfc4: no visible global function definition for ‘predict’
rrfc5 : regdat: no visible global function definition for ‘predict’
rrfc5 : regdat: no visible global function definition for ‘glm’
rrfc5: no visible global function definition for ‘predict’
rrfc6: no visible global function definition for ‘predict’
rrfc7: no visible global function definition for ‘predict’
rrfd: no visible global function definition for ‘predict’
rrfe : rdms: no visible global function definition for ‘rbinom’
rrfe: no visible global function definition for ‘predict’
Undefined global functions or variables:
  glm median predict rbinom
Consider adding
  importFrom("stats", "glm", "median", "predict", "rbinom")
to your NAMESPACE file.
Running examples in ‘roughrf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mfix
> ### Title: Four single imputation methods
> ### Aliases: mfix
> 
> ### ** Examples
> 
> dat=data.frame(continuous=c(1,2,3,4,5),categorical=c('a','a','a','a','b'))
> dat[2,]=NA
> dat
  continuous categorical
1          1           a
2         NA        <NA>
3          3           a
4          4           a
5          5           b
> summary(dat)
   continuous   categorical       
 Min.   :1.00   Length:5          
 1st Qu.:2.50   Class :character  
 Median :3.50   Mode  :character  
 Mean   :3.25                     
 3rd Qu.:4.25                     
 Max.   :5.00                     
 NA's   :1                        
> mfix(dat,1)[2,]  #median/mode imputation
Error in mmfix.data.frame(x) : mfix only works for numeric or factor
Calls: mfix -> mmfix -> mmfix.data.frame
Execution halted
.computeValueReduct: no visible global function definition for ‘combn’
.findAllReductsFromCore: no visible global function definition for
  ‘combn’
.findFirstReductsFromCore: no visible global function definition for
  ‘combn’
.findSmallestReductFamilyFromCore: no visible global function
  definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
royston.test: no visible global function definition for ‘shapiro.test’
royston.test: no visible global function definition for ‘cor’
royston.test: no visible global function definition for ‘qnorm’
royston.test: no visible global function definition for ‘pnorm’
royston.test: no visible global function definition for ‘cov’
royston.test: no visible global function definition for ‘mahalanobis’
royston.test: no visible global function definition for ‘qqplot’
royston.test: no visible global function definition for ‘qchisq’
royston.test: no visible global function definition for ‘ppoints’
royston.test: no visible global function definition for ‘abline’
royston.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
Package in Depends field not imported from: ‘hash’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
P: no visible global function definition for ‘has.key’
get_rand_int: no visible global function definition for ‘runif’
last: no visible global function definition for ‘tail’
rand_partitions: no visible global function definition for ‘hash’
Undefined global functions or variables:
  has.key hash runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
evalMedian: no visible global function definition for ‘xtabs’
evalMode: no visible global function definition for ‘xtabs’
rpartScore: no visible global function definition for ‘model.extract’
rpartScore: no visible global function definition for ‘var’
rpartScore: no visible binding for global variable ‘var’
splitAbs: no visible global function definition for ‘xtabs’
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
'library' or 'require' call to ‘RODBC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
rpart.rules.push: no visible global function definition for ‘sqlSave’
rpart.rules.table : <anonymous>: no visible global function definition
  for ‘setNames’
rpart.subrules.table : <anonymous>: no visible global function
  definition for ‘setNames’
Undefined global functions or variables:
  setNames sqlSave
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘codelists.Rmd’
'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
Found the following files/directories:
  ‘Rpdb.pdb’
Found the following files/directories:
  ‘mygraph.eps’ ‘mygraph.png’ ‘mygraph.tex’
Found the following files/directories:
  ‘Datasample.mads.txt’ ‘Datasample.medians.txt’ ‘control_plot.pdf’
  ‘correlation_plot.pdf’ ‘dataIII_qqplot.pdf’ ‘kruskalBoxplot.pdf’
  ‘plotQC.pdf’ ‘simpleBoxplot.pdf’ ‘wilcoxonBoxplot.pdf’
but_last: no visible global function definition for ‘head’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
preview_frames: no visible global function definition for ‘str’
print.EprimeFrame: no visible global function definition for ‘str’
print.FrameList: no visible global function definition for ‘str’
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘rpsychi-Ex.R’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rPython.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘rjpod’
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
Packages in Depends field not imported from:
  ‘glasso’ ‘matrixcalc’ ‘mvoutlier’ ‘pcaPP’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
rrest: no visible binding for global variable ‘glasso’
rrest: no visible global function definition for ‘pcout’
rrest: no visible global function definition for ‘var’
rrest: no visible global function definition for ‘mahalanobis’
rrlda : centerObservations: no visible global function definition for
  ‘l1median_NLM’
rrlda : df.L2glasso: no visible global function definition for
  ‘duplication.matrix’
rrlda : alt.df.L2glasso: no visible global function definition for
  ‘lower.triangle’
Undefined global functions or variables:
  duplication.matrix glasso l1median_NLM lower.triangle mahalanobis
  pcout var
Consider adding
  importFrom("stats", "mahalanobis", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
Package vignette with placeholder title ‘Vignette Title’:
  ‘rescaling_data.Rmd’
'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.
stripslash: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in ‘RSDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VeterinaryData
> ### Title: Symbolic interval data example
> ### Aliases: VeterinaryData
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(VeterinaryData)
> VeterinaryData
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'warningc' not found
Calls: <Anonymous> ... do.call -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 40-42 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
object ‘warningc’ not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
convexhull: no visible global function definition for ‘chull’
convexhull: no visible global function definition for ‘rnorm’
drawcompletegraph: no visible global function definition for ‘segments’
getbag: no visible global function definition for ‘chull’
getbag: no visible global function definition for ‘polygon’
getbag: no visible global function definition for ‘points’
inflate: no visible global function definition for ‘rnorm’
rsmed: no visible global function definition for ‘runif’
rsplot: no visible global function definition for ‘chull’
rsplot: no visible global function definition for ‘polygon’
rsplot: no visible global function definition for ‘points’
rsrings: no visible global function definition for ‘chull’
rsrings: no visible global function definition for ‘polygon’
rsrings: no visible global function definition for ‘points’
rstinterval: no visible global function definition for ‘runif’
rstinterval: no visible global function definition for ‘rnorm’
rstinterval: no visible global function definition for ‘chull’
rstinterval: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  chull points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘Rcompression’
rsem: no visible global function definition for ‘write.table’
rsem.Ascov: no visible global function definition for ‘qchisq’
rsem.Ascov: no visible global function definition for ‘pchisq’
rsem.emmusig: no visible global function definition for ‘na.omit’
rsem.emmusig: no visible global function definition for ‘qchisq’
rsem.emmusig: no visible global function definition for ‘pchisq’
rsem.fit: no visible global function definition for ‘pchisq’
rsem.fit: no visible global function definition for ‘pf’
rsem.print : print.estimate: no visible global function definition for
  ‘pnorm’
rsem.weight: no visible global function definition for ‘qchisq’
rsem.weight: no visible global function definition for ‘pchisq’
semdiag.call.eqs: no visible global function definition for
  ‘write.table’
semdiag.read.eqs: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  na.omit pchisq pf pnorm qchisq read.fwf write.table
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pf", "pnorm", "qchisq")
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Rserv.c:2150:3: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
  Rserv.c:816:4: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:817:3: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:820:22: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:821:22: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:372:2: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:375:3: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2342:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3351:4: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3358:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2088:7: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2090:7: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  oc.c:47:5: warning: ‘RAND_pseudo_bytes’ is deprecated [-Wdeprecated-declarations]
  standalone.c:220:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rserve.Rcheck/00install.out’ for details.
Non-standard files/directories found at top level:
  ‘aclocal.m4’ ‘clients’ ‘clients.txt’ ‘version’
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
addNoisyCopies: no visible global function definition for ‘rnorm’
eta: no visible global function definition for ‘var’
gaussClassifier: no visible global function definition for ‘runif’
getSigma: no visible global function definition for ‘sd’
getSigma: no visible binding for global variable ‘sd’
sfaClassify: no visible global function definition for ‘rainbow’
sfaClassify: no visible global function definition for ‘par’
sfaClassify: no visible global function definition for ‘points’
sfaClassify: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
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.
Found the following files/directories:
  ‘Database’ ‘rSQM.yaml’ ‘rSQM_Sample_Project’ ‘sample_script.R’
Package vignette with placeholder title ‘Vignette Title’:
  ‘main-vignette.Rmd’
Found the following files/directories:
  ‘Rplots.svg’
Found the following files/directories:
  ‘bitmap.jpg’ ‘bitmap.png’ ‘bitmap.webp’ ‘out.pdf’ ‘out.png’ ‘out.ps’
  ‘out.svg’
Found the following files/directories:
  ‘svgplot1.svg’ ‘svgplot10.svg’ ‘svgplot11.svg’ ‘svgplot12.svg’
  ‘svgplot13.svg’ ‘svgplot2.svg’ ‘svgplot3.svg’ ‘svgplot4.svg’
  ‘svgplot5.svg’ ‘svgplot6.svg’ ‘svgplot7.svg’ ‘svgplot8.svg’
  ‘svgplot9.svg’
Found the following files/directories:
  ‘mapCH2017.rda’
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab

Found the following assignments to the global environment:
File ‘rSymPy/R/sympy.R’:
  assign(".Jython", .jnew("org.python.util.PythonInterpreter"), 
    .GlobalEnv)
  assign(".Jython", rJython(modules = system.file("Lib", package = "rSymPy")), 
    .GlobalEnv)
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.
plotGLCM: no visible global function definition for ‘points’
Undefined global functions or variables:
  points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Skylark_example.Rmd’ using rmarkdown
Quitting from lines 171-172 (Skylark_example.Rmd) 
Error: processing vignette 'Skylark_example.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Skylark_example.Rmd’

--- re-building ‘rtrim_2_extensions.Rmd’ using rmarkdown
Quitting from lines 261-264 (rtrim_2_extensions.Rmd) 
Error: processing vignette 'rtrim_2_extensions.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘rtrim_2_extensions.Rmd’

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

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

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

--- re-building ‘TRIM_methods_v2.pdf.asis’ using asis
--- finished re-building ‘TRIM_methods_v2.pdf.asis’

SUMMARY: processing the following files failed:
  ‘Skylark_example.Rmd’ ‘rtrim_2_extensions.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘Tsttwalk.dat’
Running examples in ‘rubias-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write_gsi_sim_mixture
> ### Title: Write a mixture data frame to gsi_sim format baseline and
> ###   repunits file
> ### Aliases: write_gsi_sim_mixture
> 
> ### ** Examples
> 
> # this writes to file prefix "mixfile" in a temporary directory
> dd <- tempdir()
> prefix <- file.path(dd, "mixfile")
> 
> # print that
> prefix
[1] "/home/hornik/tmp/scratch/RtmpXmv4Dj/mixfile"
> 
> # note that in practice you will probably want to specify
> # your own directory...
> 
> # run the function
> write_gsi_sim_mixture(chinook_mix, 5, prefix)
Error: Assigned data `0` must be compatible with existing data.
ℹ Error occurred for column `repunit`.
✖ No common type for `value` <double> and `x` <character>.
Backtrace:
    █
 1. └─rubias::write_gsi_sim_mixture(chinook_mix, 5, prefix)
 2.   ├─base::`[<-`(`*tmp*`, is.na(mix), value = 0)
 3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, is.na(mix), value = 0)
 4.     └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(value))
 5.       └─base::tryCatch(...)
 6.         └─base:::tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
Execution halted
Found the following files/directories:
  ‘results’
Found the following files/directories:
  ‘somefile.xml’
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.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
  configure.in:22: warning: underquoted definition of AC_PROG_R
  configure.in:22:   run info Automake 'Extending aclocal'
  configure.in:22:   or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal
  configure.in:86: warning: the serial number must appear before any macro definition
  configure.in:362: warning: the serial number must appear before any macro definition
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.
check_ISO_code: no visible binding for global variable ‘NoAm_country’
check_ISO_code: no visible binding for global variable ‘SoAm_country’
check_ISO_code: no visible binding for global variable ‘Oceana_country’
check_ISO_code: no visible binding for global variable ‘Africa_country’
check_ISO_code: no visible binding for global variable ‘Asia_country’
check_ISO_code: no visible binding for global variable ‘Eur_country’
climate_map: no visible binding for global variable ‘data’
date_correct: no visible global function definition for ‘tail’
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for ‘na.omit’
RWBP.default: no visible global function definition for ‘kmeans’
RWBP.formula: no visible global function definition for ‘model.extract’
predict.RWBP: no visible global function definition for ‘head’
Undefined global functions or variables:
  head kmeans model.extract na.omit
Consider adding
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
weblogo: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Found the following files/directories:
  ‘RWebLogo.pdf’ ‘RWebLogo.png’
.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.
flemming.plot: no visible global function definition for ‘par’
flemming.plot: no visible global function definition for ‘segments’
flemming.plot: no visible global function definition for ‘text’
flemming.plot : triax.segments: no visible global function definition
  for ‘segments’
legend.bubbles: no visible global function definition for ‘quantile’
legend.bubbles: no visible global function definition for ‘legend’
other.methods: no visible global function definition for ‘quantile’
pejrup.plot: no visible global function definition for ‘par’
pejrup.plot: no visible global function definition for ‘segments’
pejrup.plot: no visible global function definition for ‘text’
pejrup.plot : triax.segments: no visible global function definition for
  ‘segments’
pejrup.plot: no visible global function definition for ‘legend’
rysgran.plot: no visible global function definition for ‘par’
rysgran.plot: no visible global function definition for ‘text’
rysgran.plot: no visible global function definition for ‘points’
rysgran.plot: no visible global function definition for ‘abline’
rysgran.plot: no visible global function definition for ‘mtext’
rysgran.ternary: no visible global function definition for ‘par’
rysgran.ternary: no visible global function definition for ‘points’
rysgran.ternary: no visible global function definition for ‘text’
shepard.plot: no visible global function definition for ‘par’
shepard.plot: no visible global function definition for ‘segments’
shepard.plot: no visible global function definition for ‘text’
shepard.plot : triax.segments: no visible global function definition
  for ‘segments’
shepard.plot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend mtext par points quantile segments text
Consider adding
  importFrom("graphics", "abline", "legend", "mtext", "par", "points",
             "segments", "text")
  importFrom("stats", "quantile")
to your NAMESPACE file.
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.
CV.Epidemic.Vn: no visible global function definition for ‘uniroot’
CV.Epidemic.Wn: no visible global function definition for ‘uniroot’
G.alfa: no visible global function definition for ‘dchisq’
Graf.Diagnostic: no visible global function definition for ‘stepfun’
Graf.Diagnostic: no visible global function definition for ‘title’
Graf.Diagnostic: no visible global function definition for ‘quantile’
Graf.Diagnostic: no visible global function definition for ‘legend’
Graf.Diagnostic: no visible global function definition for ‘arrows’
Graf.Diagnostic: no visible global function definition for ‘par’
Plot.ll: no visible global function definition for ‘segments’
Plot.ll: no visible global function definition for ‘axis’
SemiparChangePoint: no visible global function definition for ‘glm’
SemiparChangePoint: no visible binding for global variable ‘binomial’
SemiparChangePoint: no visible global function definition for
  ‘glm.control’
SemiparChangePoint: no visible global function definition for ‘coef’
Sn.alfa : tempfun: no visible global function definition for ‘dchisq’
Sn.alfa : d.tempfun: no visible global function definition for ‘dchisq’
Zn.alfa : tempfun: no visible global function definition for ‘dchisq’
Zn.alfa : d.tempfun: no visible global function definition for ‘dchisq’
cumsum.test: no visible global function definition for ‘var’
p.OneChange : tempfun: no visible global function definition for
  ‘dchisq’
p.OneChange: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  arrows axis binomial coef dchisq glm glm.control legend par quantile
  segments stepfun title uniroot var
Consider adding
  importFrom("graphics", "arrows", "axis", "legend", "par", "segments",
             "title")
  importFrom("stats", "binomial", "coef", "dchisq", "glm", "glm.control",
             "quantile", "stepfun", "uniroot", "var")
to your NAMESPACE file.
fit.saery.AR1: no visible global function definition for ‘qnorm’
fit.saery.MA1: no visible global function definition for ‘qnorm’
fit.saery.indep: no visible global function definition for ‘qnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘write.table’
plot.saery: no visible global function definition for ‘devAskNewPage’
plot.saery: no visible global function definition for ‘par’
plot.saery: no visible global function definition for ‘abline’
plot.saery: no visible global function definition for ‘title’
plot.saery: no visible global function definition for ‘axis’
plot.saery: no visible global function definition for ‘lines’
plot.saery: no visible global function definition for ‘legend’
pvalue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par pnorm qnorm rnorm title
  write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package in Depends field not imported from: ‘lpSolveAPI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable ‘gaussian’
glm: no visible global function definition for ‘glm.control’
glm: no visible global function definition for ‘model.response’
glm: no visible global function definition for ‘is.empty.model’
glm: no visible global function definition for ‘model.matrix’
glm: no visible global function definition for ‘model.weights’
glm: no visible global function definition for ‘model.offset’
glm: no visible global function definition for ‘model.extract’
glm: no visible global function definition for ‘glm.fit’
glm: no visible global function definition for ‘.getXlevels’
separator: no visible global function definition for ‘make.lp’
separator: no visible global function definition for ‘set.column’
separator: no visible global function definition for ‘set.rhs’
separator: no visible global function definition for ‘set.constr.type’
separator: no visible global function definition for ‘set.objfn’
separator: no visible global function definition for ‘set.bounds’
separator: no visible global function definition for ‘lp.control’
separator: no visible global function definition for ‘get.variables’
separator: no visible global function definition for ‘set.basis’
separator: no visible global function definition for
  ‘get.dual.solution’
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
propdiff.acc: no visible global function definition for ‘rbeta’
propdiff.acc: no visible global function definition for ‘rbinom’
propdiff.acc: no visible global function definition for ‘pbeta’
propdiff.alc: no visible global function definition for ‘rbeta’
propdiff.alc: no visible global function definition for ‘rbinom’
propdiff.alc: no visible global function definition for ‘qbeta’
propdiff.freq: no visible global function definition for ‘qnorm’
propdiff.mblacc: no visible global function definition for ‘rbeta’
propdiff.mblacc: no visible global function definition for ‘rbinom’
propdiff.mblacc: no visible global function definition for ‘pbeta’
propdiff.mblalc: no visible global function definition for ‘rbeta’
propdiff.mblalc: no visible global function definition for ‘rbinom’
propdiff.mblalc: no visible global function definition for ‘qbeta’
propdiff.mblmodwoc: no visible global function definition for ‘qchisq’
propdiff.mblmodwoc: no visible global function definition for ‘pbeta’
propdiff.mblwoc: no visible global function definition for ‘pbeta’
propdiff.modwoc: no visible global function definition for ‘qchisq’
propdiff.modwoc: no visible global function definition for ‘pbeta’
propdiff.woc: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
GraphBinaryForestPlot: no visible global function definition for
  ‘abline’
GraphBinaryForestPlot: no visible global function definition for ‘text’
GraphContinuousForestPlot: no visible global function definition for
  ‘abline’
GraphContinuousForestPlot: no visible global function definition for
  ‘text’
ImputeBinaryEvents: no visible global function definition for ‘rbinom’
ImputeSMD: no visible global function definition for ‘rnorm’
funnelplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
generate.sample.core: no visible global function definition for
  ‘predict’
mdh: no visible global function definition for ‘model.frame’
mdh: no visible binding for global variable ‘na.fail’
mdh: no visible global function definition for ‘.getXlevels’
mdh: no visible global function definition for ‘quantile’
mdh: no visible global function definition for ‘hist’
predict.mdh: no visible global function definition for ‘model.frame’
samur: no visible global function definition for ‘predict’
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mixer’
Running examples in ‘SanzCircos-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_circos_links
> ### Title: make_circos_links
> ### Aliases: make_circos_links
> 
> ### ** Examples
> 
> 
> links_df <- data.frame(chrom = c(rep("chr1", 5), rep("chr2", 5)),
+ band = c(rep("band1", 3), rep("band2", 2), "band1", rep("band2", 4)),
+ link = c(1, 2, 3, 1, 2, 1, 1, 3, 4, 5),
+ start = c(1, 3, 5, 10, 35, 1, 5, 8, 13, 15),
+ end = c(3, 5, 10, 35, 39, 5, 8, 13, 15, 21))
> 
> links <- make_circos_links(links_df, "chrom", "band", "link", "start", "end", status = TRUE)
Warning: `as.tibble()` is deprecated as of tibble 2.0.0.
Please use `as_tibble()` instead.
The signature and semantics have changed, see `?as_tibble`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: Assigned data `as.character(df[[chromosome_grouping]][i])` must be compatible with existing data.
ℹ Error occurred for column `V2`.
✖ Lossy cast from `value` <character> to `x` <logical>.
* Locations: 1.
Backtrace:
     █
  1. └─SanzCircos::make_circos_links(...)
  2.   ├─dplyr::bind_rows(...)
  3.   │ ├─dplyr:::flatten_bindable(dots_values(...))
  4.   │ └─rlang::dots_values(...)
  5.   └─pbapply::pblapply(...)
  6.     └─base::lapply(X, FUN, ...)
  7.       └─SanzCircos:::FUN(X[[i]], ...)
  8.         ├─base::`[<-`(`*tmp*`, 1, 2, value = "chr1")
  9.         └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 2, value = "chr1")
 10.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 11.             └─tibble:::tbl_subassign_row(xj, i, value, value_arg)
 12.               └─base::tryCatch(...)
 13.                 └─base:::tryCatchList(expr, classes, parentenv, handlers)
 14.                   └
Execution halted
Found the following files/directories:
  ‘exemple.QCM.xml’ ‘exemple.VF.xml’ ‘exemple.affichages.xml’
  ‘exemple.categorie.xml’ ‘exemple.image.xml’ ‘exemple.libre.xml’
  ‘exemple.numerique.xml’ ‘exemple.ouverte.xml’ ‘exemple.qroc.xml’
  ‘exemple.question.xml’ ‘exemple.xml’
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.
SASPECT: no visible global function definition for ‘dbinom’
my.SOnePro: missing arguments not allowed in calls to ‘c’
my.ttest: no visible global function definition for ‘var’
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘SASPECT.result.txt’
Found the following files/directories:
  ‘stateLung-R01.pdf’ ‘stateLung-R01.txt’
loads: no visible global function definition for ‘untar’
saves: no visible global function definition for ‘tar’
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
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.
Found the following files/directories:
  ‘insulin_receptor_IR_beta_pY1146_stats.csv’
  ‘insulin_receptor_exp_dataset.csv’ ‘pe_datasets’ ‘pe_plots’
  ‘ps1_datasets’ ‘ps1_plots’ ‘ps2_datasets’ ‘ps2_plots’ ‘sim_datasets’
  ‘sim_datasets_sum’ ‘sim_plots’
Found the following files/directories:
  ‘tdata_R.label’ ‘tdata_R.out’
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.
Missing or unexported objects:
  ‘Rmosek::mosek_lptoprob’ ‘Rmosek::mosek_qptoprob’
Non-standard file/directory found at top level:
  ‘src-java’
ChooseBest: no visible global function definition for ‘head’
GetScores: no visible global function definition for ‘write.table’
ReportTable: no visible binding for global variable ‘sd’
ReportTable: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
plot.scair: no visible global function definition for ‘par’
plot.scair: no visible global function definition for ‘points’
plot.scar: no visible global function definition for ‘par’
plot.scar: no visible global function definition for ‘points’
predict.scair: no visible global function definition for ‘approx’
predict.scar: no visible global function definition for ‘approx’
scair: no visible global function definition for ‘gaussian’
scair: no visible global function definition for ‘runif’
scair: no visible global function definition for ‘rnorm’
scar: no visible global function definition for ‘gaussian’
scar: no visible global function definition for ‘glm.fit’
scar: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx gaussian glm.fit par points rnorm runif
Consider adding
  importFrom("graphics", "par", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘buildtree.Rmd’
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘schoolmath/R/prime.factor.R’:
  data(primlist)
See section ‘Good practice’ in ‘?data’.
score.GGUM: no visible global function definition for ‘dnorm’
score.GGUM: no visible global function definition for ‘hist’
score.GGUM: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘EAP_est1.txt’
CreatePssm: no visible binding for global variable ‘training’
Undefined global functions or variables:
  training
'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.
Found the following calls to attach():
File ‘scriptests/R/source.pkg.R’:
  attach(NULL, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
  attach(envir, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘untitled_consensus_cluster’
Running ‘test-all.R’ [6s/10s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("scrubr")
  Loading required package: scrubr
  ── 1. Error: coord_within works (@test-coords.R#84)  ───────────────────────────
  st_crs(x) == st_crs(y) is not TRUE
  Backtrace:
   1. base::suppressMessages(coord_within(dframe(zz), country = "Israel"))
   3. scrubr::coord_within(dframe(zz), country = "Israel")
   5. sf:::st_join.sf(z, ctry, join = sf::st_within)
   6. sf:::join(x, y, ...)
   7. sf:::st_geos_binop("within", x, y, sparse = sparse, prepared = prepared)
   8. base::stopifnot(st_crs(x) == st_crs(y))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 43 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: coord_within works (@test-coords.R#84) 
  
  Error: testthat unit tests failed
  Execution halted
lahiri.design: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘flush.console’
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘flush.console’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘quantile’
initialize,sdcTargetMatrixClass: no visible global function definition
  for ‘flush.console’
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
.ACF.compute: no visible global function definition for ‘pnorm’
.ACF.compute: no visible global function definition for ‘qnorm’
.ACF.compute: no visible global function definition for ‘pchisq’
.ACF.plot: no visible global function definition for ‘abline’
.ADF.compute: no visible global function definition for ‘qnorm’
.ADF.compute: no visible global function definition for ‘chisq.test’
.ADF.compute: no visible global function definition for ‘qchisq’
.ADF.compute: no visible global function definition for ‘pchisq’
.ADF.plot: no visible global function definition for ‘abline’
.CADF.plot: no visible global function definition for ‘points’
.DeltaADF.plot: no visible global function definition for ‘abline’
.RPADF.compute: no visible global function definition for ‘pchisq’
.RPADF.compute: no visible global function definition for ‘qchisq’
.RPADF.plot: no visible global function definition for ‘abline’
.RPADF.plot: no visible global function definition for ‘rect’
.fmin: no visible global function definition for ‘optimize’
.fobj: no visible global function definition for ‘pchisq’
.gen.plot: no visible global function definition for ‘axis’
.gen.plot: no visible global function definition for ‘box’
.gen.plot: no visible global function definition for ‘abline’
.lcv: no visible global function definition for ‘bw.nrd0’
.lcv: no visible global function definition for ‘nlm’
ADF: no visible binding for global variable ‘p.adjust.methods’
ADF: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  abline axis box bw.nrd0 chisq.test nlm optimize p.adjust
  p.adjust.methods pchisq pnorm points qchisq qnorm rect
Consider adding
  importFrom("graphics", "abline", "axis", "box", "points", "rect")
  importFrom("stats", "bw.nrd0", "chisq.test", "nlm", "optimize",
             "p.adjust", "p.adjust.methods", "pchisq", "pnorm", "qchisq",
             "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘MC p-value.ps’ ‘Output.csv’ ‘Rh.ps’ ‘Th.ps’ ‘dataratio .Rdata’
  ‘featuresRmax.csv’ ‘featuresT.csv’
dimplot: no visible global function definition for ‘par’
dimplot: no visible global function definition for ‘barplot’
dimplot: no visible global function definition for ‘axis’
find.traj: no visible global function definition for ‘flush.console’
nullprob: no visible global function definition for ‘pbinom’
pbox: no visible global function definition for ‘rect’
pbox: no visible global function definition for ‘par’
prim.traj: no visible global function definition for ‘flush.console’
prim.trajauto: no visible global function definition for
  ‘flush.console’
resampstats: no visible binding for global variable ‘sd’
scatterbox: no visible binding for global variable ‘box’
sd.start: no visible global function definition for ‘read.csv’
sd.start: no visible global function definition for ‘par’
sd.start: no visible global function definition for ‘graphics.off’
sd.start: no visible global function definition for ‘hist’
sd.start: no visible global function definition for ‘plot.ecdf’
sd.start: no visible global function definition for ‘write.csv’
sd.start: no visible global function definition for ‘flush.console’
trajplot: no visible global function definition for ‘points’
trajplot: no visible global function definition for ‘flush.console’
trajplot: no visible global function definition for ‘lm’
trajplot: no visible global function definition for ‘predict.lm’
trajplot: no visible global function definition for ‘identify’
Undefined global functions or variables:
  axis barplot box flush.console graphics.off hist identify lm par
  pbinom plot.ecdf points predict.lm read.csv rect sd write.csv
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "axis", "barplot", "box", "hist", "identify",
             "par", "points", "rect")
  importFrom("stats", "lm", "pbinom", "plot.ecdf", "predict.lm", "sd")
  importFrom("utils", "flush.console", "read.csv", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘demofile.txt’
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sealasso: no visible global function definition for ‘lars’
weight.calc: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
adx: no visible global function definition for ‘abline’
adx: no visible global function definition for ‘legend’
dx: no visible global function definition for ‘abline’
dx: no visible global function definition for ‘legend’
maxd: no visible global function definition for ‘abline’
maxd: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘rainbow’
pc: no visible global function definition for ‘abline’
pc: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘points’
pcu: no visible global function definition for ‘rainbow’
pcu: no visible global function definition for ‘abline’
pcu: no visible global function definition for ‘legend’
pcu: no visible global function definition for ‘points’
rmsd: no visible global function definition for ‘abline’
rmsd: no visible global function definition for ‘legend’
rsd: no visible global function definition for ‘abline’
rsd: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "points")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘seastests-vignette.Rmd’
Packages in Depends field not imported from:
  ‘NADA’ ‘lubridate’ ‘survival’
  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:
  ‘examplePlots0404104041.pdf’ ‘myfit104035.pdf’ ‘myfit104037.pdf’
  ‘myfit104041.pdf’ ‘myfit1_survregCall.txt’ ‘myfit304041.pdf’
  ‘myfit3_survregCall.txt’
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.
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.
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Package suggested but not available for checking: ‘rsbml’
.read.SeerStatTXT: no visible global function definition for
  ‘read.table’
.write.SeerStatTXT: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘testrun1.dic’ ‘testrun1.txt’ ‘testrun2.dic’ ‘testrun2.txt’
Found the following files/directories:
  ‘SM-Ex-H04 GA Co 2010 hatch-ge mean popdens-d15 a60.pdf’ ‘SM-Ex-c30
  Kentucky All Co Map w hatching-defaults.pdf’ ‘SM-Ex-c64 GA
  Counties10-PC age 65 and up-def.pdf’
  ‘SM-Ex-c80-WashBalt-County-CSA-def.pdf’ ‘SM-Ex-s01 States Map of
  Cancer Mortality-defaults.pdf’ ‘SM-Ex-s02 States Map of Cancer
  Mortality-w hatching.pdf’ ‘SM-Ex-sr11 Seer Reg 17 Map stB-A
  srB-D.pdf’ ‘SM-Ex-tr74-WA-Dem-All-Census-Tracts-PCgt65-def.pdf’
  ‘SM-Ex-tr78-WA-Dem-P-Tract-trB-sr.pdf’
Found the following files/directories:
  ‘SeerMapperRegs00-Test-Res.pdf’
Error(s) in re-building vignettes:
  ...
--- re-building ‘segmentr.Rmd’ using rmarkdown
Loading required package: segmentr
Loading required package: tidyr
Loading required package: tibble
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: lubridate

Attaching package: 'lubridate'

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

    date

Loading required package: magrittr

Attaching package: 'magrittr'

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

    extract

Loading required package: purrr

Attaching package: 'purrr'

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

    set_names

Killed
get.infectiousness: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
get_statistics_from_file: no visible global function definition for
  ‘read.csv’
glm_anova: no visible global function definition for ‘aov’
glm_anova: no visible global function definition for ‘glm’
glm_anova: no visible global function definition for ‘gaussian’
glm_anova: no visible global function definition for ‘anova’
glm_anova: no visible global function definition for ‘quasipoisson’
glm_anova: no visible global function definition for ‘sd’
glm_anova: no visible global function definition for ‘p.adjust’
ttest_cohens_d: no visible global function definition for ‘t.test’
ttest_cohens_d: no visible global function definition for ‘sd’
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘expression.csv’ ‘group.csv’
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of ‘deriv’ to ‘derivs’
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta predict runif splinefun uniroot
Consider adding
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: ‘sem’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘Rprof.out’
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.
'library' or 'require' calls in package code:
  ‘XML’ ‘boot’ ‘sem’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘boot:::const’ ‘stats:::AIC.logLik’ ‘stats:::BIC.logLik’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘addPath.plsm’ ‘endogenous’ ‘predecessors’ ‘qSquared’ ‘reorder’
  ‘resempls’ ‘residuals.sempls’
Package vignette with placeholder title ‘Vignette Title’:
  ‘semPower.Rmd’
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-package-SEMrushR-.Rmd’
.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.
'library' or 'require' call to ‘rtiff’ which was already attached by Depends.
  Please remove these calls from your code.
gconv: no visible global function definition for ‘convolve’
sens.analysis.aberrant.rank: no visible global function definition for
  ‘pnorm’
sens.analysis.mh: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
mscorev: no visible global function definition for ‘quantile’
senmwCI : funcCI: no visible global function definition for ‘qnorm’
senmwCI : funcCI2: no visible global function definition for ‘qnorm’
separable1k: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for ‘gray’
sensitivitySGD: no visible global function definition for ‘tail’
sensitivitySGL: no visible global function definition for ‘tail’
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
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.
Found the following files/directories:
  ‘total’
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.

Found the following calls to attach():
File ‘session/R/session.R’:
  attach(sub("file:", "", i))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘RSession.Rda’
setpath: no visible global function definition for ‘cov’
setpath: no visible global function definition for ‘median’
setpath: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for ‘runif’
random.number.test: no visible global function definition for ‘rnorm’
setRNG: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: ‘loomR’
Unknown package ‘SDMTools’ in Rd xrefs
'library' or 'require' call to ‘graphics’ which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for ‘qnorm’
severity: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
L_exp: no visible global function definition for ‘pnorm’
L_hNV: no visible global function definition for ‘pnorm’
L_trunc: no visible global function definition for ‘pnorm’
L_trunc_mufest: no visible global function definition for ‘pnorm’
dgp: no visible global function definition for ‘runif’
dgp: no visible global function definition for ‘rnorm’
eff.sfa: no visible global function definition for ‘predict’
fitted.sfa: no visible global function definition for ‘predict’
predict.sfa: no visible global function definition for ‘coef’
print.sfa: no visible global function definition for ‘coef’
residuals.sfa: no visible global function definition for ‘fitted’
sfa: no visible global function definition for ‘model.frame’
sfa: no visible global function definition for ‘model.response’
sfa.fit: no visible global function definition for ‘lm’
sfa.fit: no visible global function definition for ‘resid’
sfa.fit: no visible global function definition for ‘var’
sfa.fit: no visible global function definition for ‘optim’
summary.sfa: no visible global function definition for ‘logLik’
summary.sfa: no visible global function definition for ‘pchisq’
te.eff.sfa: no visible global function definition for ‘residuals’
te.eff.sfa: no visible global function definition for ‘pnorm’
u.sfa: no visible global function definition for ‘residuals’
u.sfa: no visible global function definition for ‘dnorm’
u.sfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
.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.
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.
UQnormalize.count: no visible binding for global variable ‘quantile’
plotNScores: no visible global function definition for ‘par’
plotNScores: no visible global function definition for ‘hist’
plotNScores: no visible global function definition for ‘title’
plotScores: no visible global function definition for ‘par’
plotScores: no visible global function definition for ‘hist’
plotScores: no visible global function definition for ‘title’
sgRSEA: no visible binding for global variable ‘sd’
sgRSEA: no visible global function definition for ‘p.adjust’
sgRSEA.mean: no visible binding for global variable ‘sd’
sgRSEA.mean: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  hist p.adjust par quantile sd title
Consider adding
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "p.adjust", "quantile", "sd")
to your NAMESPACE file.
Running examples in ‘sgRSEA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sgRSEA
> ### Title: Perform a permutation test which computes gene scores and their
> ###   significance
> ### Aliases: sgRSEA
> 
> ### ** Examples
> 
> data(melanoma808)
> dat = UQnormalize(melanoma808, trt=c('PLX7_R1','PLX7_R2'), ctrl=c('D7_R1','D7_R2'))
> results = sgRSEA(dat=dat, multiplier=30)
Error in sum(ifelse(zj >= 0, zj, 0)) : 
  invalid 'type' (character) of argument
Calls: sgRSEA ... Tmaxmean.Null.Tss2 -> T.maxmean -> tapply -> lapply -> FUN
Execution halted
'library' or 'require' call to ‘foreign’ which was already attached by Depends.
  Please remove these calls from your code.
Package suggested but not available for checking: ‘hydromad’
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 vignette with placeholder title ‘Vignette Title’:
  ‘SI.Rmd’
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
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.
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.
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.
Found the following files/directories:
  ‘3_FindHaplo_Example2_modified.txt’
  ‘4_Example3_HapPerPop_Weighted.txt’
  ‘4_Example3_IndelDistanceMatrixMullerMod.txt’
  ‘4_FindHaplo_Example2_modified.txt’ ‘FindHaplo.txt’
  ‘Haplotypes_DefaultNames.txt’ ‘Haplotypes_sequentialNames.txt’
  ‘Interaction.txt’ ‘Modules_summary.txt’
  ‘NINA.ThresholdEstimation.txt’ ‘NINA_Network.pdf’ ‘Network.pdf’
  ‘PercThr Estimation.pdf’ ‘PercThresholdEstimation.txt’
  ‘PercolatedNetwork.pdf’ ‘PopulationDistances.r.txt’ ‘Weighted.txt’
  ‘ex1.fas’ ‘ex2.2.fas’ ‘ex2.fas’ ‘ex2_unique.fas’ ‘ex3.fas’
  ‘simulated_sequences_rep1.fas’ ‘simulated_sequences_rep2.fas’
  ‘simulated_sequences_tips_rep1.fas’
  ‘simulated_sequences_tips_rep2.fas’
dSepAdji: no visible global function definition for ‘as’
dag2cpdagAdj: no visible global function definition for ‘as’
randomDAG: no visible global function definition for ‘rbinom’
structIntervDist: no visible global function definition for ‘as’
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
.cluster: no visible global function definition for ‘kmeans’
.plot.sigclust: no visible global function definition for ‘par’
.plot.sigclust: no visible global function definition for ‘density’
.plot.sigclust: no visible global function definition for ‘runif’
.plot.sigclust: no visible global function definition for ‘dnorm’
.plot.sigclust: no visible global function definition for ‘lines’
.plot.sigclust: no visible global function definition for ‘points’
.plot.sigclust: no visible global function definition for ‘title’
.plot.sigclust: no visible global function definition for ‘text’
.plot.sigclust: no visible global function definition for ‘qnorm’
.plot.sigclust: no visible global function definition for ‘abline’
.plot.sigclust: no visible global function definition for ‘quantile’
.plot.sigclust: no visible global function definition for ‘legend’
.simnull: no visible global function definition for ‘rnorm’
.vareigen: no visible global function definition for ‘mad’
.vareigen: no visible global function definition for ‘cov’
sigclust: no visible global function definition for ‘sd’
sigclust: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Sight.Est: no visible global function definition for ‘glm’
Sight.Est: no visible global function definition for ‘binomial’
Sight.Est: no visible global function definition for ‘coef’
Sight.Est: no visible global function definition for ‘terms’
Sight.Est: no visible binding for global variable ‘binomial’
covtheta: no visible global function definition for ‘cov’
print.sightest: no visible global function definition for ‘qnorm’
summary.sightest: no visible global function definition for ‘qnorm’
vardiff: no visible global function definition for ‘vcov’
vardiff: no visible global function definition for ‘coef’
vardiff: no visible global function definition for ‘terms’
varlog.lam: no visible global function definition for ‘vcov’
varlog.lam: no visible global function definition for ‘coef’
varlog.lam: no visible global function definition for ‘terms’
Undefined global functions or variables:
  binomial coef cov glm qnorm terms vcov
Consider adding
  importFrom("stats", "binomial", "coef", "cov", "glm", "qnorm", "terms",
             "vcov")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘animate.Rmd’ using rmarkdown
--- finished re-building ‘animate.Rmd’

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

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

--- re-building ‘dynamic.Rmd’ using rmarkdown
Quitting from lines 27-45 (dynamic.Rmd) 
Error: processing vignette 'dynamic.Rmd' failed with diagnostics:
Assigned data `runif(15, 500, 750)` must be compatible with existing data.
✖ Existing data has 75 rows.
✖ Assigned data has 15 rows.
ℹ Only vectors of size 1 are recycled.
--- failed re-building ‘dynamic.Rmd’

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

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Package vignette with placeholder title ‘Vignette Title’:
  ‘getting-started.Rmd’
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.
Found the following files/directories:
  ‘ExportFigtree1.tre’
'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.
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.
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include/boost/graph/detail/adjacency_list.hpp:2239:43: warning: ‘p.Edge::color’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SimilaR.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
cumallcausehr: no visible global function definition for ‘integrate’
plotbe: no visible global function definition for ‘lines’
plotbe: no visible global function definition for ‘legend’
plotcph: no visible global function definition for ‘confint’
plotcph: no visible global function definition for ‘abline’
plotcph: no visible global function definition for ‘axis’
plotcph: no visible global function definition for ‘polygon’
plotcph: no visible global function definition for ‘lines’
simCR: no visible global function definition for ‘rnorm’
simEBMT: no visible global function definition for ‘model.matrix’
simexit: no visible global function definition for ‘runif’
simexitinner: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix polygon rnorm
  runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
Found the following files/directories:
  ‘simu.pheno’ ‘usedpars.txt’
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘HISTORY’
Package vignette with placeholder title ‘Vignette Title’:
  ‘SimplifyStats_Vignette.Rmd’
Package in Depends field not imported from: ‘mclust’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for ‘Mclust’
Simpsons: no visible global function definition for ‘lm’
Simpsons: no visible global function definition for ‘abline’
Simpsons: no visible global function definition for ‘par’
Simpsons: no visible global function definition for ‘legend’
Simpsons: no visible global function definition for ‘txtProgressBar’
Simpsons: no visible global function definition for ‘setTxtProgressBar’
Simpsons: no visible global function definition for ‘quantile’
plot.Simpson: no visible global function definition for ‘lm’
plot.Simpson: no visible global function definition for ‘abline’
plot.Simpson: no visible global function definition for ‘par’
plot.Simpson: no visible global function definition for ‘legend’
Undefined global functions or variables:
  Mclust abline legend lm par quantile setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(simrel)
  > 
  > test_check("simrel")
  ── 1. Error: Prepare Design (@test-utils.R#44)  ────────────────────────────────
  Can't join on 'q' x 'q' because of incompatible types (list / list)
  Backtrace:
   1. testthat::expect_identical(prepare_design(opts), dgn)
   3. testthat:::compare.default(act$val, exp$val)
   5. dplyr:::all.equal.tbl_df(x, y, ...)
   6. dplyr:::equal_data_frame(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 169 | SKIPPED: 21 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: Prepare Design (@test-utils.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘crop_device.pdf’
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘abind’ ‘svUnit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for ‘abind’
simSummary_unitTests: no visible global function definition for
  ‘clearLog’
simSummary_unitTests: no visible global function definition for
  ‘runTest’
simSummary_unitTests: no visible global function definition for
  ‘svSuite’
simSummary_unitTests: no visible global function definition for ‘Log’
simSummary_unitTests: no visible global function definition for ‘stats’
simSummary_unitTests: no visible global function definition for
  ‘metadata’
simSummary_unitTests: no visible global function definition for
  ‘errorLog’
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
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.
Found the following files/directories:
  ‘agency.csv’ ‘calendar.csv’ ‘routes.txt’ ‘shapes.txt’
  ‘stop_times.txt’ ‘stops.txt’ ‘translations.txt’ ‘trips.txt’
Found the following files/directories:
  ‘helicopter.pdf’
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
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 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.
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.
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.
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.
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.
Grad.sph: no visible global function definition for ‘dist’
IMDS: no visible global function definition for ‘cmdscale’
IMDS: no visible global function definition for ‘as.dist’
IMDS: no visible global function definition for ‘runif’
IMDS: no visible global function definition for ‘optim’
idistSph: no visible global function definition for ‘dist’
obj.sph: no visible global function definition for ‘dist’
plot.imds: no visible binding for global variable ‘lines’
plot.imds: no visible global function definition for ‘text’
plot.imds: no visible global function definition for ‘rect’
Undefined global functions or variables:
  as.dist cmdscale dist lines optim rect runif text
Consider adding
  importFrom("graphics", "lines", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘corpcor’ ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Fourier2d: no visible global function definition for ‘fft’
kernel2dsmooth: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
Found the following files/directories:
  ‘my_new_social_media_plot.png’
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.
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.
Package in Depends field not imported from: ‘snow’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KS.test: no visible global function definition for ‘quantile’
KS.test : Fgaus: no visible global function definition for ‘pnorm’
KS.test: no visible global function definition for ‘setNames’
cs.test: no visible global function definition for ‘pbinom’
cs.test: no visible global function definition for ‘pnorm’
cs.test: no visible global function definition for ‘setNames’
kde: no visible global function definition for ‘quantile’
kde : Fgaus: no visible global function definition for ‘pnorm’
kde: no visible global function definition for ‘par’
kre: no visible global function definition for ‘quantile’
kre: no visible global function definition for ‘lines’
ns.test: no visible global function definition for ‘complete.cases’
ns.test: no visible global function definition for ‘qnorm’
ns.test: no visible global function definition for ‘pnorm’
ns.test: no visible global function definition for ‘pchisq’
ns.test: no visible global function definition for ‘setNames’
ns.test: no visible global function definition for ‘qt’
quant.test: no visible global function definition for ‘complete.cases’
quant.test: no visible global function definition for ‘pbinom’
quant.test: no visible global function definition for ‘pnorm’
quant.test: no visible global function definition for ‘setNames’
quant.test: no visible global function definition for ‘quantile’
quant.test: no visible global function definition for ‘phyper’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘setNames’
runs.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
Found the following files/directories:
  ‘geneSet.set’ ‘snplistdb.sqlite’
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘mvtnorm’ ‘combinat’
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for ‘chisq.test’
maxsel: no visible global function definition for ‘complete.cases’
maxsel.asymp.test: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘colorspace’ ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.args: no visible global function definition for ‘is’
write.sbams: no visible global function definition for ‘as’
write.sbams: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  as is write.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
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.
Warning: no function found corresponding to methods exports from ‘SoDA’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘base::WHAT’
Packages in Depends field not imported from:
  ‘MASS’ ‘magic’ ‘ppls’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.hnx.B.initialW: no visible global function definition for
  ‘normalize.vector’
get.hnx.B.initialW: no visible global function definition for ‘adiag’
hclust.wrap: no visible global function definition for ‘hclust’
hclust.wrap: no visible global function definition for ‘dist’
hclust.wrap: no visible global function definition for ‘cutree’
my.normdata.gen: no visible global function definition for ‘mvrnorm’
my.normdata.gen: no visible global function definition for ‘rnorm’
odc.clust: no visible binding for global variable ‘kmeans’
odc.cv: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible global function definition for ‘tr’
odc.optimallambda2: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible binding for global variable ‘sd’
sodc.clust: no visible binding for global variable ‘kmeans’
Undefined global functions or variables:
  adiag cutree dist ginv hclust kmeans mvrnorm normalize.vector rnorm
  sd tr
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rnorm",
             "sd")
to your NAMESPACE file.
Ssimpute.als: no visible global function definition for ‘rnorm’
Ssvd.als: no visible global function definition for ‘rnorm’
cs.default: no visible binding for global variable ‘weighted.mean’
simpute.als: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
compileDatabase: no visible global function definition for ‘use_data’
Undefined global functions or variables:
  use_data
Package vignette with placeholder title ‘Vignette Title’:
  ‘SolveRationalMatrixEquation.Rmd’
soma: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
bm: no visible global function definition for ‘rnorm’
bm: no visible global function definition for ‘ts’
fbm: no visible global function definition for ‘fft’
fbm: no visible global function definition for ‘rnorm’
fbm: no visible global function definition for ‘ts’
gbm: no visible global function definition for ‘rnorm’
gbm: no visible global function definition for ‘ts’
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for ‘pbinom’
kfweOrd: no visible global function definition for ‘qnbinom’
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘someMTP’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘somspace.Rmd’
Non-standard files/directories found at top level:
  ‘README.markdown’ ‘build_package.sh’ ‘upload.sh’
Found the following files/directories:
  ‘asc.gif’ ‘bg.gif’ ‘desc.gif’ ‘jquery-1.4.2.js’
  ‘jquery.tablesorter.js’ ‘sample.html’ ‘style.css’
convert_municipality_names: no visible global function definition for
  ‘read.csv’
regression_plot: no visible binding for global variable ‘loess’
regression_plot: no visible global function definition for
  ‘colorRampPalette’
regression_plot: no visible global function definition for
  ‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
  for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
  for ‘pnorm’
regression_plot: no visible global function definition for
  ‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘splineSearch.xls’
Package suggested but not available for checking: ‘SciencesPo’

Package which this enhances but not available for checking: ‘RecordLinkage’
Package suggested but not available for checking: ‘r2cytoscape’
exploreSP23Design: no visible global function definition for
  ‘txtProgressBar’
exploreSP23Design: no visible global function definition for
  ‘setTxtProgressBar’
generateClinicalTrialData : <anonymous>: no visible global function
  definition for ‘runif’
generateClinicalTrialData: no visible global function definition for
  ‘rbinom’
generateClinicalTrialData: no visible global function definition for
  ‘rexp’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘pnorm’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.b: no visible global function definition for ‘qnorm’
mHP.b: no visible global function definition for ‘uniroot’
mHP.c : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.c: no visible global function definition for ‘uniroot’
mHP.c: no visible global function definition for ‘qnorm’
performInterimLook: no visible global function definition for ‘optim’
performInterimLook: no visible global function definition for
  ‘constrOptim’
performInterimLook: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  Miwa constrOptim optim pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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.
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.
f.I2.cont: no visible global function definition for ‘combn’
f.I2.dich: no visible global function definition for ‘combn’
f.pstar.cont: no visible global function definition for ‘combn’
f.pstar.dich: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Starting.Rmd’
Running examples in ‘spatial.tools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tahoe_highrez_training
> ### Title: Point and polygon files for use with spatial.tools
> ### Aliases: tahoe_highrez_training
> ### Keywords: data
> 
> ### ** Examples
> 
> library("raster")
Loading required package: sp
> library("rgdal")
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 3.0.4, released 2020/01/28
 Path to GDAL shared files: 
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 7.0.0, March 1st, 2020, [PJ_VERSION: 700]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
> tahoe_highrez_training_polygons <- readOGR(
+ 	dsn=system.file("external", package="spatial.tools"),layer="tahoe_highrez_training")
OGR data source with driver: ESRI Shapefile 
Source: "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/spatial.tools/external", layer: "tahoe_highrez_training"
with 8 features
It has 2 fields
> spplot(tahoe_highrez_training_polygons,zcol="Class")
Warning in extend.limits(range(as.numeric(z), finite = TRUE)) :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 
  'from' must be a finite number
Calls: spplot ... <Anonymous> -> levelplot.formula -> seq -> seq.default
Execution halted
Running ‘testthat.R’ [43s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spbabel)
  > 
  > test_check("spbabel")
  ── 1. Failure: sf conversion works (@test-sf.R#34)  ────────────────────────────
  `map_table(st_as_sf(as(as(nc, "Spatial"), "SpatialLinesDataFrame")))` produced warnings.
  
  ── 2. Failure: sf conversion works (@test-sf.R#35)  ────────────────────────────
  `map_table(...)` produced warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 85 | SKIPPED: 4 | WARNINGS: 5 | FAILED: 2 ]
  1. Failure: sf conversion works (@test-sf.R#34) 
  2. Failure: sf conversion works (@test-sf.R#35) 
  
  Error: testthat unit tests failed
  Execution halted
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’
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.
'library' or 'require' call to ‘leaps’ which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for ‘glm’
modSearch: no visible binding for global variable ‘binomial’
modSearch: no visible global function definition for ‘na.omit’
modSearch: no visible global function definition for ‘as.formula’
speff: no visible binding for global variable ‘na.pass’
speff: no visible global function definition for ‘model.matrix’
speff: no visible global function definition for ‘terms’
speff: no visible global function definition for ‘model.response’
speff: no visible global function definition for ‘as.formula’
speff: no visible global function definition for ‘predict’
speff: no visible global function definition for ‘na.omit’
speff: no visible global function definition for ‘glm’
speff: no visible binding for global variable ‘na.omit’
speffSurv: no visible global function definition for ‘model.matrix’
speffSurv: no visible global function definition for ‘terms’
speffSurv: no visible global function definition for ‘model.response’
speffSurv: no visible global function definition for ‘as.formula’
speffSurv: no visible global function definition for ‘uniroot’
summary.speff: no visible global function definition for ‘qnorm’
summary.speff: no visible global function definition for ‘pnorm’
summary.speffSurv: no visible global function definition for ‘qnorm’
summary.speffSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
Found the following files/directories:
  ‘.neig’
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 in Depends field not imported from: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for ‘runif’
rgl.sphMW: no visible global function definition for ‘plot3d’
rgl.sphcirc: no visible global function definition for ‘rotate3d’
rgl.sphcirc: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘open3d’
rgl.sphgrid: no visible global function definition for ‘plot3d’
rgl.sphgrid: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘text3d’
rgl.sphpoints: no visible global function definition for ‘points3d’
rgl.sphsun: no visible global function definition for ‘plot3d’
rgl.sphtext: no visible global function definition for ‘text3d’
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘spiders.Rmd’
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
Packages in Depends field not imported from:
  ‘lars’ ‘parallel’ ‘randomForest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘mbgraphic’
'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.
spi: no visible global function definition for ‘read.table’
spi: no visible global function definition for ‘ecdf’
spi: no visible global function definition for ‘qnorm’
spi: no visible global function definition for ‘colorRampPalette’
spi: no visible global function definition for ‘filled.contour’
spi: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘spi.txt’
Running examples in ‘spm12r-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: install_spm12
> ### Title: Install SPM12 file into directory
> ### Aliases: install_spm12
> 
> ### ** Examples
> 
> tdir = tempfile()
> dir.create(tdir)
> in_ci <- function() {
+ nzchar(Sys.getenv("CI"))
+ }
> if (.Platform$OS.type == "unix" | in_ci()) { # windows problem
+ res = install_spm12(install_dir = tdir)
+ res = install_spm12(install_dir = tdir)
+ }
cloning into '/home/hornik/tmp/scratch/Rtmp8gFztm/file2710451890ae/spm12'...
Error in git2r::clone("https://github.com/muschellij2/spm12r", branch = "gh-pages",  : 
  Error in 'git2r_clone': failed to connect to github.com: Connection timed out
Calls: install_spm12 -> <Anonymous>
Execution halted
R2.global: no visible global function definition for ‘var’
calculer.var.exp: no visible global function definition for ‘var’
creer.noeud: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘cov’
spodt: no visible global function definition for ‘model.frame’
spodt.tree: no visible global function definition for ‘plot.new’
spodt.tree: no visible global function definition for ‘par’
spodt.tree: no visible global function definition for ‘plot.window’
spodt.tree: no visible global function definition for ‘text’
spodt.tree: no visible global function definition for ‘segments’
test.spodt: no visible global function definition for ‘model.frame’
test.spodt: no visible global function definition for ‘hist’
test.spodt: no visible global function definition for ‘abline’
tracer.noeud: no visible global function definition for ‘text’
tracer.noeud: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
Ell.Theta: no visible global function definition for ‘ell.theta’
confid.int.theta: no visible global function definition for ‘qchisq’
confid.int.theta : sim.c: no visible global function definition for
  ‘runif’
confid.int.theta: no visible global function definition for ‘quantile’
dd.est: no visible global function definition for ‘ecdf’
ks.sporm : Simul: no visible global function definition for ‘runif’
ks.stat: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘ecdf’
test.theta: no visible global function definition for ‘ecdf’
test.theta : sim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ecdf ell.theta qchisq quantile runif
Consider adding
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
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.
Missing or unexported objects:
  ‘rgdal::checkCRSArgs_ng’ ‘rgdal::new_proj_and_gdal’
Package vignette with placeholder title ‘Vignette Title’:
  ‘spreadr_vignette.Rmd’
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.
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.
'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.
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 ‘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.
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.
Running ‘testthat.R’ [17s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #    Copyright 2015 Province of British Columbia
  > #
  > #    Licensed under the Apache License, Version 2.0 (the "License");
  > #    you may not use this file except in compliance with the License.
  > #    You may obtain a copy of the License at
  > #
  > #       http://www.apache.org/licenses/LICENSE-2.0
  > #
  > #    Unless required by applicable law or agreed to in writing, software
  > #    distributed under the License is distributed on an "AS IS" BASIS,
  > #    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  > #    See the License for the specific language governing permissions and
  > #    limitations under the License.
  > 
  > library(testthat)
  > library(ssdtools)
  
  Attaching package: 'ssdtools'
  
  The following objects are masked from 'package:stats':
  
      dgamma, dweibull, pgamma, pweibull, qgamma, qweibull, rgamma,
      rweibull
  
  > 
  > test_check("ssdtools")
  ── 1. Failure: ssd_gof fitdistscens (@test-gof.R#46)  ──────────────────────────
  as.data.frame(ssd_gof(fluazinam_dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ── 2. Failure: manual (@test-schwarz-tillmans.R#24)  ───────────────────────────
  as.data.frame(ssd_gof(dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 269 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 2 ]
  1. Failure: ssd_gof fitdistscens (@test-gof.R#46) 
  2. Failure: manual (@test-schwarz-tillmans.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
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
mem.usage: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
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.
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.
.expandLevels: no visible global function definition for ‘na.omit’
.ffStack: no visible global function definition for ‘na.omit’
.ffffStack: no visible global function definition for ‘na.omit’
Stack : <anonymous>: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-data.frame: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-ffdf: no visible global function definition for ‘na.omit’
ffStack,ffdf-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.
genericPlot: no visible global function definition for ‘dev.new’
genericPlot: no visible global function definition for ‘par’
genericPlot: no visible global function definition for ‘rainbow’
genericPlot: no visible global function definition for ‘lines’
genericPlot: no visible global function definition for ‘legend’
genericPlot: no visible global function definition for ‘dev.copy2pdf’
genericPlot: no visible global function definition for ‘dev.copy2eps’
genericPlot: no visible global function definition for ‘dev.print’
genericPlot: no visible binding for global variable ‘png’
genericPlot: no visible binding for global variable ‘tiff’
plotStrains: no visible global function definition for ‘rainbow’
plotStrains: no visible global function definition for ‘dev.new’
plotStrains: no visible global function definition for ‘par’
plotStrains: no visible global function definition for ‘lines’
plotStrains: no visible global function definition for ‘legend’
plotStrains: no visible global function definition for ‘dev.copy2pdf’
plotStrains: no visible global function definition for ‘dev.copy2eps’
plotStrains: no visible global function definition for ‘dev.print’
plotStrains: no visible binding for global variable ‘png’
plotStrains: no visible binding for global variable ‘tiff’
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par")
to your NAMESPACE file.
Found the following files/directories:
  ‘Rplot001.pdf’
Non-standard file/directory found at top level:
  ‘Licence’
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.

Found the following calls to attach():
File ‘stam/R/stkde.sig.r’:
  attach(samdata)
See section ‘Good practice’ in ‘?attach’.
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.
Package which this enhances but not available for checking: ‘Zelig’
'library' or 'require' call to ‘codetools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘codetools’ ‘gss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘starsdata’
Running examples in ‘stars-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: st_as_sf
> ### Title: Convert stars object into an sf object
> ### Aliases: st_as_sf st_as_sfc.stars st_as_sf.stars
> 
> ### ** Examples
> 
> tif = system.file("tif/L7_ETMs.tif", package = "stars")
> x = read_stars(tif)
> x = x[,,,6] # a band with lower values in it
> x[[1]][x[[1]] < 30] = NA # set lower values to NA
> x[[1]] = x[[1]] < 100 # make the rest binary
> x
stars object with 3 dimensions and 1 attribute
attribute(s):
 L7_ETMs.tif    
 Mode :logical  
 FALSE:16452    
 TRUE :78796    
 NA's :27600    
dimension(s):
     from  to  offset delta refsys point values    
x       1 349  288776  28.5     NA FALSE   NULL [x]
y       1 352 9120761 -28.5     NA FALSE   NULL [y]
band    6   6      NA    NA     NA    NA   NULL    
> (p = st_as_sf(x)) # removes NA areas
Simple feature collection with 95248 features and 1 field
geometry type:  POLYGON
dimension:      XY
bbox:           xmin: 288776.3 ymin: 9110729 xmax: 298722.8 ymax: 9120761
CRS:            NA
First 10 features:
     V1                       geometry
1  TRUE POLYGON ((288776.3 9120761,...
2  TRUE POLYGON ((288804.8 9120761,...
3  TRUE POLYGON ((288833.3 9120761,...
4  TRUE POLYGON ((288861.8 9120761,...
5  TRUE POLYGON ((288890.3 9120761,...
6  TRUE POLYGON ((288918.8 9120761,...
7  TRUE POLYGON ((288947.3 9120761,...
8  TRUE POLYGON ((288975.8 9120761,...
9  TRUE POLYGON ((289004.3 9120761,...
10 TRUE POLYGON ((289032.8 9120761,...
> (p = st_as_sf(x[,,,1], merge = TRUE)) # glues polygons together
Error in CPL_polygonize(file, mask_name, "GTiff", "Memory", "foo", options,  : 
  basic_string::_M_construct null not valid
Calls: st_as_sf ... st_as_sf.stars -> gdal_polygonize -> CPL_polygonize
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘stars1.Rmd’ using rmarkdown
--- finished re-building ‘stars1.Rmd’

--- re-building ‘stars2.Rmd’ using rmarkdown
--- finished re-building ‘stars2.Rmd’

--- re-building ‘stars3.Rmd’ using rmarkdown
--- finished re-building ‘stars3.Rmd’

--- re-building ‘stars4.Rmd’ using rmarkdown
--- finished re-building ‘stars4.Rmd’

--- re-building ‘stars5.Rmd’ using rmarkdown
Quitting from lines 67-69 (stars5.Rmd) 
Error: processing vignette 'stars5.Rmd' failed with diagnostics:
basic_string::_M_construct null not valid
--- failed re-building ‘stars5.Rmd’

SUMMARY: processing the following file failed:
  ‘stars5.Rmd’

Error: Vignette re-building failed.
Execution halted
Unexported objects imported by ':::' calls:
  ‘s2dverification:::.KnownLatNames’ ‘s2dverification:::.KnownLonNames’
  See the note in ?`:::` about the use of this operator.
Found the following files/directories:
  ‘testmat.sdml’ ‘testmat2.sdml’
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.
inspect: no visible global function definition for ‘par’
inspect: no visible global function definition for ‘abline’
inspect: no visible global function definition for ‘lines’
inspect: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘dev.off’
plotfit: no visible global function definition for ‘par’
plotfit: no visible global function definition for ‘lines’
plotfit: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘legend’
plothill: no visible global function definition for ‘par’
plothill: no visible global function definition for ‘abline’
plothill: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘par’
plotmultifit: no visible global function definition for ‘lines’
plotmultifit: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘pexp’
plotmultifit: no visible global function definition for ‘plnorm’
plotmultifit: no visible global function definition for ‘ppois’
plotmultifit: no visible global function definition for ‘legend’
plotols: no visible global function definition for ‘dev.off’
plotols: no visible global function definition for ‘lm’
plotols: no visible global function definition for ‘par’
plotols: no visible global function definition for ‘abline’
plotols: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
Running examples in ‘statsr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bandit_posterior
> ### Title: bandit posterior
> ### Aliases: bandit_posterior
> 
> ### ** Examples
> 
> data = data.frame(machine = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), 
+                   outcome = c("W", "L", "W", "L", "L", "W", "L", "L", "L", "W"))
> bandit_posterior(data)
m1_good m2_good 
    0.5     0.5 
> plot_bandit_posterior(data)
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: Assigned data `prior` must be compatible with row subscript `1`.
✖ 1 row must be assigned.
✖ Assigned data has 2 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─statsr::plot_bandit_posterior(data)
 2.   ├─base::`[<-`(...)
 3.   └─tibble:::`[<-.tbl_df`(...)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
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.
Running ‘testthat.R’ [3s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("stemmatology")
  > test_check("stemmatology")
  ── 1. Error: can be imported from URL (@test-import.TEIApparatus.R#55)  ────────
  Timeout was reached: [github.com] Connection timed out after 10001 milliseconds
  Backtrace:
   1. testthat::expect_equal(...)
   4. stemmatology::import.TEIApparatus(file = "https://github.com/Jean-Baptiste-Camps/stemmatology-utils/raw/master/test/Yvain.xml")
   6. xml2:::read_xml.character(file)
   7. xml2:::read_xml.connection(...)
   9. base::open.connection(x, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 90 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: can be imported from URL (@test-import.TEIApparatus.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Found the following files/directories:
  ‘corrviz.html’
StratPhyloCongruence: no visible global function definition for ‘runif’
StratPhyloCongruence: no visible global function definition for
  ‘txtProgressBar’
StratPhyloCongruence: no visible global function definition for
  ‘setTxtProgressBar’
StratPhyloCongruence: no visible global function definition for ‘pnorm’
StratPhyloCongruence: no visible global function definition for ‘sd’
geoscalePhylo: no visible global function definition for ‘data’
geoscalePhylo: no visible global function definition for ‘par’
geoscalePhylo: no visible global function definition for ‘text’
geoscalePhylo: no visible global function definition for ‘segments’
geoscalePhylo: no visible global function definition for ‘rect’
geoscalePhylo: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following files/directories:
  ‘myNewStrat.R’
Missing or unexported object: ‘limma::ebayes’
Package vignette with placeholder title ‘Vignette Title’:
  ‘strider.Rmd’
Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
Warning: no function found corresponding to methods exports from ‘stsm.class’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
stsm.model: no visible global function definition for ‘is.ts’
stsm.model: no visible global function definition for ‘var’
stsm.model: no visible global function definition for ‘frequency’
stsm.model: no visible global function definition for ‘na.omit’
stsm.model: no visible global function definition for ‘fft’
stsm.model: no visible global function definition for ‘new’
stsm.sgf: no visible global function definition for ‘frequency’
char2numeric,stsm: no visible global function definition for
  ‘frequency’
set.cpar,stsm: no visible global function definition for ‘validObject’
set.nopars,stsm: no visible global function definition for
  ‘validObject’
set.pars,stsm: no visible global function definition for ‘validObject’
transPars,stsm: no visible global function definition for ‘var’
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘EmiStatR_output’ ‘ExamplePlot-event.pdf’ ‘ExamplePlot-season.pdf’
  ‘Output1_MC-uncertainty_360min-event.pdf’
  ‘Output1_MC-uncertainty_360min-season.pdf’ ‘gof.RData’ ‘gof.csv’
  ‘gofGoF_results.RData’ ‘gofGoF_results.csv’ ‘mc.RData’ ‘sim1.RData’
  ‘summ.RData’ ‘variance.RData’
Running examples in ‘stylo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: perform.svm
> ### Title: Support Vector Machines classifier
> ### Aliases: perform.svm
> 
> ### ** Examples
> 
> ## Not run: 
> ##D perform.svm(training.set, test.set)
> ## End(Not run)
> 
> # classifying the standard 'iris' dataset:
> data(iris)
> x = subset(iris, select = -Species)
> train = rbind(x[1:25,], x[51:75,], x[101:125,])
> test = rbind(x[26:50,], x[76:100,], x[126:150,])
> train.classes = c(rep("s",25), rep("c",25), rep("v",25))
> test.classes = c(rep("s",25), rep("c",25), rep("v",25))
> 
> perform.svm(train, test, train.classes, test.classes)
Error in svm.default(x, y, scale = scale, ..., na.action = na.action) : 
  Need numeric dependent variable for regression.
Calls: perform.svm -> svm -> svm.formula -> svm.default
Execution halted
identifyGraph: no visible global function definition for ‘phyper’
mytriangle: no visible global function definition for ‘symbols’
plotGraph: no visible global function definition for ‘par’
updateOrgEnvir: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par phyper read.table symbols
Consider adding
  importFrom("graphics", "par", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘ROCR’ ‘penalized’
  Please remove these calls from your code.
ELF: no visible global function definition for ‘pt’
ELF: no visible global function definition for ‘qnorm’
ELF: no visible global function definition for ‘lm’
ELF: no visible global function definition for ‘lowess’
ELF: no visible global function definition for ‘dnorm’
ELF: no visible global function definition for ‘approx’
subtype: no visible global function definition for ‘runif’
subtype: no visible global function definition for ‘hclust’
subtype: no visible global function definition for ‘dist’
subtype: no visible global function definition for ‘cutree’
subtype: no visible global function definition for ‘pt’
subtype: no visible global function definition for ‘heatmap’
test_subtype_only: no visible global function definition for ‘pt’
test_subtype_only: no visible global function definition for ‘survdiff’
test_subtype_only: no visible global function definition for ‘survfit’
test_subtype_only: no visible global function definition for ‘title’
ufun: no visible global function definition for ‘dnorm’
ufun: no visible global function definition for ‘lowess’
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
'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.
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.
Found the following files/directories:
  ‘CFH.scores.full.vcf’
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.
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.
.p.1gen: warning in formatC(id, wid = 6): partial argument match of
  ‘wid’ to ‘width’
.p.1gen: warning in formatC(s, wid = 4): partial argument match of
  ‘wid’ to ‘width’
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of ‘dig’ to
  ‘digits’
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of ‘wid’ to
  ‘width’
predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)]
  %*% koeff))))), nc = 1): partial argument match of ‘nc’ to ‘ncol’
ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr =
  ncol(X)): partial argument match of ‘nr’ to ‘nrow’
aggtrees: no visible global function definition for ‘predict’
coef.pelora: no visible global function definition for ‘fitted’
dlda: no visible binding for global variable ‘var’
logreg: no visible global function definition for ‘glm’
logreg: no visible binding for global variable ‘binomial’
logreg: no visible global function definition for ‘predict’
plot.pelora: no visible global function definition for ‘text’
plot.wilma: no visible global function definition for ‘fitted’
plot.wilma: no visible global function definition for ‘text’
predict.pelora: no visible global function definition for ‘fitted’
predict.pelora: no visible global function definition for ‘coef’
predict.wilma: no visible global function definition for ‘fitted’
print.wilma: no visible global function definition for ‘fitted’
ridge.coef: no visible binding for global variable ‘var’
sign.change: no visible binding for global variable ‘cov’
standardize.genes: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  binomial coef cov fitted glm predict sd text var
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "binomial", "coef", "cov", "fitted", "glm",
             "predict", "sd", "var")
to your NAMESPACE file.
HCLtree: no visible global function definition for ‘hclust’
HCLtree: no visible global function definition for ‘as.dist’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matplot’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matlines’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘axis’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matplot’
plotProfilesWithinBicluster: no visible global function definition for
  ‘title’
plotProfilesWithinBicluster: no visible global function definition for
  ‘axis’
plotProfilesWithinBicluster: no visible global function definition for
  ‘par’
plotProfilesWithinBicluster: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matlines’
plotProfilesWithinBicluster: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘boa’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for ‘as.mcmc.list’
superdiag: no visible global function definition for ‘as.mcmc’
superdiag: no visible global function definition for ‘runif’
superdiag: no visible global function definition for ‘geweke.diag’
superdiag: no visible global function definition for ‘heidel.diag’
superdiag: no visible global function definition for ‘raftery.diag’
superdiag: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘gam’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
TrainSuperMDS: no visible global function definition for ‘rnorm’
TrainSuperMDSOnce: no visible global function definition for ‘cmdscale’
TrainSuperMDSOnce: no visible global function definition for ‘quantile’
distmat: no visible global function definition for ‘dist’
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
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.
Est.PH: no visible global function definition for ‘coxph’
Inf.Cval: no visible global function definition for ‘rexp’
Inf.Cval: no visible global function definition for ‘var’
Inf.Cval.Delta: no visible global function definition for ‘rexp’
Inf.Cval.Delta: no visible global function definition for ‘var’
cvC: no visible global function definition for ‘coxph’
cvC: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
pearson: no visible global function definition for ‘cor’
plot.survcorr: no visible global function definition for ‘pnorm’
plot.survcorr: no visible global function definition for ‘par’
plot.survcorr: no visible global function definition for ‘points’
survcorr: no visible global function definition for ‘model.frame’
survcorr: no visible global function definition for ‘qnorm’
survcorr: no visible global function definition for ‘runif’
survcorr: no visible global function definition for ‘pnorm’
survcorr: no visible global function definition for ‘var’
survcorr: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cor model.frame par pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
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.
'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.
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.
Running examples in ‘survsup-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nar
> ### Title: Add a numbers at risk table to a Kaplan-Meier plot
> ### Aliases: nar
> 
> ### ** Examples
> 
> library(survsup); library(ggplot2); library(dplyr); library(survival)

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

> 
> retinopathy %>%
+     survfit(Surv(futime, status) ~ trt, data = .) %>%
+    plot_survfit() %>%
+ 	   nar()
Error in `$<-.data.frame`(`*tmp*`, "y", value = NA_real_) : 
  replacement has 1 row, data has 0
Calls: %>% ... withVisible -> <Anonymous> -> nar -> $<- -> $<-.data.frame
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘survsup_intro.Rmd’ using rmarkdown
Quitting from lines 92-96 (survsup_intro.Rmd) 
Error: processing vignette 'survsup_intro.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘survsup_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
fitModel: no visible global function definition for ‘var’
fitModel: no visible global function definition for ‘cov’
svpls: no visible global function definition for ‘pt’
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
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.
.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.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
processSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
.formatResult : capture.str: no visible global function definition for
  ‘str’
createLog: no visible global function definition for ‘sessionInfo’
protocol_junit.svSuiteData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svSuiteData: no visible global function definition for
  ‘addChildren’
protocol_junit.svSuiteData: no visible global function definition for
  ‘saveXML’
protocol_junit.svTestData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svTestData: no visible global function definition for
  ‘addChildren’
Undefined global functions or variables:
  addChildren saveXML sessionInfo str xmlNode
Consider adding
  importFrom("utils", "sessionInfo", "str")
to your NAMESPACE file.
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: ‘swephRdata’
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.
Warning in min(matches) :
  no non-missing arguments to min; returning Inf
Warning in getBiocvrFromRvr(myyaml) :
  NAs introduced by coercion to integer range
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘SWMPrExtension-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: seasonal_dot
> ### Title: Seasonal Dot Plot
> ### Aliases: seasonal_dot seasonal_dot.swmpr
> 
> ### ** Examples
> 
> dat_wq <- elksmwq
> #dat_wq <- subset(dat_wq, subset = c('2010-01-01 0:00', '2017-01-01 0:00'))
> dat_wq <- qaqc(dat_wq, qaqc_keep = c(0, 3, 5))
> 
> x <-
+   seasonal_dot(dat_wq, param = 'do_mgl'
+                , lm_trend = TRUE
+                , lm_lab = TRUE
+                , plot_title = TRUE)
Error: Aesthetics must be either length 1 or the same as the data (48): y
Backtrace:
    █
 1. ├─SWMPrExtension::seasonal_dot(...)
 2. └─SWMPrExtension:::seasonal_dot.swmpr(...)
 3.   ├─ggplot2::ggplot_build(plt)
 4.   └─ggplot2:::ggplot_build.ggplot(plt)
 5.     └─ggplot2:::by_layer(function(l, d) l$compute_aesthetics(d, plot))
 6.       └─ggplot2:::f(l = layers[[i]], d = data[[i]])
 7.         └─l$compute_aesthetics(d, plot)
 8.           └─ggplot2:::f(..., self = self)
 9.             └─ggplot2:::check_aesthetics(evaled, n)
Execution halted
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.
Running examples in ‘SympluR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: symplurContentRetweets
> ### Title: Symplur API - Content/Retweets
> ### Aliases: symplurContentRetweets
> ### Keywords: content retweets
> 
> ### ** Examples
> 
> LCSMDemoDataContentRetweets <- symplurContentRetweets(
+     "09/01/2017",
+     "09/08/2017",
+     databases = "#LCSMDemoData",
+     50)
What is your Symplur API clientId? If none, just hit enter to try #LCSMDemoData: 
What is your Symplur API clientSecret? If none, just hit enter to try #LCSMDemoData: 
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE,  : 
  arguments imply differing number of rows: 0, 1
Calls: symplurContentRetweets ... as.data.frame -> as.data.frame.list -> do.call -> <Anonymous>
Execution halted
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.
mainNetFunction: no visible global function definition for ‘png’
mainNetFunction: no visible global function definition for ‘lines’
mainNetFunction: no visible global function definition for ‘legend’
mainNetFunction: no visible global function definition for ‘dev.off’
plotROC: no visible global function definition for ‘lines’
simulatedData: no visible global function definition for ‘rpois’
simulatedData : <anonymous>: no visible global function definition for
  ‘rpois’
simulatedData : rlognormpois: no visible global function definition for
  ‘rnorm’
simulatedData : rlognormpois: no visible global function definition for
  ‘rpois’
Undefined global functions or variables:
  dev.off legend lines png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for ‘LowRankQP’
gaps.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘lines’
path.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘legend’
synth: no visible binding for global variable ‘sd’
synth: no visible binding for global variable ‘var’
synth: no visible global function definition for ‘LowRankQP’
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘test.csv’
.checkDimAndTest: no visible global function definition for
  ‘chisq.test’
.checkDimAndTest: no visible global function definition for
  ‘fisher.test’
plotTable1Heatmap: no visible global function definition for ‘par’
plotTable1Heatmap: no visible global function definition for ‘image’
plotTable1Heatmap: no visible global function definition for ‘abline’
plotTable1Heatmap: no visible global function definition for ‘axis’
plotTable1Heatmap: no visible global function definition for ‘text’
plotTable1Heatmap: no visible global function definition for ‘legend’
plotTable1Heatmap: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
Found the following files/directories:
  ‘.xls’ ‘attenu.xls’ ‘chick1.xls’ ‘chick2.xls’ ‘generic1.xls’
  ‘hands.xls’ ‘table1.xls’
Found the following files/directories:
  ‘myhtmlcode.html’
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘perturb’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for ‘grid.rect’
cellgram: no visible global function definition for ‘gpar’
cellgram: no visible global function definition for ‘grid.segments’
cellgram: no visible global function definition for ‘grid.circle’
cellgram: no visible global function definition for ‘grid.polygon’
cellgram: no visible global function definition for ‘grid.text’
cellgram: no visible global function definition for ‘unit’
compare: no visible global function definition for ‘sd’
tableplot.colldiag: no visible global function definition for
  ‘colldiag’
tableplot.colldiag: no visible global function definition for ‘xtabs’
tableplot.default: no visible global function definition for
  ‘grid.newpage’
tableplot.default: no visible global function definition for
  ‘grid.layout’
tableplot.default: no visible global function definition for ‘unit’
tableplot.default: no visible global function definition for
  ‘pushViewport’
tableplot.default: no visible global function definition for ‘viewport’
tableplot.default: no visible global function definition for
  ‘grid.text’
tableplot.default: no visible global function definition for
  ‘upViewport’
tableplot.default: no visible global function definition for ‘gpar’
tableplot.default: no visible global function definition for
  ‘grid.rect’
tableplot.default: no visible global function definition for
  ‘popViewport’
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
Package suggested but not available for checking: ‘pmatch’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
--- finished re-building ‘example.Rmd’

--- re-building ‘fda-example.Rmd’ using rmarkdown
Quitting from lines 242-244 (fda-example.Rmd) 
Error: processing vignette 'fda-example.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- failed re-building ‘fda-example.Rmd’

--- re-building ‘single-style.Rmd’ using rmarkdown
--- finished re-building ‘single-style.Rmd’

--- re-building ‘summary-example.Rmd’ using rmarkdown
--- finished re-building ‘summary-example.Rmd’

SUMMARY: processing the following file failed:
  ‘fda-example.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘spruce.taper.pars.rdata’
'library' or 'require' calls in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘tashudata’
Running ‘testthat.R’ [21s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(taxa)
  
  Attaching package: 'taxa'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("taxa")
  ── 1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 607 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#52) 
  2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#56) 
  3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘nameNode.sqlite’
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.
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:
Assigned data `as.numeric(results[1:length(results)])` must be compatible with existing data.
✖ Existing data has 1 row.
✖ Assigned data has 3 rows.
ℹ Only vectors of size 1 are recycled.
--- failed re-building ‘intro_to_tbrf.Rmd’

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

Error: Vignette re-building failed.
Execution halted
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for ‘hist’
mapper1D: no visible global function definition for ‘dist’
mapper1D: no visible global function definition for ‘as.dist’
mapper1D: no visible global function definition for ‘hclust’
mapper1D: no visible global function definition for ‘cutree’
mapper2D: no visible global function definition for ‘dist’
mapper2D: no visible global function definition for ‘as.dist’
mapper2D: no visible global function definition for ‘hclust’
mapper2D: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘RSEIS’ ‘pracma’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CalcCorners: no visible global function definition for ‘abline’
ConvDiffCoef: no visible global function definition for ‘pascal’
ConvolveTrace: no visible global function definition for ‘filter’
DeconTrace: no visible global function definition for ‘as.Zpg’
DeconTrace: no visible global function definition for ‘butter’
DeconTrace: no visible global function definition for ‘filter’
GetDPZ: no visible global function definition for ‘data’
MakeDPZ: no visible global function definition for ‘bilinear’
MakeDPZ: no visible global function definition for ‘fft’
MakeDPZ: no visible global function definition for ‘lines’
MakeDPZ: no visible global function definition for ‘legend’
MatchCoefDPZ : CalcMisfit: no visible global function definition for
  ‘fft’
MatchCoefDPZ : CalcMisfit: no visible global function definition for
  ‘filter’
MatchCoefDPZ : generate: no visible global function definition for
  ‘runif’
MatchCoefDPZ : generate: no visible global function definition for
  ‘rnorm’
MatchCoefDPZ: no visible global function definition for ‘fft’
MatchCoefDPZ: no visible global function definition for ‘filter’
MatchCoefDPZ: no visible global function definition for ‘Zpg’
MatchCoefDPZ: no visible global function definition for ‘lines’
MatchCoefDPZ: no visible global function definition for ‘abline’
Metropolis: no visible global function definition for ‘runif’
PZ2Coef: no visible global function definition for ‘Poly’
PlotResp: no visible global function definition for ‘fft’
PlotResp: no visible global function definition for ‘filter’
PlotResp: no visible global function definition for ‘lines’
Undefined global functions or variables:
  Poly Zpg abline as.Zpg bilinear butter data fft filter legend lines
  pascal rnorm runif
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "fft", "filter", "rnorm", "runif")
  importFrom("utils", "data")
to your NAMESPACE file.
Running examples in ‘TeachingDemos-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: simfun
> ### Title: Create a function to simulate data
> ### Aliases: simfun
> ### Keywords: datagen design
> 
> ### ** Examples
> 
> # Create a function to simulate heights for a given dataset
> 
> simheight <- simfun( {h <- c(64,69); height<-h[sex]+ rnorm(10,0,3)}, drop='h' )
> 
> my.df <- data.frame(sex=rep(c('Male','Female'),each=5))
> simdat <- simheight(my.df)
> t.test(height~sex, data=simdat)
Error in t.test.formula(height ~ sex, data = simdat) : 
  grouping factor must have exactly 2 levels
Calls: t.test -> t.test.formula
Execution halted
S3 methods shown with full name in documentation object 'mean.tensor':
  ‘mean.tensor’

S3 methods shown with full name in documentation object 'solve.tensor':
  ‘solve.tensor’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/terra.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘ExtinctionRateChanges.txt’ ‘ExtinctionRates.txt’
  ‘MassExtinctionTimes.txt’ ‘SpeciationRateChanges.txt’
  ‘SpeciationRates.txt’ ‘SurvivalProbabilities.txt’ ‘analysis_conifer’
  ‘input_tree.tre’ ‘run_1’ ‘run_2’ ‘samples_numCategories.txt’
Packages suggested but not available for checking: 'btergm', 'Zelig'

Package which this enhances but not available for checking: ‘xergm’
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.
transfer: no visible global function definition for ‘rgamma’
transfer: no visible global function definition for ‘rnorm’
transfer: no visible global function definition for ‘rnbinom’
transfer: no visible global function definition for ‘rpois’
transfer: no visible global function definition for ‘rbinom’
transfer: no visible global function definition for ‘runif’
plot,transfer: no visible global function definition for ‘barplot’
plot,transfer: no visible global function definition for ‘axis’
plot,transfer: no visible global function definition for ‘par’
plot,transfer: no visible global function definition for ‘hist’
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘tmp.test.data.csv’
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.
Running ‘testthat.R’ [25s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(themetagenomics)
  Loading required package: Rcpp
  > 
  > test_check("themetagenomics")
  ── 1. Failure: prepare_data works with multiclass factor (@test-prepare.R#92)  ─
  `prepare_data(...)` did not produce any warnings.
  
  ── 2. Error: prepare_data works with multiclass factor and continuous (@test-pre
  undefined columns selected
  Backtrace:
   1. testthat::expect_equal(...)
   5. base::`[.data.frame`(x$modelframe, , c("Multi1", "Multi3", "Day"))
  
  ── 3. Error: prepare_data works with multiclass factor and spline (@test-prepare
  undefined columns selected
  Backtrace:
   1. testthat::expect_equal(...)
   5. base::`[.data.frame`(x$modelframe, , c("Multi1", "Multi3", "Day"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 45 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: prepare_data works with multiclass factor (@test-prepare.R#92) 
  2. Error: prepare_data works with multiclass factor and continuous (@test-prepare.R#139) 
  3. Error: prepare_data works with multiclass factor and spline (@test-prepare.R#168) 
  
  Error: testthat unit tests failed
  Execution halted
Package unavailable to check Rd xrefs: ‘dada2’
Running ‘testthat.R’ [11s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(theseus)
  > 
  > test_check("theseus")
  ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
  attempting to coerce non-factor
  Backtrace:
   1. base::table(...)
   2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
   3. base::as.character.factor(df[[tax_level]])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Thinknum: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
coef_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘abline’
coef_traceplot : <anonymous>: no visible global function definition for
  ‘lines’
coef_traceplot: no visible global function definition for ‘text’
ee.GEE.aux : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline combn lines rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for ‘printCoefmat’
threesls: no visible global function definition for ‘cor’
threesls: no visible global function definition for ‘pt’
tsls.formula: no visible global function definition for ‘model.matrix’
tsls.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
.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.
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').
Running examples in ‘tidybayes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare_levels
> ### Title: Compare the value of draws of some variable from a Bayesian
> ###   model for different levels of a factor
> ### Aliases: compare_levels
> ### Keywords: manip
> 
> ### ** 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(ggplot2)
> 
> data(RankCorr, package = "tidybayes")
> 
> # Let's do all pairwise comparisons of b[i,1]:
> RankCorr %>%
+   spread_draws(b[i,j]) %>%
+   filter(j == 1) %>%
+   compare_levels(b, by = i) %>%
+   median_qi()
Error: Assigned data `draws[, c(".chain", ".iteration", ".draw")]` must be compatible with existing data.
✖ Existing data has 12000 rows.
✖ Element 1 of assigned data has 1000 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
     █
  1. └─`%>%`(...)
  2.   ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3.   └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       └─`_fseq`(`_lhs`)
  6.         └─magrittr::freduce(value, `_function_list`)
  7.           └─function_list[[i]](value)
  8.             └─tidybayes::spread_draws(., b[i, j])
  9.               └─base::lapply(...)
 10.                 └─tidybayes:::FUN(X[[i]], ...)
 11.                   └─tidybayes:::spread_draws_(...)
 12.                     └─tidybayes:::spread_draws_long_(...)
 13.                       ├─base::`[<-`(...)
 14.                       └─tibble:::`[<-.tbl_df`(...)
 15.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tidydice.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 147-150 (tidydice.Rmd) 
Error: processing vignette 'tidydice.Rmd' failed with diagnostics:
Must extract column with a single valid subscript.
✖ The subscript `target_txt` can't be `NA`.
--- failed re-building ‘tidydice.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_difference
> ### Title: Plot difference smooth from a GAM.
> ### Aliases: plot_difference
> 
> ### ** Examples
> 
> library(mgcv)
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
> set.seed(10)
> data <- gamSim(4)
Factor `by' variable example
> model <- gam(y ~ fac + s(x2) + s(x2, by = fac) + s(x0), data = data)
> 
> plot_difference(model, x2, list(fac = c("1", "2")))
Error in table(predictors$Terms) - table(predictors[predictors$Label %in%  : 
  non-conformable arrays
Calls: plot_difference -> %>% -> eval -> eval
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plot-smooths.Rmd’ using rmarkdown
Quitting from lines 172-177 (plot-smooths.Rmd) 
Error: processing vignette 'plot-smooths.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘plot-smooths.Rmd’

--- re-building ‘predict-gam.Rmd’ using rmarkdown
--- finished re-building ‘predict-gam.Rmd’

SUMMARY: processing the following file failed:
  ‘plot-smooths.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [12s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  ── 1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15)  ────
  paste(as.character(ovid[[1]]), collapse = " ") not equal to td$text[1].
  names for current but not for target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 297 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [59s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytransit)
  > 
  > test_check("tidytransit")
  ── 1. Error: travel_times from stop with departures from transfer stops (@test-r
  Assigned data `c("stop0", "Zero", 46.9596, 7.39071, NA, 0)` must be compatible with row subscript `nrow(g2$stops) + 1`.
  ✖ 1 row must be assigned.
  ✖ Assigned data has 6 rows.
  ℹ Only vectors of size 1 are recycled.
  Backtrace:
   1. base::`[<-`(...)
   2. tibble:::`[<-.tbl_df`(...)
   3. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4. tibble:::vectbl_recycle_rhs(...)
   5. base::tryCatch(...)
   6. base:::tryCatchList(expr, classes, parentenv, handlers)
   7. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 106 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: travel_times from stop with departures from transfer stops (@test-raptor.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
'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
Running examples in ‘timeperiodsR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: last_n_quarters
> ### Title: Start and end of last n quarters
> ### Aliases: last_n_quarters
> 
> ### ** Examples
> 
> ## To get start, end and sequence of last 2 quarters, 
> ## exclude current quarter
> last2quarters <- last_n_quarters(n = 2)
> 
> ## include current quarter
> last2quarters_2 <- last_n_quarters(n = 2, include_current = TRUE)
Error in seq.int(0, to0 - from, by) : 'to' must be a finite number
Calls: last_n_quarters -> custom_period -> seq.Date
Execution halted
'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
'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.
author.search: no visible binding for global variable ‘na.omit’
reference.list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf segments text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘_paramEst.txt’
Non-standard files/directories found at top level:
  ‘DESCRIPTION.orig’ ‘README.rst’
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
ls.tree: no visible global function definition for ‘lm’
ls.tree: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
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.
Found the following significant warnings:
  Warning: replacing previous import ‘sf::st_make_valid’ by ‘lwgeom::st_make_valid’ when loading ‘tmap’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tmap.Rcheck/00install.out’ for details.
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.
Package suggested but not available for checking: ‘corpus.JSS.papers’
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.
Found the following files/directories:
  ‘test-001.png’ ‘test-002.png’ ‘test-003.png’ ‘test-004.png’
  ‘test-005.png’ ‘test-006.png’ ‘test-007.png’ ‘test-008.png’
  ‘test-009.png’ ‘test-010.png’ ‘test-011.png’ ‘test-012.png’
  ‘test-013.png’ ‘test-014.png’ ‘test-015.png’ ‘test-016.png’
  ‘test-017.png’ ‘test-018.png’ ‘test-019.png’ ‘test-020.png’
  ‘test-021.png’ ‘test-022.png’ ‘test-023.png’ ‘test-024.png’
  ‘test-025.png’ ‘test-026.png’ ‘test-027.png’ ‘test-028.png’
  ‘test-029.png’ ‘test-030.png’ ‘test-031.png’ ‘test-032.png’
  ‘test-033.png’ ‘test-034.png’ ‘test-035.png’ ‘test-036.png’
  ‘test-037.png’ ‘test-038.png’ ‘test-039.png’ ‘test-040.png’
  ‘test-041.png’ ‘test-042.png’ ‘test-043.png’ ‘test-044.png’
  ‘test-045.png’ ‘test-046.png’ ‘test-047.png’ ‘test-048.png’
  ‘test-049.png’ ‘test-050.png’ ‘test.pdf’
ConfA: no visible global function definition for ‘qf’
EstM2Sn: no visible global function definition for ‘nlm’
EstM2Sn: no visible global function definition for ‘qnorm’
TV.model: no visible global function definition for ‘dev.new’
TV.model: no visible global function definition for ‘points’
betaBino: no visible global function definition for ‘pbinom’
doseD: no visible global function definition for ‘lm’
doseD: no visible global function definition for ‘dev.new’
doseD: no visible global function definition for ‘par’
doseD: no visible global function definition for ‘axTicks’
doseD: no visible global function definition for ‘axis’
doseD: no visible global function definition for ‘lines’
doseD: no visible global function definition for ‘abline’
doseD: no visible global function definition for ‘legend’
setD: no visible global function definition for ‘dev.new’
setD: no visible global function definition for ‘par’
setD: no visible global function definition for ‘pbinom’
setD: no visible global function definition for ‘abline’
setD: no visible global function definition for ‘axis’
setD: no visible global function definition for ‘rect’
setD: no visible global function definition for ‘lines’
setD: no visible global function definition for ‘text’
setD: no visible global function definition for ‘axTicks’
setD: no visible global function definition for ‘legend’
spoD : spoD_A: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘01_spontaneous lethality.txt’ ‘02.sample size.txt’
  ‘03.dosestrategy.txt’ ‘doseD4.txt’ ‘setD.txt’ ‘spoDa.txt’ ‘spoDb.txt’
align1d : obj: no visible global function definition for ‘dist’
align2d : obj: no visible global function definition for ‘dist’
align2d : pen: no visible global function definition for ‘dist’
align2d: no visible global function definition for ‘dist’
sumt: no visible global function definition for ‘optim’
tpe1d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘cmdscale’
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following calls to attach():
File ‘track/R/track.attach.R’:
  attach(what = NULL, pos = pos, name = name)
See section ‘Good practice’ in ‘?attach’.
Running examples in ‘traitdataform-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rbind.traitdata
> ### Title: Combine trait datasets
> ### Aliases: rbind.traitdata
> 
> ### ** Examples
> 
> 
> pulldata("carabids")
The dataset 'carabids' is now available for use! 

> 
> dataset1 <- as.traitdata(carabids,
+   taxa = "name_correct",
+   traits = c("body_length", "antenna_length", "metafemur_length"),
+   units = "mm",
+   keep = c(datasetID = "source_measurement", measurementRemarks = "note"),
+   metadata = as.metadata(
+     bibliographicCitation = c(
+         "van der Plas et al. (2017) Methods in Ecol. & Evol., doi: 10.1111/2041-210x.12728"
+        ),
+     author = "Fons van der Plas",
+     license = "http://creativecommons.org/publicdomain/zero/1.0/"
+     )
+ )
Input is taken to be a species -- trait matrix. If this is not the case, please provide parameters!
> 
> 
> traits1 <- as.thesaurus(
+  body_length = as.trait("body_length",
+    expectedUnit = "mm", valueType = "numeric",
+    identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_length"),
+  antenna_length = as.trait("antenna_length",
+    expectedUnit = "mm", valueType = "numeric",
+    identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Antenna_length"),
+  metafemur_length = as.trait("metafemur_length",
+    expectedUnit = "mm", valueType = "numeric",
+    identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length")
+ )
> 
> dataset1Std <- standardize.traits(dataset1, thesaurus = traits1)
Error in UseMethod("droplevels") : 
  no applicable method for 'droplevels' applied to an object of class "character"
Calls: standardize.traits -> droplevels
Execution halted
Running ‘testthat.R’ [5s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(traitdataform)
  > 
  > test_check("traitdataform")
  ── 1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10)  ─────────
  Value hashes to 2448e3596a, not bc9f97d273
  
  ── 2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11)  ─────────
  Value hashes to 4381d5bd4d, not 74f9a02a12
  
  ── 3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64)
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dataset2, thesaurus = traits2)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnitStd)
  
  ── 4. Error: factor level harmonizationworks (@test.standardize.R#81)  ─────────
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dd1)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnit)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 64 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10) 
  2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11) 
  3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64) 
  4. Error: factor level harmonizationworks (@test.standardize.R#81) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘traitdataform.Rmd’ using rmarkdown
Quitting from lines 310-312 (traitdataform.Rmd) 
Error: processing vignette 'traitdataform.Rmd' failed with diagnostics:
no applicable method for ‘droplevels’ applied to an object of class "character"
--- failed re-building ‘traitdataform.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘taxidata’
microsoftTranslate: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
rtrapezoid: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Build_JTree: no visible global function definition for ‘flush.console’
Run_JTree: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LikAge: no visible global function definition for ‘read.table’
bd.ME.optim: no visible global function definition for ‘optim’
bd.ME.optim.rho: no visible global function definition for ‘optim’
bd.ME.optim.rho.all: no visible global function definition for ‘optim’
bd.MEyule.optim: no visible global function definition for ‘optimize’
bd.MEyule.optim: no visible global function definition for ‘optim’
bd.age.optim.matlab: no visible global function definition for
  ‘read.table’
bd.groups.conf: no visible global function definition for ‘uniroot’
bd.shifts.plot: no visible global function definition for ‘lines’
bdsky.stt.optim: no visible global function definition for ‘optim’
create.mat: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines optim optimize read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for ‘hist’
plot.treeperm: no visible global function definition for ‘points’
plot.treeperm: no visible global function definition for ‘text’
treeperm.formula: no visible global function definition for
  ‘model.frame’
treeperm.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘trimr-vignette.Rmd’
cinbag: no visible global function definition for ‘var’
trimTrees: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for ‘odd’
HtoGp: no visible global function definition for ‘even’
plot.pirls.gam: no visible global function definition for ‘par’
plot.pirls.gam: no visible global function definition for ‘title’
plot.pirls.gam: no visible global function definition for ‘lines’
plot.pirls.gam: no visible global function definition for ‘rug’
plot.pirls.gam: no visible global function definition for ‘mtext’
test.trioGxE: no visible global function definition for ‘write.table’
trioGxE: no visible global function definition for ‘quantile’
trioGxE: no visible global function definition for ‘qtnorm’
trioplot: no visible global function definition for ‘quantile’
trioplot: no visible global function definition for ‘formula’
trioplot: no visible global function definition for ‘gam’
trioplot: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par qtnorm quantile rug
  title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘GTFS-table-relationships.Rmd’
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').
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.
tfDetails: no visible global function definition for ‘start’
tfDetails: no visible global function definition for ‘end’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for ‘pnorm’
plrt: no visible global function definition for ‘uniroot’
plrt: no visible global function definition for ‘optimize’
simulatedata: no visible global function definition for ‘rnorm’
tsc.test: no visible global function definition for ‘shapiro.test’
tsc.test: no visible global function definition for ‘p.adjust’
tsc.test: no visible global function definition for ‘glm’
tsc.test : f: no visible global function definition for ‘pnorm’
tsc.test: no visible global function definition for ‘uniroot’
tsc.test: no visible global function definition for ‘optimize’
variance: no visible global function definition for ‘density’
variance: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
vintageMap: no visible global function definition for ‘read.table’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘frequency’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘frequency’
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for ‘cov’
FAfitStats.TSFmodel: no visible global function definition for ‘cov’
FAfitStats.default: no visible global function definition for ‘cor’
FAfitStats.default: no visible global function definition for
  ‘factanal’
FAfitStats.default: no visible global function definition for ‘pchisq’
FAmodelFitStats: no visible global function definition for ‘pchisq’
checkResiduals.TSFmodel: no visible global function definition for
  ‘cov’
distribution.factorsEstEval: no visible global function definition for
  ‘par’
distribution.factorsEstEval: no visible binding for global variable
  ‘par’
distribution.factorsEstEval: no visible global function definition for
  ‘density’
distribution.factorsEstEval: no visible global function definition for
  ‘matplot’
distribution.factorsEstEval: no visible global function definition for
  ‘title’
summary.TSFmodel: no visible global function definition for ‘start’
summary.TSFmodel: no visible global function definition for ‘end’
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
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.
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.
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.
Found the following files/directories:
  ‘XMIwords.txt’
TT.GS : TT.GS.sp: no visible global function definition for ‘qt’
TT.GS : TT.GS.sp: no visible global function definition for ‘runif’
TT.GS : TT.GS.sp: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
.saveDevice: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
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.
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.
TwoCop: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Found the following files/directories:
  ‘debug.txt’
txtacf: no visible binding for global variable ‘na.fail’
txtacf: no visible global function definition for ‘acf’
txtboxplot : <anonymous>: no visible global function definition for
  ‘boxplot.stats’
txtboxplot: no visible global function definition for ‘boxplot.stats’
txtdensity: no visible global function definition for ‘density’
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
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.
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.
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.
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.
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘upm-primer.Rmd’ using rmarkdown
Quitting from lines 70-71 (upm-primer.Rmd) 
Error: processing vignette 'upm-primer.Rmd' failed with diagnostics:
A variable(s) is listed by user as factors but data type in design matrix is not actually a factor. Reformat.
--- failed re-building ‘upm-primer.Rmd’

SUMMARY: processing the following file failed:
  ‘upm-primer.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘USAboundariesData’
readSEER: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000cdp/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000tract/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000tract\").\n")
    cat("Type help(package=\"UScensus2000tract\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘ushr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summarize_model
> ### Title: Summarize model output
> ### Aliases: summarize_model
> 
> ### ** Examples
> 
> 
> set.seed(1234567)
> 
> simulated_data <- simulate_data(nsubjects = 20)
Joining, by = "id"
> 
> model_output <- ushr(data = simulated_data)
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
> 
> summarize_model(model_output, data = simulated_data)
Joining, by = c("id", "Model")
Joining, by = "id"
Error: Assigned data `values` must be compatible with existing data.
ℹ Error occurred for column `ShortLifespan`.
✖ No common type for `value` <character> and `x` <double>.
Backtrace:
     █
  1. └─ushr::summarize_model(model_output, data = simulated_data)
  2.   └─`%>%`(...)
  3.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.         └─ushr:::`_fseq`(`_lhs`)
  7.           └─magrittr::freduce(value, `_function_list`)
  8.             ├─base::withVisible(function_list[[k]](value))
  9.             └─function_list[[k]](value)
 10.               └─base::replace(., is.na(.), "")
 11.                 ├─base::`[<-`(`*tmp*`, list, value = "")
 12.                 └─tibble:::`[<-.tbl_df`(`*tmp*`, list, value = "")
 13.                   └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(va
Execution halted
histw: no visible global function definition for ‘plot.new’
histw: no visible global function definition for ‘plot.window’
histw: no visible global function definition for ‘axis’
histw: no visible global function definition for ‘rect’
histw: no visible global function definition for ‘lines’
uwham.boot: no visible binding for global variable ‘var’
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Package vignette with placeholder title ‘Vignette Title’:
  ‘intro-to-varbundle.Rmd’
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.
Found the following files/directories:
  ‘Output.txt’ ‘Overlap.csv’ ‘Polar coordinates.csv’
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
compute_KL : rtnorm: no visible global function definition for ‘runif’
compute_KL : rtnorm: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘qnorm’
compute_KL: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘pnorm’
compute_KL: no visible global function definition for ‘var’
compute_KL: no visible global function definition for ‘rbinom’
compute_KL: no visible global function definition for ‘rnorm’
compute_KL: no visible global function definition for ‘sd’
vbsr: no visible global function definition for ‘qchisq’
vbsr: no visible global function definition for ‘var’
vbsr: no visible global function definition for ‘pchisq’
vbsr: no visible global function definition for ‘sd’
vbsr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘VBTree_vignette.Rmd’
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.
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.
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.
'library' or 'require' call to ‘stats’ which was already attached by Depends.
  Please remove these calls from your code.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of ‘arg’ to
  ‘args’
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
Found the following files/directories:
  ‘Fig3-1_triple_labels_sub_and_superscripts.tiff’
  ‘Fig3-2_Euler_3set_simple_with_subscripts.tiff’
  ‘Pairwise_Venn_diagram.tiff’ ‘Quad_Venn_diagram.tiff’
  ‘Quintuple_Venn_diagram.tiff’ ‘Single_Venn_diagram.tiff’
  ‘Triple_Venn_diagram.tiff’ ‘Venn_2set_complex.tiff’
  ‘Venn_4set_pretty.tiff’ ‘Venn_5set_pretty.tiff’
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.
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.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
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.
Missing or unexported object: ‘jsonlite::rbind.pages’
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vortexRguide.Rmd’ using rmarkdown
Quitting from lines 293-297 (vortexRguide.Rmd) 
Error: processing vignette 'vortexRguide.Rmd' failed with diagnostics:
Some items of .SDcols are not column names: [N]
--- failed re-building ‘vortexRguide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘test’ ‘testname.rda’ ‘testname.txt’
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.
'library' or 'require' call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
Non-standard file/directory found at top level:
  ‘vwr-Ex.R’
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’ ‘stringdist’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for ‘detectCores’
ald: no visible global function definition for ‘mclapply’
coltheart.N: no visible global function definition for ‘detectCores’
coltheart.N: no visible global function definition for ‘mclapply’
hamming.distance: no visible global function definition for
  ‘stringdist’
ldknn: no visible global function definition for ‘detectCores’
ldknn: no visible global function definition for ‘mclapply’
ldknn.odds: no visible global function definition for ‘glm’
ldknn.odds: no visible binding for global variable ‘binomial’
ldknn.odds: no visible global function definition for ‘coefficients’
levenshtein.damerau.distance: no visible global function definition for
  ‘stringdist’
levenshtein.distance: no visible global function definition for
  ‘stringdist’
plot.ldknn.run: no visible global function definition for ‘histogram’
plot.ldknn.run: no visible global function definition for
  ‘theEconomist.theme’
plot.ldknn.run: no visible global function definition for ‘xyplot’
plot.ldknn.run: no visible global function definition for ‘as.layer’
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
summary.whc: no visible global function definition for ‘printCoefmat’
wahc.fit: no visible global function definition for ‘pt’
wahc.fit: no visible global function definition for ‘cor’
whc: no visible global function definition for ‘model.frame’
whc: no visible global function definition for ‘model.matrix’
whc: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
Found the following files/directories:
  ‘linout.csv’ ‘linout.pdf’ ‘out.csv’ ‘out.pdf’ ‘tabel_out.csv’
Found the following files/directories:
  ‘weisseritz’
Foreign function call to a different package:
  .C("comwr", ..., PACKAGE = "wavethresh")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘rPeaks’
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
onesamplemeantest: no visible global function definition for ‘pnorm’
twosamplemeantest: no visible global function definition for ‘pnorm’
wcq: no visible global function definition for ‘var’
wcq: no visible global function definition for ‘pnorm’
wcq.fdrc: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘rgeolocate’
Package vignette with placeholder title ‘Vignette Title’:
  ‘weco-vignette.Rmd’
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.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
Found the following files/directories:
  ‘Bundesliga.xml’ ‘myfile.xml’
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘WindCurves_Info.Rmd’
plotTrait: no visible global function definition for ‘points’
plotTrait: no visible global function definition for ‘legend’
test.windex: no visible global function definition for ‘hist’
test.windex: no visible global function definition for ‘abline’
test.windex: no visible global function definition for ‘legend’
windex: no visible global function definition for ‘sd’
windex: no visible global function definition for ‘var’
windex: no visible global function definition for ‘dist’
windex: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline dist hist legend points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘foo’
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.
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
Found the following files/directories:
  ‘aphiainfo.csv’ ‘tax.csv’
Package unavailable to check Rd xrefs: ‘cleaver’
simul.wsvm: no visible binding for global variable ‘mixture.example’
Undefined global functions or variables:
  mixture.example
Package vignette with placeholder title ‘Vignette Title’:
  ‘wTOvignette.Rmd’
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
Found the following files/directories:
  ‘Rout.a1’ ‘Rout.b1’ ‘Rout.d10’ ‘Rout.d11’ ‘Rout.d12’ ‘Rout.dat’
  ‘Rout.ftr’ ‘Rout.html’ ‘Rout.spc’ ‘Rout_Profiler.txt’ ‘Rout_err.html’
  ‘Rout_log.html’ ‘gra_Rout’
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
Found the following files/directories:
  ‘xgb.txt’
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.
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘results.txt’
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
LPGM: no visible global function definition for ‘flush.console’
PGM: no visible global function definition for ‘flush.console’
PGM.path.neighborhood: no visible global function definition for
  ‘runif’
PGMSim: no visible global function definition for ‘rpois’
PGMSim: no visible global function definition for ‘par’
WPGMSim: no visible global function definition for ‘rpois’
XMRF.Sim: no visible global function definition for ‘cov2cor’
XMRF.Sim: no visible global function definition for ‘rbinom’
XMRF.Sim: no visible global function definition for ‘rnorm’
glm.generic: no visible global function definition for ‘flush.console’
mymult: no visible global function definition for ‘rmultinom’
plot.GMS: no visible global function definition for ‘pdf’
plot.GMS: no visible global function definition for ‘dev.off’
plotNet: no visible global function definition for ‘pdf’
plotNet: no visible global function definition for ‘dev.off’
print.GMS: no visible global function definition for ‘str’
processSeq: no visible binding for global variable ‘quantile’
processSeq: no visible binding for global variable ‘var’
processSeq: no visible global function definition for ‘ks.test’
rmpois : <anonymous>: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
Found the following files/directories:
  ‘ggm.fit.net.pdf’
Running examples in ‘Xplortext-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LexHCca
> ### Title: Hierarchical Clustering of Documents on Textual Correspondence
> ###   Analysis Coordinates (LexHCca)
> ### Aliases: LexHCca
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(open.question)
> res.TD<-TextData(open.question, var.text=c(9,10), Fmin=10, Dmin=10, stop.word.tm=TRUE,
+         context.quali=c("Gender","Age_Group","Education"), context.quanti=c("Age"))
> res.LexCA<-LexCA(res.TD, graph=FALSE, ncp=8)
Error in which(unlist(lapply(listModa, is.numeric))) : 
  argument to 'which' is not logical
Calls: LexCA -> as.matrix -> t -> tab.disjonctif -> which
Execution halted
Running examples in ‘xslt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xslt
> ### Title: XSLT 1.0 Transformations
> ### Aliases: xslt xml_xslt xslt_version
> 
> ### ** Examples
> 
> doc <- read_xml(system.file("examples/cd_catalog.xml", package = "xslt"))
> style <- read_xml(system.file("examples/cd_catalog.xsl", package = "xslt"))
> html <- xml_xslt(doc, style)
Error in doc_xslt_apply(doc$doc, stylesheet$doc, paramstr) : 
  function 'enterRNGScope' not provided by package 'Rcpp'
Calls: xml_xslt -> xml_xslt.xml_document -> doc_xslt_apply
Execution halted
Found the following files/directories:
  ‘xSub_ACLED_EGY_adm0_year.csv’
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
Package vignette with placeholder title ‘Vignette Title’:
  ‘xyz-vignette.Rmd’
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS’
big.read.table: no visible global function definition for ‘read.table’
big.read.table: no visible global function definition for ‘object.size’
sparkline: no visible global function definition for ‘is.ts’
sparkline: no visible global function definition for ‘time’
sparkline: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘CO2.csv’
bootstrapswapcurve: no visible global function definition for ‘ts’
fitted: no visible global function definition for ‘ts’
forwardrates: no visible global function definition for ‘ts’
residuals: no visible global function definition for ‘ts’
tZC_NS: no visible global function definition for ‘cmpfun’
tZC_NS_extra: no visible global function definition for ‘cmpfun’
tZC_SV: no visible global function definition for ‘cmpfun’
tZC_SV_extra: no visible global function definition for ‘cmpfun’
ycextra: no visible global function definition for ‘new’
ycinter: no visible global function definition for ‘new’
ycplot: no visible global function definition for ‘par’
ycplot: no visible global function definition for ‘points’
ycplot: no visible global function definition for ‘abline’
ycplot: no visible global function definition for ‘hist’
ycplot: no visible global function definition for ‘lines’
ycplot: no visible global function definition for ‘density’
ycplot: no visible global function definition for ‘qqnorm’
ycplot: no visible global function definition for ‘qqline’
ycsummary: no visible global function definition for ‘shapiro.test’
ycsummary: no visible global function definition for ‘pf’
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
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.
Missing or unexported object: ‘devtools::use_data’
Package vignette with placeholder title ‘Vignette Title’:
  ‘ZipRadius.Rmd’
S3 methods shown with full name in documentation object 'merge':
  ‘cbind.zoocat’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.9Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
Missing or unexported object: ‘devtools::use_package’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
File ‘abundant/libs/abundant.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘acc/libs/acc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rARPACK’ ‘sparseLDA’
  All declared Imports should be used.
File ‘ACDm/libs/ACDm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘acepack/libs/acepack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
File ‘acrt/libs/acrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
File ‘adagio/libs/adagio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Missing or unexported object: ‘devtools::clean_source’
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘AdaptFit/R/aspm.R’:
  assign("group.vec.Handan", group.vec, pos = 1)
  assign("X.Declan", X, pos = 1)
  assign("Z.Jaida", Z, pos = 1)
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R       1.3Mb
    data    1.3Mb
    files   1.7Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data  20.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
File ‘AdMit/libs/AdMit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
File ‘ADMMnet/libs/ADMMnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("aemo")
  Loading required package: aemo
  ── 1. Failure: AEMO data URLs still correct (@test-aemo.R#34)  ─────────────────
  GET(co_url)$status not equal to 200.
  1/1 mismatches
  [1] 404 - 200 == 204
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: AEMO data URLs still correct (@test-aemo.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
File ‘AhoCorasickTrie/libs/AhoCorasickTrie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
File ‘akima/libs/akima.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 198-205 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
invalid 'times' argument
--- failed re-building ‘ALA4R.Rmd’

SUMMARY: processing the following file failed:
  ‘ALA4R.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘taxize’
  All declared Imports should be used.
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘allelic/libs/allelic.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’
File ‘allelic/libs/allelic.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘tibble’
  All declared Imports should be used.
File ‘alphabetr/libs/alphabetr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘magrittr’
  All declared Imports should be used.
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Running examples in ‘anchoredDistr-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotMAD
> ### Title: Plot the data contained in MADproject object slots.
> ### Aliases: plotMAD plotMAD,MADproject,ANY-method
> ###   plotMAD,MADproject,character-method
> 
> ### ** Examples
> 
> data(pumping)
> plotMAD(pumping, "realizations")
Error: Assigned data `x@observations` must be compatible with existing data.
✖ Existing data has 300 rows.
✖ Assigned data has 100 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
     █
  1. ├─anchoredDistr::plotMAD(pumping, "realizations")
  2. └─anchoredDistr::plotMAD(pumping, "realizations")
  3.   ├─base::`$<-`(...)
  4.   └─tibble:::`$<-.tbl_df`(...)
  5.     └─tibble:::tbl_subassign(...)
  6.       └─tibble:::vectbl_recycle_rhs(...)
  7.         └─base::tryCatch(...)
  8.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
  9.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.               └─value[[3L]](cond)
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘anchoredDistr.Rmd’ using rmarkdown
Quitting from lines 85-86 (anchoredDistr.Rmd) 
Error: processing vignette 'anchoredDistr.Rmd' failed with diagnostics:
Assigned data `x@observations` must be compatible with existing data.
✖ Existing data has 300 rows.
✖ Assigned data has 100 rows.
ℹ Only vectors of size 1 are recycled.
--- failed re-building ‘anchoredDistr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘anchors/libs/anchors.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘V8’
  All declared Imports should be used.
installed size is 63.6Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    62.0Mb
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘evd’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(aoos)
  > 
  > test_check("aoos")
  ── 1. Failure: Type inheritance (@test-S4-types.R#75)  ─────────────────────────
  inherits(Child(), "Test2") isn't true.
  
  ── 2. Failure: Type with VIRTUAL (@test-S4-types.R#111)  ───────────────────────
  names(Test(x = 2)) == "x" isn't true.
  
  ── 3. Failure: Type with VIRTUAL (@test-S4-types.R#112)  ───────────────────────
  inherits(Test(), "Type") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 187 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Type inheritance (@test-S4-types.R#75) 
  2. Failure: Type with VIRTUAL (@test-S4-types.R#111) 
  3. Failure: Type with VIRTUAL (@test-S4-types.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [9s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apa)
  > 
  > test_check("apa")
  ── 1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#13
  Assigned data `<list>` must be compatible with existing data.
  ℹ Error occurred for column `df_n`.
  ✖ No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  ── 2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anov
  Assigned data `<list>` must be compatible with existing data.
  ℹ Error occurred for column `df_n`.
  ✖ No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 105 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 2 ]
  1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#135) 
  2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anova-apa.R#181) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
Running ‘testthat.R’ [13s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apex)
  Loading required package: ape
  Loading required package: phangorn
  > 
  > test_check("apex")
  ── 1. Error: (unknown) (@test_export.R#8)  ─────────────────────────────────────
  subscript out of bounds
  Backtrace:
   1. apex::multidna2genind(x, mlst = TRUE, gapIsNA = TRUE)
   2. adegenet::df2genind(xdfnum, ploidy = 1, ind.names = x@labels)
   3. base::vapply(...)
   4. adegenet:::FUN(X[[i]], ...)
   5. base::rowSums(out[, i, drop = FALSE], na.rm = TRUE)
   6. base::is.data.frame(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
  1. Error: (unknown) (@test_export.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘apex.Rmd’ using rmarkdown
Quitting from lines 294-299 (apex.Rmd) 
Error: processing vignette 'apex.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘apex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘APIS/libs/APIS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
File ‘apple/libs/apple.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
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.
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/aqr.Rcheck/00install.out’ for details.
File ‘aqr/libs/aqr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.3Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘gmm’ ‘graphics’ ‘sandwich’ ‘stats4’ ‘utils’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.6Mb
File ‘ash/libs/ash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ASPBay/libs/ASPBay.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘arules’ ‘arulesViz’ ‘dplyr’ ‘methods’ ‘plotly’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
File ‘AssotesteR/libs/AssotesteR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘AtmRay/libs/AtmRay.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See ‘/data/gannet/ripley/R/packages/tests-clang/autocogs.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
Running examples in ‘autocogs-Ex.R’ failed
The error most likely occurred in:

> ### Name: cog_spec
> ### Title: Cognostic Specification
> ### Aliases: cog_spec as_cog_specs
> 
> ### ** Examples
> 
> # example cog specifications
> # display like normal
> cog_spec(); TRUE
$keep_layer
[1] TRUE

$remove
character(0)

attr(,"class")
[1] "cog_spec"
[1] TRUE
> # remove scagnostics
> cog_spec(scagnostics = FALSE)
$keep_layer
[1] TRUE

$remove
[1] "scagnostics"

attr(,"class")
[1] "cog_spec"
> # remove layer
> cog_spec(.keep_layer = FALSE); FALSE
$keep_layer
[1] FALSE

$remove
character(0)

attr(,"class")
[1] "cog_spec"
[1] FALSE
> 
> # set up data
> p <- ggplot2::qplot(Sepal.Length, Sepal.Width, data = iris, geom = c("point", "smooth"))
> dt <- tibble::data_frame(panel = list(p))
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
> 
> # compute cognostics like normal
> add_panel_cogs(dt)
Error in switch(as.character(layer$stat_params$method), loess = "geom_smooth_loess",  : 
  EXPR must be a length 1 vector
Calls: add_panel_cogs ... get_layer_info -> layer_info -> layer_info.ggplot -> lapply -> FUN
Execution halted
Running ‘testthat.R’ [13s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(autocogs)
  > 
  > test_check("autocogs")
  ── 1. Failure: ggplot2 layers (@test-layers.R#20)  ─────────────────────────────
  `{ ... }` produced warnings.
  
  ── 2. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246)  ─────────────────────
  EXPR must be a length 1 vector
  Backtrace:
    1. ggplot2::qplot(cty, hwy, data = mpg, geom = "smooth")
    9. autocogs:::expect_auto_cogs(...)
   11. autocogs:::plot_cogs(.)
   19. autocogs:::get_layer_info(p, keep = keep_layers, ...)
   21. autocogs:::layer_info.ggplot(p, keep = keep, ...)
   22. base::lapply(...)
   23. autocogs:::FUN(X[[i]], ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 241 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Failure: ggplot2 layers (@test-layers.R#20) 
  2. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
File ‘BaBooN/libs/BaBooN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   3.8Mb
Namespace in Imports field not imported from: ‘glpkAPI’
  All declared Imports should be used.
Running examples in ‘BacArena-Ex.R’ failed
The error most likely occurred in:

> ### Name: HeatMapFeeding
> ### Title: Function for plotting heatmap of feeding between two selected
> ###   cell models
> ### Aliases: HeatMapFeeding HeatMapFeeding,Eval-method
> 
> ### ** Examples
> 
> sim <- sihumi_test
> HeatMapFeeding(object = sim, speciesA = 1, speciesB = 2, var_nr = 78)
Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr],  :
  sim_step 1 : No crossfeeding found. Try other metaboites or time points.
Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr],  :
  sim_step 2 : No crossfeeding found. Try other metaboites or time points.
Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr],  :
  sim_step 3 : No crossfeeding found. Try other metaboites or time points.
Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr],  :
  sim_step 4 : No crossfeeding found. Try other metaboites or time points.
Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr],  :
  sim_step 5 : No crossfeeding found. Try other metaboites or time points.
Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr],  :
  sim_step 6 : No crossfeeding found. Try other metaboites or time points.
Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr],  :
  sim_step 7 : No crossfeeding found. Try other metaboites or time points.
Error in if (z[h, 1] == names(object@specs)[speciesA]) d[h, 1] <- 1 else if (z[h,  : 
  argument is of length zero
Calls: HeatMapFeeding -> HeatMapFeeding
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘BacArena-Introduction.Rmd’ using rmarkdown
Loading required package: sybil
Loading required package: Matrix
Loading required package: lattice
Loading required package: ReacTran
Loading required package: rootSolve
Loading required package: deSolve
Loading required package: shape
BacArena paper: https://doi.org/10.1371/journal.pcbi.1005544
 Tutorials: https://bacarena.github.io
 Model import from SBML: https://github.com/euba/BacArena/wiki/Model-import
 Development and help: https://github.com/euba/bacarena
Warning in simEnv(arena, time = 10) :
  If growth is limited by maximum weight for an organism (max_weight=TRUE) it is recommended to use minimize total flux (sec_obj='mtf').
Quitting from lines 231-232 (BacArena-Introduction.Rmd) 
Error: processing vignette 'BacArena-Introduction.Rmd' failed with diagnostics:
Faceting variables must have at least one value
--- failed re-building ‘BacArena-Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 93.7Mb
  sub-directories of 1Mb or more:
    libs  92.5Mb
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(bagRboostR)
  > 
  > test_package("bagRboostR")
  ── 1. Error: bagging returns a character vector of predicted classes (@test_bagg
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. bagRboostR::bagging(...) tests/test_bagging.R:6:4
   2. base::droplevels(t[, outcome.label])
  
  ── 2. Error: samme returns a character vector of predicted classes (@test_samme.
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. bagRboostR::samme(activity ~ ., train, test, 3, ntree = 5, trace = F) tests/test_samme.R:6:2
   2. base::droplevels(t[, outcome.label])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 37 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: bagging returns a character vector of predicted classes (@test_bagging.R#6) 
  2. Error: samme returns a character vector of predicted classes (@test_samme.R#6) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
Package suggested but not available for checking: ‘mzR’
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
File ‘BALD/libs/BALD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘docopt’
  All declared Imports should be used.
Running examples in ‘BANEScarparkinglite-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_range_crude
> ### Title: Download records from a specified range from the Bath: Hacked
> ###   datastore
> ### Aliases: get_range_crude
> 
> ### ** Examples
> 
> # Records for 1st June 2016
> raw_data <- get_range_crude("2016-06-01 00:00:00", "2016-06-01 23:59:59")
Making request to Socrata Open Data API...
Error in open.connection(con, "rb") : HTTP error 404.
Calls: get_range_crude ... datasource_connection -> read_connection -> open -> open.connection
Execution halted
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File ‘Barnard/libs/Barnard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.1Mb
    libs   5.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.2Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
File ‘base64enc/libs/base64enc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BASIX/libs/BASIX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘using-the-basket-package.Rmd’ using rmarkdown
Quitting from lines 91-92 (using-the-basket-package.Rmd) 
Error: processing vignette 'using-the-basket-package.Rmd' failed with diagnostics:
Assigned data `x$p0` must be compatible with existing data.
✖ Existing data has 30000 rows.
✖ Assigned data has 6 rows.
ℹ Only vectors of size 1 are recycled.
--- failed re-building ‘using-the-basket-package.Rmd’

SUMMARY: processing the following file failed:
  ‘using-the-basket-package.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘batman/libs/batman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: get_similar_players
> ### Title: Similar players to archetypoids
> ### Aliases: get_similar_players
> 
> ### ** Examples
> 
> (s0 <- Sys.time())
[1] "2020-03-31 10:12:51 BST"
> # Turn off temporarily some negligible warnings from the 
> # archetypes package to avoid missunderstandings. The code works well.
> oldw <- getOption("warn")
> options(warn = -1)
> library(Anthropometry)
> df <- do_join_games_bio("ACB", acb_games_1718, acb_players_1718)
> df1 <- do_add_adv_stats(df)
> df2 <- do_stats(df1, "Total", "2017-2018", "ACB", "Regular Season")
Joining, by = c("Name", "Team", "CombinID", "Position", "Nationality", "GP", "GS")
> df3 <- df2[which(df2$Position == "Guard")[1:31], c("MP", "PTS", "Name")]
> preproc <- preprocessing(df3[,1:2], stand = TRUE, percAccomm = 1)
> set.seed(4321)
> lass <- stepArchetypesRawData(preproc$data, 1:2, numRep = 20, verbose = FALSE)
> res <- archetypoids(2, preproc$data, huge = 200, step = FALSE, ArchObj = lass,
+                     nearest = "cand_ns", sequ = TRUE)
> cases <- anthrCases(res)
> df3[cases,]
Error: Must subset rows with a valid subscript vector.
✖ The subscript `cases` has the wrong type `anthrCases`.
ℹ It must be logical, numeric, or character.
Backtrace:
     █
  1. ├─df3[cases, ]
  2. └─tibble:::`[.tbl_df`(df3, cases, )
  3.   └─tibble:::tbl_subset_row(xo, i = i, i_arg)
  4.     └─tibble:::vectbl_as_row_index(i, x, i_arg)
  5.       └─tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
  6.         ├─tibble:::subclass_row_index_errors(...)
  7.         │ ├─base::tryCatch(...)
  8.         │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
  9.         │ │   └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.         │ │     └─base:::doTryCatch(return(expr), name, parentenv, handler)
 11.         │ └─base::force(expr)
 12.         └─vctrs::vec_as_location(i, n, arg = as_label(i_arg))
Execution halted
installed size is 78.3Mb
  sub-directories of 1Mb or more:
    libs  76.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  rcpparma_hello_world.cpp:930:4: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:930:12: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:939:4: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:939:12: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/BayesBD.Rcheck/00install.out’ for details.
File ‘BayesComm/libs/BayesComm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bayescount/libs/bayescount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
installed size is 73.1Mb
  sub-directories of 1Mb or more:
    libs  72.2Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  16.0Mb
File ‘bayesGARCH/libs/bayesGARCH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BayesGPfit/libs/BayesGPfit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bayesianETAS/libs/bayesianETAS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shinytest’ ‘testthat’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.9Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘bayesloglin/libs/bayesloglin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  30.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   4.1Mb
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘carData’ ‘runjags’
  All declared Imports should be used.
Running ‘testthat.R’ [19s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BayesPostEst)
  > 
  > test_check("BayesPostEst")
  ── 1. Failure: pars subsetting works (@test_mcmcTab.R#61)  ─────────────────────
  object$Variable not equal to factor(c(sprintf("b[%s]", 1:3))).
  Types not compatible: character is not integer
  
  ── 2. Failure: pars subsetting works (@test_mcmcTab.R#83)  ─────────────────────
  object$Variable not equal to factor(c(sprintf("b[%s]", 1:2))).
  Types not compatible: character is not integer
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 52 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: pars subsetting works (@test_mcmcTab.R#61) 
  2. Failure: pars subsetting works (@test_mcmcTab.R#83) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘bayesQR/libs/bayesQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  15.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
File ‘BayesTree/libs/BayesTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 133.8Mb
  sub-directories of 1Mb or more:
    libs  133.7Mb
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘locfit’ ‘secr’
  All declared Imports should be used.
File ‘BCBCSF/libs/BCBCSF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
File ‘Bclim/libs/Bclim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  sparseFactor.cpp:33:10: warning: explicitly assigning value of variable of type 'Rcpp::IntegerVector' (aka 'Vector<13>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/BClustLonG.Rcheck/00install.out’ for details.
File ‘bcpa/libs/bcpa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
File ‘bcv/libs/bcv.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Running ‘testthat.R’ [145s/161s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(beadplexr)
  > 
  > test_check("beadplexr")
  ── 1. Error: ident_bead_pop() works (@test_identify_assay_analyte.R#39)  ───────
  Assigned data `c("A", "B")` must be compatible with existing data.
  ✖ Existing data has 5126 rows.
  ✖ Assigned data has 2 rows.
  ℹ Only vectors of size 1 are recycled.
  Backtrace:
   1. base::`$<-`(`*tmp*`, BeadID, value = c("A", "B"))
   2. tibble:::`$<-.tbl_df`(`*tmp*`, BeadID, value = c("A", "B"))
   3. tibble:::tbl_subassign(...)
   4. tibble:::vectbl_recycle_rhs(...)
   5. base::tryCatch(...)
   6. base:::tryCatchList(expr, classes, parentenv, handlers)
   7. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 398 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: ident_bead_pop() works (@test_identify_assay_analyte.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 108.9Mb
  sub-directories of 1Mb or more:
    libs  107.4Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘png’
  All declared Imports should be used.
File ‘BenfordTests/libs/BenfordTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
File ‘betategarch/libs/betategarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Note: found 4 marked Latin-1 strings
  Note: found 611 marked UTF-8 strings
installed size is 135.0Mb
  sub-directories of 1Mb or more:
    include  134.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
File ‘BiasedUrn/libs/BiasedUrn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  11.1Mb
possible bashism in configure line 12 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 22 (echo -n):
  echo -n "  checking for OS..."
File ‘biganalytics/libs/biganalytics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: browse_opening
> ### Title: Browse opening
> ### Aliases: browse_opening
> 
> ### ** Examples
> 
> f <- system.file("extdata", "Kasparov.gz", package = "bigchess")
> con <- gzfile(f,encoding = "latin1")
> df <- read.pgn(con,quiet = TRUE,ignore.other.games = TRUE,stat.moves = FALSE)
> # Analyze best Kasparov openings:
> bo <- browse_opening(subset(df,grepl("Kasparov",White)))
Error in UseMethod("droplevels") : 
  no applicable method for 'droplevels' applied to an object of class "character"
Calls: browse_opening -> tree_move -> droplevels
Execution halted
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
File ‘bigGP/libs/bigGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘biglars/libs/biglars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
File ‘biglm/libs/biglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      2.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
possible bashism in configure line 14 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 24 (echo -n):
  echo -n "  checking for OS..."
File ‘bigReg/libs/bigReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs     12.3Mb
possible bashism in configure line 13 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 23 (echo -n):
  echo -n "  checking for OS..."
File ‘bigtabulate/libs/bigtabulate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lattice’ ‘zoo’
  All declared Imports should be used.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
File ‘bild/libs/bild.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
File ‘binom/libs/binom.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘binostics/libs/binostics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
Package suggested but not available for checking: ‘msa’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Package suggested but not available for checking: ‘BiocVersion’
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘fs’
  All declared Imports should be used.
File ‘bioPN/libs/bioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.3Mb
    extdata   1.7Mb
Running examples in ‘bios2mds-Ex.R’ failed
The error most likely occurred in:

> ### Name: bios2mds-package
> ### Title: From BIOlogical Sequences to MultiDimensional Scaling
> ### Aliases: bios2mds-package bios2mds
> ### Keywords: package
> 
> ### ** Examples
> 
> # The MSA files provided with the package correspond to the sequence 
> # alignment of non-olfactory class A G-protein-coupled receptors from
> # H. sapiens and D. melanogaster prepared by Deville et al. (2009).  
> 
> # loading GPCR data
> data(gpcr)
> 
> # building distance matrices between the aligned GPCR sequences from
> # H. sapiens and D. melanogaster
> human <- import.fasta(system.file("msa/human_gpcr.fa", package = "bios2mds"))
> drome <- import.fasta(system.file("msa/drome_gpcr.fa", package = "bios2mds"))
> 
> #active <- mat.dif(human, human)
> # or
> active <- gpcr$dif$sapiens.sapiens
> 
> #sup <- mat.dif(drome, human)
> # or
> sup <- gpcr$dif$melanogaster.sapiens
> 
> # performing MDS analysis of the GPCR sequences from H. sapiens 
> mmds_active <- mmds(active, group.file=system.file(
+ "csv/human_gpcr_group.csv",package = "bios2mds"))
Error in rbind(col, matrix(c(names[i], levels(element[, 2])[element[j,  : 
  number of columns of matrices must match (see arg 2)
Calls: mmds -> col.group -> rbind
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Namespaces in Imports field not imported from:
  ‘esquisse’ ‘rgdal’
  All declared Imports should be used.
Running examples in ‘biscale-Ex.R’ failed
The error most likely occurred in:

> ### Name: bi_class
> ### Title: Create Classes for Bivariate Maps
> ### Aliases: bi_class
> 
> ### ** Examples
> 
> # quantile breaks, 2x2
> data <- bi_class(stl_race_income, x = pctWhite, y = medInc, style = "quantile", dim = 2)
Warning in bi_class(stl_race_income, x = pctWhite, y = medInc, style = "quantile",  :
  The 'sf' package is not loaded, and the class 'sf' attribute of the given data set has been lost. Load 'sf' to retain the class when using 'bi_class'.
Error: All columns in a tibble must be vectors.
✖ Column `geometry` is a `sfc_POLYGON/sfc` object.
Backtrace:
     █
  1. └─biscale::bi_class(...)
  2.   ├─dplyr::mutate(.data, bi_x = cut(!!xQ, breaks = bins_x, include.lowest = TRUE))
  3.   └─dplyr:::mutate.data.frame(...)
  4.     ├─base::as.data.frame(mutate(tbl_df(.data), ...))
  5.     ├─dplyr::mutate(tbl_df(.data), ...)
  6.     └─dplyr::tbl_df(.data)
  7.       ├─tibble::as_tibble(data, .name_repair = "check_unique")
  8.       └─tibble:::as_tibble.data.frame(data, .name_repair = "check_unique")
  9.         └─tibble:::lst_to_tibble(unclass(x), .rows, .name_repair)
 10.           └─tibble:::check_valid_cols(x)
Execution halted
Running ‘testthat.R’ [5s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biscale)
  > 
  > test_check("biscale")
  ── 1. Error: sf warning is triggered (@test_bi_class.R#10)  ────────────────────
  All columns in a tibble must be vectors.
  ✖ Column `geometry` is a `sfc_POLYGON/sfc` object.
  Backtrace:
    1. testthat::expect_warning(...)
    6. biscale::bi_class(...)
    8. dplyr:::mutate.data.frame(...)
   11. dplyr::tbl_df(.data)
   13. tibble:::as_tibble.data.frame(data, .name_repair = "check_unique")
   14. tibble:::lst_to_tibble(unclass(x), .rows, .name_repair)
   15. tibble:::check_valid_cols(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 82 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: sf warning is triggered (@test_bi_class.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
File ‘bitops/libs/bitops.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘corrgram’ ‘rpivotTable’ ‘shinyAce’
  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: ‘RQuantLib’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RGtk2’ ‘cairoDevice’ ‘ergm’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘haven’ ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
installed size is 55.3Mb
  sub-directories of 1Mb or more:
    libs  53.4Mb
Package suggested but not available for checking: ‘bigrf’

Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
installed size is 60.5Mb
  sub-directories of 1Mb or more:
    libs  59.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
File ‘blockmodels/libs/blockmodels.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘blockTools/libs/blockTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
File ‘Bmix/libs/Bmix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
File ‘BMRV/libs/BMRV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
installed size is 371.1Mb
  sub-directories of 1Mb or more:
    include    8.8Mb
    lib      361.9Mb
installed size is 81.1Mb
  sub-directories of 1Mb or more:
    libs  80.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
File ‘bootruin/libs/bootruin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
File ‘bqtl/libs/bqtl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’
File ‘brainwaver/libs/brainwaver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Branching/libs/Branching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: get_brmap
> ### Title: Get Brazilian maps from different geographic levels
> ### Aliases: get_brmap
> ### Keywords: IBGE geographic levels shapefile spatial
> 
> ### ** Examples
> 
> ## Retrieving the map from the State of Rio de Janeiro
> rio_map <- get_brmap(geo = "State",
+                      geo.filter = list(State = 33),
+                      class = "sf")
Error: All columns in a tibble must be vectors.
✖ Column `geometry` is a `sfc_MULTIPOLYGON/sfc` object.
Backtrace:
     █
  1. └─brazilmaps::get_brmap(...)
  2.   └─`%>%`(...)
  3.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.         └─brazilmaps:::`_fseq`(`_lhs`)
  7.           └─magrittr::freduce(value, `_function_list`)
  8.             └─function_list[[i]](value)
  9.               ├─dplyr::filter(., brmap[[(names(geo.filter)[i])]] %in% geo.filter[[i]])
 10.               └─dplyr:::filter.data.frame(...)
 11.                 ├─base::as.data.frame(filter(tbl_df(.data), ..., .preserve = .preserve))
 12.                 ├─dplyr::filter(tbl_df(.data), ..., .preserve = .preserve)
 13.                 └─dplyr::tbl_df(.data)
 14.                   ├─tibble::as_tibble(data, .name_repair = "chec
Execution halted
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     3.5Mb
    doc   2.6Mb
Error(s) in re-building vignettes:
--- re-building ‘broom_mixed_intro.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Registered S3 methods overwritten by 'broom.mixed':
  method         from 
  augment.lme    broom
  augment.merMod broom
  glance.lme     broom
  glance.merMod  broom
  glance.stanreg broom
  tidy.brmsfit   broom
  tidy.gamlss    broom
  tidy.lme       broom
  tidy.merMod    broom
  tidy.rjags     broom
  tidy.stanfit   broom
  tidy.stanreg   broom
Loading required package: brms
Loading required package: Rcpp
Loading 'brms' package (version 2.12.0). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').

Attaching package: 'brms'

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

    ar

Loading required package: dotwhisker
Loading required package: ggplot2
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 68-82 (broom_mixed_intro.rmd) 
Error: processing vignette 'broom_mixed_intro.rmd' failed with diagnostics:
Aesthetics must be either length 1 or the same as the data (6): xmin and xmax
--- failed re-building ‘broom_mixed_intro.rmd’

SUMMARY: processing the following file failed:
  ‘broom_mixed_intro.rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin    2.7Mb
    doc    1.1Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is 42.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  40.4Mb
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
installed size is 105.5Mb
  sub-directories of 1Mb or more:
    libs  104.7Mb
File ‘BTYDplus/libs/BTYDplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘modeldata’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘bvarsv/libs/bvarsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘bvls/libs/bvls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
File ‘bytescircle/libs/bytescircle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘here’ ‘withr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
File ‘CAMAN/libs/CAMAN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.2Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘details’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Namespace in Imports field not imported from: ‘g.data’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘animation’ ‘devtools’ ‘gapminder’ ‘knitr’ ‘rlist’ ‘rmarkdown’
  ‘roxygen2’ ‘sde’ ‘shiny’ ‘tidyverse’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘fs’ ‘janitor’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  ../inst/include/SignificantIntervalSearchFais.h:97:17: warning: 'saveSignificantInterval' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ../inst/include/SignificantIntervalSearchFais.h:100:17: warning: 'saveTestableInterval' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
See ‘/data/gannet/ripley/R/packages/tests-clang/CASMAP.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
File ‘catIrt/libs/catIrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cat/libs/cat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.1Mb
Namespace in Imports field not imported from: ‘prettydoc’
  All declared Imports should be used.
File ‘cbird/libs/cbird.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 217.4Mb
  sub-directories of 1Mb or more:
    libs  216.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par points
  text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
File ‘cccp/libs/cccp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CDLasso/libs/CDLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.3Mb
File ‘CDVine/libs/CDVine.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
File ‘cec2013/libs/cec2013.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   7.0Mb
File ‘censNID/libs/censNID.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
File ‘cents/libs/cents.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
File ‘cgAUC/libs/cgAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cgh/libs/cgh.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/changepoint.np.Rcheck/00install.out’ for details.
File ‘changepoint/libs/changepoint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ChargeTransport/libs/ChargeTransport.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cheb/libs/cheb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘foreach’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
File ‘ChIPtest/libs/ChIPtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Namespace in Imports field not imported from: ‘forcats’
  All declared Imports should be used.
File ‘CHsharp/libs/CHsharp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
File ‘CIFsmry/libs/CIFsmry.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sp’
  All declared Imports should be used.
File ‘ClickClust/libs/ClickClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: merge_results
> ### Title: Merge two slidingwin analyses.
> ### Aliases: merge_results
> 
> ### ** Examples
> 
> 
> #Simple test example
> #Create data from a subset of our test dataset
> #Just use two years
> biol_data <- Mass[1:2, ]
> clim_data <- MassClimate[grep(pattern = "1979|1986", x = MassClimate$Date), ]
> 
> output <- slidingwin(xvar = list(Temp = clim_data$Temp),
+                     cdate = clim_data$Date, 
+                     bdate = biol_data$Date, 
+                     baseline = lm(Mass ~ 1, data = biol_data),
+                     range = c(1, 0), 
+                     type = "relative", stat = "mean", 
+                     func = c("lin"), cmissing = FALSE, cinterval = "day")
Initialising, please wait...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  ||||||||||||||||||||||||                                               |  33%
  |                                                                            
  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%Error in min(modlist$ModelAICc) : invalid 'type' (list) of argument
Calls: slidingwin -> basewin -> %in%
Execution halted
Namespaces in Imports field not imported from:
  ‘car’ ‘emmeans’
  All declared Imports should be used.
Running examples in ‘ClinReport-Ex.R’ failed
The error most likely occurred in:

> ### Name: report.quali.hlev
> ### Title: 'Hierarchical Qualitative' statistics reporting (experimental)
> ### Aliases: report.quali.hlev
> 
> ### ** Examples
> 
> 
> data(adverse_event)
> 
> test=report.quali.hlev(data=adverse_event,subjid="SUBJID",var_upper="PTNAME",
+ var_lower="SOCNAME",lower.levels="System Organ Class",upper.levels="Prefered Terms",x1="randtrt")
Error in match.names(clabs, names(xi)) : 
  names do not match previous names
Calls: report.quali.hlev -> report.quali.hlev -> rbind -> rbind -> match.names
Execution halted
File ‘clogitboost/libs/clogitboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clogitL1/libs/clogitL1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘KernSmooth’
  All declared Imports should be used.
possible bashism in cleanup line 15 (brace expansion):
  rm -f src/*.{o,so,mod}
  possible bashism in cleanup line 17 (brace expansion):
  rm -f config.{log,status}
  possible bashism in cleanup line 22 (brace expansion):
  rm -f vignettes/*.{tex,aux,bbl,blg,log,toc,idx,ind,ilg,out,synctex.gz}
File ‘clustering.sc.dp/libs/clustering.sc.dp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: clusterlab
> ### Title: clusterlab
> ### Aliases: clusterlab
> 
> ### ** Examples
> 
> synthetic <- clusterlab(centers=4,r=8,sdvec=c(2.5,2.5,2.5,2.5),   
+ alphas=c(1,1,1,1),centralcluster=FALSE,   
+ numbervec=c(50,50,50,50)) # for a six cluster solution)   
***clusterlab***
mode: circle
simulating clusters...
Error: More than one expression parsed
Backtrace:
    █
 1. └─clusterlab::clusterlab(...)
 2.   ├─ggplot2::ggplot(...)
 3.   ├─ggplot2:::ggplot.default(...)
 4.   └─ggplot2::aes_string(x = "PC1", y = "PC2", colour = identitymatrix$cluster)
 5.     └─base::lapply(...)
 6.       └─ggplot2:::FUN(X[[i]], ...)
 7.         └─rlang::parse_expr(x)
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 43-45 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
More than one expression parsed
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘purrr’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
File ‘ClusterStability/libs/ClusterStability.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clusteval/libs/clusteval.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘ClustMMDD/libs/ClustMMDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
File ‘clv/libs/clv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cmprsk/libs/cmprsk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Imports includes 42 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.3Mb
File ‘COBRA/libs/COBRA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
File ‘codadiags/libs/codadiags.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘readr’
  All declared Imports should be used.
Running ‘testthat.R’ [84s/214s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat) 
  > library(codyn)
  > test_check("codyn")
  ── 1. Failure: rank_shift loads and returns correct result (@test_rank_shift.R#1
  result[, 1] inherits from `character` not `factor`.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 359 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: rank_shift loads and returns correct result (@test_rank_shift.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘coenoflex/libs/coenoflex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  24.3Mb
Error(s) in re-building vignettes:
--- re-building ‘collateral.Rmd’ using rmarkdown
Quitting from lines 221-229 (collateral.Rmd) 
Error: processing vignette 'collateral.Rmd' failed with diagnostics:
Input must be a vector, not a `safely_mapped` object.
--- failed re-building ‘collateral.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘collUtils/libs/collUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: plot.colocal
> ### Title: Making scatter plots for signal proportions before and after
> ###   d-type or z-type normalization
> ### Aliases: plot.colocal
> 
> ### ** Examples
> 
> ## a simulated 3D example data.
> data("twolines")
> 
> twolines.results <- nsinc.d(data = twolines, membership = "membership",
+                             dim = 3, r.model = "r.med")
The method is 'nsinc.d'!
The input data has dimension of 3!
The input study region is 'NULL'!
The observed study region is [-0.994687642,0.991983793] X [-0.994783715,0.984829183] X [-0.25846953,0.343853326]!

 The default full r range for colocalization index of type d is [0.00550850564633427,2.03825393738339]!

The r.model = 'r.med'!
r.min = 0.722833786275035 is used!
r.max = 0.722833786275035 is used!
Because of r.min = r.max, r.count = 1 and r.adjust = 0 are used!
Bi-direction colocalization is considered!
index.d for r = 0.722833786275035 is -0.224788967716664 ;
The average coolocalization index of type d over all choosen r's is = -0.224788967716664!
> 
> plot(twolines.results)
Error in levels(P.all$type) <- c(expression(paste(italic(P), sep = "")),  : 
  unimplemented type 'expression' in 'HashTableSetup'
Calls: plot -> plot.colocal -> <Anonymous>
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Package suggested but not available for checking: ‘CAM’

Suggests orphaned package: ‘flare’
File ‘compareC/libs/compareC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  27.0Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  22.9Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘checkmate’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Running ‘testthat.R’ [11s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(compstatr)
  > 
  > test_check("compstatr")
  ── 1. Failure: correct output is returned on sample data (@test_projectXY.R#36) 
  sf::st_crs(results)[[1]] not equal to 4269.
  Types not compatible: character is not double
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 225 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: correct output is returned on sample data (@test_projectXY.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘concaveman-Ex.R’ failed
The error most likely occurred in:

> ### Name: concaveman
> ### Title: concaveman: A very fast 2D concave hull algorithm.
> ### Aliases: concaveman concaveman-package concaveman concaveman.matrix
> ###   concaveman.sf concaveman.SpatialPoints
> 
> ### ** Examples
> 
> data(points)
> polygons <- concaveman(points)
Error: All columns in a tibble must be vectors.
✖ Column `geometry` is a `sfc_POINT/sfc` object.
Backtrace:
     █
  1. ├─concaveman::concaveman(points)
  2. └─concaveman:::concaveman.sf(points)
  3.   └─`%>%`(...)
  4.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  5.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  7.         └─concaveman:::`_fseq`(`_lhs`)
  8.           └─magrittr::freduce(value, `_function_list`)
  9.             ├─base::withVisible(function_list[[k]](value))
 10.             └─function_list[[k]](value)
 11.               ├─dplyr::summarise(...)
 12.               └─dplyr:::summarise.data.frame(...)
 13.                 ├─base::as.data.frame(summarise(tbl_df(.data), ...))
 14.                 ├─dplyr::summarise(tbl_df(.data), ...)
 15.                 └─dplyr::tbl_df(.data)
 16.                   ├─tibble::as_tibble(d
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘ConConPiWiFun/libs/ConConPiWiFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘concreg/libs/concreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘compiler’ ‘rlang’
  All declared Imports should be used.
Running examples in ‘concurve-Ex.R’ failed
The error most likely occurred in:

> ### Name: curve_corr
> ### Title: Computes Consonance Intervals for Correlations
> ### Aliases: curve_corr
> 
> ### ** Examples
> 
> 
> GroupA <- rnorm(50)
> GroupB <- rnorm(50)
> joe <- curve_corr(x = GroupA, y = GroupB, alternative = "two.sided", method = "pearson")
> tibble::tibble(joe[[1]])
Error: All columns in a tibble must be vectors.
✖ Column `joe[[1]]` is a `data.frame/concurve` object.
Backtrace:
    █
 1. └─tibble::tibble(joe[[1]])
 2.   └─tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
 3.     └─tibble:::check_valid_col(res, col_names[[j]], j)
 4.       └─tibble:::check_valid_cols(set_names(list(x), name))
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘examples.Rmd’ using rmarkdown
Quitting from lines 51-52 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
All columns in a tibble must be vectors.
✖ Column `intervalsdf[[1]]` is a `data.frame/concurve` object.
--- failed re-building ‘examples.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Missing or unexported object: ‘xlsx::CellBlock.default’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
File ‘condSURV/libs/condSURV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape’
  All declared Imports should be used.
File ‘constrainedKriging/libs/constrainedKriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 70.6Mb
  sub-directories of 1Mb or more:
    libs  69.4Mb
Namespaces in Imports field not imported from:
  ‘geosphere’ ‘igraph’ ‘methods’ ‘rgdal’ ‘sf’
  All declared Imports should be used.
File ‘contoureR/libs/contoureR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘formattable’ ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘magrittr’
  ‘readr’ ‘readxl’ ‘tidyverse’
  All declared Imports should be used.
Running examples in ‘convergEU-Ex.R’ failed
The error most likely occurred in:

> ### Name: country_ranking
> ### Title: Ranking of EU countries by time
> ### Aliases: country_ranking
> 
> ### ** Examples
> 
> 
> # Example 1
> # Sorted dataframe in the format years by countries:
> require(tibble)
Loading required package: tibble
> myTB  <- tibble::tribble(
+ ~years, ~UK, ~DE, ~IT,
+ 1988,   1201, 868, 578,
+ 1989,   1150, 978, 682,
+ 1990,   998,  1250, 332,
+ 1991,  1600,  1350, 802
+ )
> 
> # Country ranking according to the indicator higher is the best:
> res <- country_ranking(myTB,timeName="years")
Error: Assigned data `rank(unlist(ord_MS[auxMS, -posizTime]), ties.method = "min")` must be compatible with row subscript `auxMS`.
✖ 1 row must be assigned.
✖ Assigned data has 3 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─convergEU::country_ranking(myTB, timeName = "years")
 2.   ├─base::`[<-`(...)
 3.   └─tibble:::`[<-.tbl_df`(...)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
Namespace in Imports field not imported from: ‘mcc’
  All declared Imports should be used.
File ‘cord/libs/cord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘rmarkdown’ ‘shinyWidgets’ ‘shinydashboard’
  ‘shinyjs’
  All declared Imports should be used.
Running examples in ‘corpus-Ex.R’ failed
The error most likely occurred in:

> ### Name: text_locate
> ### Title: Searching for Terms
> ### Aliases: text_count text_detect text_locate text_match text_sample
> ###   text_subset
> 
> ### ** Examples
> 
> text <- c("Rose is a rose is a rose is a rose.",
+           "A rose by any other name would smell as sweet.",
+           "Snow White and Rose Red")
> 
> text_count(text, "rose")
[1] 4 1 1
> text_detect(text, "rose")
[1] TRUE TRUE TRUE
> text_locate(text, "rose")
Error in sum(colwidths) : invalid 'type' (list) of argument
Calls: <Anonymous> ... print.corpus_text_locate -> format.corpus_text_locate
Execution halted
Running ‘testthat.R’ [11s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 601 | SKIPPED: 5 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘profr’ ‘xtable’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Package suggested but not available for checking: ‘xcms’
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.6Mb
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   6.9Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
File ‘COUSCOus/libs/COUSCOus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
File ‘covBM/libs/covBM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘dplyr’ ‘ggridges’ ‘markdown’ ‘shinyjs’ ‘tidyr’
  All declared Imports should be used.
Running ‘testthat.R’ [6s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(covid19us)
  > 
  > test_check("covid19us")
  ── 1. Failure: get_states_daily works (@test-all.R#21)  ────────────────────────
  nrow(too_early) not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 2. Error: other funs work (@test-all.R#53)  ─────────────────────────────────
  Can't subset columns that don't exist.
  ✖ The column `ssl_no_verify` doesn't exist.
  Backtrace:
    1. covid19us::get_tracker_urls()
   30. vctrs:::stop_subscript_oob(...)
   31. vctrs:::stop_subscript(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: get_states_daily works (@test-all.R#21) 
  2. Error: other funs work (@test-all.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
File ‘CoxBoost/libs/CoxBoost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘coxinterval/libs/coxinterval.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Namespace in Imports field not imported from: ‘coxme’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
File ‘CoxPlus/libs/CoxPlus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘coxrobust/libs/coxrobust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘cents’
  All declared Imports should be used.
File ‘cpm/libs/cpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgetsRGtk2’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘cr17-Ex.R’ failed
The error most likely occurred in:

> ### Name: fitCuminc
> ### Title: Cumulative Incidences Curves
> ### Aliases: fitCuminc
> 
> ### ** Examples
> 
> fitCuminc(time = LUAD$time, risk = LUAD$event, group = LUAD$gender, cens = "alive")
19 cases omitted due to missing values
Warning in cuminc(ftime = time, fstatus = risk, group = group, cencode = cens) :
  NAs introduced by coercion
Error in cuminc(ftime = time, fstatus = risk, group = group, cencode = cens) : 
  NAs in foreign function call (arg 3)
Calls: fitCuminc -> cuminc
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in cuminc(ftime = time, fstatus = risk, group = group, cencode = cens) :
  NAs introduced by coercion
Quitting from lines 176-180 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
NAs in foreign function call (arg 3)
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespaces in Imports field not imported from:
  ‘gdistance’ ‘raster’
  All declared Imports should be used.
File ‘credule/libs/credule.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
File ‘crrp/libs/crrp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘crrSC/libs/crrSC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘crskdiag/libs/crskdiag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  27.8Mb
Namespace in Imports field not imported from: ‘survminer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
Note: found 59670 marked Latin-1 strings
  Note: found 16 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is 113.2Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    libs  110.1Mb
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘pkgbuild’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.6Mb
File ‘cusp/libs/cusp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
File ‘cvxbiclustr/libs/cvxbiclustr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cvxclustr/libs/cvxclustr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   5.9Mb
File ‘cycleRtools/libs/cycleRtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
File ‘DALY/libs/DALY.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘expm’
  All declared Imports should be used.
File ‘darts/libs/darts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
Namespace in Imports field not imported from: ‘DatabaseConnectorJars’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   4.4Mb
Namespace in Imports field not imported from: ‘miniUI’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinyFiles’ ‘shinycssloaders’ ‘shinyjs’ ‘shinythemes’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
.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.
File ‘datamap/libs/datamap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘future’ ‘iterators’ ‘readr’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   5.5Mb
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
installed size is 51.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  49.6Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
File ‘dblcens/libs/dblcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dplyr’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
File ‘DCluster/libs/DCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
installed size is 50.3Mb
  sub-directories of 1Mb or more:
    libs  50.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
File ‘DDHFm/libs/DDHFm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
File ‘decon/libs/decon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘UScensus2010’
  All declared Imports should be used.
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.
File ‘deformula/libs/deformula.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘assertthat’
  All declared Imports should be used.
installed size is 87.3Mb
  sub-directories of 1Mb or more:
    libs  84.6Mb
File ‘delt/libs/delt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
File ‘DendSer/libs/DendSer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘denpro/libs/denpro.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
File ‘depth/libs/depth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   3.4Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
File ‘desire/libs/desire.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.6Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.4Mb
File ‘dfphase1/libs/dfphase1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 53.6Mb
  sub-directories of 1Mb or more:
    libs  53.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
File ‘dgof/libs/dgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc           9.7Mb
    htmlwidgets   5.9Mb
Error(s) in re-building vignettes:
--- re-building ‘dialr.Rmd’ using rmarkdown
Quitting from lines 135-150 (dialr.Rmd) 
Error: processing vignette 'dialr.Rmd' failed with diagnostics:
Input must be a vector, not a `phone` object.
--- failed re-building ‘dialr.Rmd’

--- re-building ‘oneshot.Rmd’ using rmarkdown
Warning: ph_valid() is soft deprecated as of dialr 0.2.0
please use is_valid() instead
Warning: ph_possible() is soft deprecated as of dialr 0.2.0
please use is_possible() instead
Warning: ph_region() is soft deprecated as of dialr 0.2.0
please use get_region() instead
Warning: ph_type() is soft deprecated as of dialr 0.2.0
please use get_type() instead
Warning: ph_format() is soft deprecated as of dialr 0.2.0
please use format.phone() instead
Warning: ph_format() is soft deprecated as of dialr 0.2.0
please use format.phone() instead
--- finished re-building ‘oneshot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘DiceOptim/libs/DiceOptim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 37 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘clValid’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
File ‘diffIRT/libs/diffIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘sf’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
File ‘diffrprojects/libs/diffrprojects.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
File ‘DiffusionRgqd/libs/DiffusionRgqd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DiffusionRimp/libs/DiffusionRimp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
File ‘DiffusionRjgqd/libs/DiffusionRjgqd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
File ‘dils/libs/dils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DIME/libs/DIME.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
File ‘DIRECT/libs/DIRECT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘splancs’ ‘utils’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
File ‘dismo/libs/dismo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘dissUtils/libs/dissUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
File ‘distory/libs/distory.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘dkDNA/libs/dkDNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  16.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   4.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Running examples in ‘DMwR2-Ex.R’ failed
The error most likely occurred in:

> ### Name: centralImputation
> ### Title: Fill in NA values with central statistics
> ### Aliases: centralImputation
> ### Keywords: models
> 
> ### ** Examples
> 
> data(algae,package="DMwR2")
> cleanAlgae <- centralImputation(algae)
Error: `i` must have one dimension, not 2.
Execution halted
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
File ‘documair/libs/documair.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  12.1Mb
Error(s) in re-building vignettes:
--- re-building ‘dodgr.Rmd’ using rmarkdown
Quitting from lines 323-330 (dodgr.Rmd) 
Error: processing vignette 'dodgr.Rmd' failed with diagnostics:
`x` must be a vector, not a `sfc_LINESTRING/sfc` object.
--- failed re-building ‘dodgr.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 359-375 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
graphical parameter "col.axis" has the wrong length
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
Namespaces in Imports field not imported from:
  ‘bit64’ ‘rstudioapi’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘tools’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘broom’ ‘colorspace’ ‘colourpicker’ ‘cowplot’
  ‘igraph’ ‘magrittr’ ‘shinyBS’ ‘shinyWidgets’ ‘shinydashboard’
  ‘shinythemes’ ‘tidyverse’ ‘visNetwork’
  All declared Imports should be used.
File ‘drmdel/libs/drmdel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’ ‘xtable’
  All declared Imports should be used.
File ‘dse/libs/dse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DStree/libs/DStree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.4Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.6Mb
File ‘dualtrees/libs/dualtrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  32.6Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘tools’
  All declared Imports should be used.
File ‘dynpred/libs/dynpred.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FNN’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs       12.5Mb
    shiny_app   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   3.7Mb
File ‘EasyABC/libs/EasyABC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’
  All declared Imports should be used.
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 ‘ebdbNet/libs/ebdbNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EBEN/libs/EBEN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EBglmnet/libs/EBglmnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘methods’ ‘mgcv’ ‘rappdirs’ ‘rgdal’ ‘scales’ ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
File ‘ecolMod/libs/ecolMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import ‘sf::st_make_valid’ by ‘lwgeom::st_make_valid’ when loading ‘edbuildmapr’
See ‘/data/gannet/ripley/R/packages/tests-clang/edbuildmapr.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Running ‘test-all.R’ [18s/45s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Failure: moves_calc gets the correct results (@test-calculators.R#210)  ──
  `moves` not equal to `correct_result`.
  Component "sid": Modes: character, numeric
  Component "sid": Attributes: < target is NULL, current is list >
  Component "sid": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 509 | SKIPPED: 0 | WARNINGS: 29 | FAILED: 1 ]
  1. Failure: moves_calc gets the correct results (@test-calculators.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
installed size is 113.4Mb
  sub-directories of 1Mb or more:
    libs  112.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc       4.4Mb
    extdata   5.1Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
installed size is 43.3Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
File ‘eiwild/libs/eiwild.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: sfx_explode
> ### Title: splits line by vertex
> ### Aliases: sfx_explode
> 
> ### ** Examples
> 
> {
+ # Do not run
+ data(emisco)
+ emisco <- emisco[1:100, "V8"]
+ dfco <- sfx_explode(emisco)
+ etm <- to_munich(sdf = dfco)
+ names(etm)
+ class(etm)
+ head(etm$Emissions)
+ head(etm$Street)
+ write.table(x = etm$Emissions, file = paste0(tempfile(), "_Emissions.txt"),
+ row.names = FALSE, sep = " ", quote = FALSE)
+ write.table(x = etm$Street, file = paste0(tempfile(), "_Street.txt"),
+ row.names = FALSE, sep = " ", quote = FALSE)
+ }
Error in to_munich(sdf = dfco) : 
  All emissions must have units. Check ?units::set_units
Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘tidyr’
  All declared Imports should be used.
File ‘elec.strat/libs/elec.strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
File ‘EL/libs/EL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘elsa/libs/elsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘AER’ ‘pROC’ ‘pander’
  All declared Imports should be used.
Running examples in ‘emax.glm-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.em.glm.summary
> ### Title: Error bar plot of coefficients and errors to inspect class
> ###   overlap.
> ### Aliases: plot.em.glm.summary
> 
> ### ** Examples
> 
> x <- model.matrix(~ factor(wool) + factor(tension), warpbreaks)
> y <- warpbreaks$breaks
> 
> m <- em.glm(x = x, y = y, K = 2, b.init = "random")
> m.sum <- summary(m)
> 
> plot(m.sum)
Warning in xy.coords(x, y, xlabel, ylabel, log) :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot ... plot2 -> plot -> plot.default -> localWindow -> plot.window
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rtsne’ ‘uwot’
  All declared Imports should be used.
File ‘EMC/libs/EMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
File ‘emdist/libs/emdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  18.5Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata  10.2Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.1Mb
File ‘emoa/libs/emoa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 23639 marked Latin-1 strings
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    lib    4.0Mb
    libs   1.4Mb
File ‘endogMNP/libs/endogMNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘bitops’ ‘rjson’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SPECIES’ ‘ade4’
  All declared Imports should be used.
File ‘EntropyEstimation/libs/EntropyEstimation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘broom’ ‘crosstalk’ ‘dplyr’ ‘ggraph’ ‘igraph’ ‘plotly’
  ‘rmarkdown’ ‘shinythemes’
  All declared Imports should be used.
File ‘enviPick/libs/enviPick.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EnviroStat/libs/EnviroStat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    3.3Mb
    help   3.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Running examples in ‘EpiCurve-Ex.R’ failed
The error most likely occurred in:

> ### Name: EpiCurve
> ### Title: Plot an Epidemic Curve
> ### Aliases: EpiCurve
> ### Keywords: ~documentation
> 
> ### ** Examples
> 
> # library(Epicurve)
> date <- seq(as.timeDate("2017-05-10 21:35:22"), as.timeDate("2017-05-12 06:15:12"), by="12 min")
> val <- rep(1, length(date))
> tri <- rep(c("Alive", "Died","Unknown"), length.out=length(date))
> DF <- data.frame(date, val, tri)
> names(DF) <- c("date","value", "tri")
> 
> 
> EpiCurve(DF,
+          date = "date",
+          freq = "value",
+          period = "hour",
+          split = 4,
+          cutvar = "tri",
+          ylabel="Number of cases",
+          xlabel= "From 2017-05-10 21:35:22 To 2017-05-12 06:15:12",
+          title = "Epidemic Curve")
Error: Column `DateFactor` is unknown
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘EpiCurve.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: ISOweek
Loading required package: scales
Quitting from lines 149-156 (EpiCurve.Rmd) 
Error: processing vignette 'EpiCurve.Rmd' failed with diagnostics:
Column `DateFactor` is unknown
--- failed re-building ‘EpiCurve.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(epikit)
  > 
  > test_check("epikit")
  ── 1. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  ── 2. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 107 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: case_fatality_rate_df will add a total row to stratified analysis (@test-proportion.R#152) 
  2. Failure: case_fatality_rate_df will add a total row to stratified analysis and merge CI (@test-proportion.R#173) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘graphics’ ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggplot2’ ‘knitr’ ‘pander’
  All declared Imports should be used.
File ‘equivalence/libs/equivalence.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
File ‘erboost/libs/erboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.1Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plyr’ ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘colorRamps’ ‘colourpicker’ ‘dichromat’ ‘leaflet’
  ‘lwgeom’ ‘raster’ ‘shinycssloaders’ ‘shinydashboard’ ‘shinyjs’ ‘tmap’
  ‘viridis’ ‘zip’
  All declared Imports should be used.
File ‘ESGtoolkit/libs/ESGtoolkit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [6s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estatapi)
  このサービスは、政府統計総合窓口(e-Stat)のAPI機能を使用していますが、サービスの内容は国によって保証されたものではありません。
  > 
  > test_check("estatapi")
  ── 1. Failure: estat_getStatsData processes the API response as expected  ──────
  estat_getStatsData(...) not identical to readRDS("result_getStatsData.rds").
  Objects equal but not identical
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 22 | SKIPPED: 12 | WARNINGS: 7 | FAILED: 1 ]
  1. Failure: estat_getStatsData processes the API response as expected 
  
  Error: testthat unit tests failed
  Execution halted
File ‘EstHer/libs/EstHer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
File ‘etasFLP/libs/etasFLP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: etm
> ### Title: Computation of the empirical transition matrix
> ### Aliases: etm etm.data.frame
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(sir.cont)
> 
> # Modification for patients entering and leaving a state
> # at the same date
> # Change on ventilation status is considered
> # to happen before end of hospital stay
> sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ]
> for (i in 2:nrow(sir.cont)) {
+   if (sir.cont$id[i]==sir.cont$id[i-1]) {
+     if (sir.cont$time[i]==sir.cont$time[i-1]) {
+       sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5
+     }
+   }
+ }
> 
> ### Computation of the transition probabilities
> # Possible transitions.
> tra <- matrix(ncol=3,nrow=3,FALSE)
> tra[1, 2:3] <- TRUE
> tra[2, c(1, 3)] <- TRUE
> 
> # etm
> tr.prob <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1)
> 
> tr.prob
Multistate model with 3 transient state(s)
 and 0 absorbing state(s)

Possible transitions:
 from to
    0  1
    0  2
    1  0
    1  2

Estimate of P(1, 183)
  0 1 2
0 0 0 1
1 0 0 1
2 0 0 1

> summary(tr.prob)
Error in object$n.risk[, trs.sep[i, 1]] : subscript out of bounds
Calls: summary -> summary.etm -> ci.transfo -> lapply -> FUN
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘etmCIF_tutorial.Rnw’ using Sweave
Error: processing vignette 'etmCIF_tutorial.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘etmCIF_tutorial.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [13s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eudract)
  > 
  > test_check("eudract")
  ── 1. Error: (unknown) (@test_bea.R#37)  ───────────────────────────────────────
  invalid value for 'stringsAsFactors'
  Backtrace:
   1. base::options(stringsAsFactors = old)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 53 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: (unknown) (@test_bea.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Running examples in ‘evaluator-Ex.R’ failed
The error most likely occurred in:

> ### Name: exposure_histogram
> ### Title: Display a histogram of losses for a scenario
> ### Aliases: exposure_histogram
> 
> ### ** Examples
> 
> data(mc_simulation_results)
> result <- mc_simulation_results[[1, "results"]]
> exposure_histogram(result)
Error: `data` must be a data frame, or other object coercible by `fortify()`, not a list
Backtrace:
    █
 1. └─evaluator::exposure_histogram(result)
 2.   ├─ggplot2::ggplot(simulation_result, aes(x = .data$ale))
 3.   └─ggplot2:::ggplot.default(simulation_result, aes(x = .data$ale))
 4.     ├─ggplot2::fortify(data, ...)
 5.     └─ggplot2:::fortify.default(data, ...)
Execution halted
Namespaces in Imports field not imported from:
  ‘devtools’ ‘msm’
  All declared Imports should be used.
File ‘evdbayes/libs/evdbayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘exactLoglinTest/libs/exactLoglinTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘exif/libs/exif.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘RColorBrewer’ ‘Rcpp’ ‘e1071’ ‘foreach’ ‘gam’ ‘ggplot2’
  ‘glmnet’ ‘nnet’ ‘polspline’ ‘repmis’ ‘splines’ ‘xgboost’
  All declared Imports should be used.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
File ‘extremis/libs/extremis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘extWeibQuant/libs/extWeibQuant.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ezglm/libs/ezglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [32s/85s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fable)
  Loading required package: fabletools
  > 
  > test_check("fable")
  ── 1. Failure: Automatic ETS selection (@test-ets.R#14)  ───────────────────────
  tidy(model(UKLungDeaths[1:24, ], ETS(mdeaths)))$estimate not equal to c(1, 2134).
  names for target but not for current
  
  ── 2. Failure: Manual ETS selection (@test-ets.R#51)  ──────────────────────────
  tidy(refit(fable_fit, USAccDeaths_tbl))$estimate == tidy(fable_fit)$estimate not identical to c(rep(TRUE, 2), rep(FALSE, 12)).
  names for target but not for current
  
  ── 3. Failure: Manual ETS selection (@test-ets.R#62)  ──────────────────────────
  tidy(fable_fit)$estimate[3:14] not identical to c(cmp$level[12], cmp$season[12:2]).
  names for target but not for current
  
  ── 4. Failure: Manual ETS selection (@test-ets.R#87)  ──────────────────────────
  coef$estimate[1:4] not identical to c(0.5, 0.006, 1e-04, 0.975).
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 100 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Automatic ETS selection (@test-ets.R#14) 
  2. Failure: Manual ETS selection (@test-ets.R#51) 
  3. Failure: Manual ETS selection (@test-ets.R#62) 
  4. Failure: Manual ETS selection (@test-ets.R#87) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘factorcpt/libs/factorcpt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘forcats’ ‘formula.tools’
  All declared Imports should be used.
File ‘factorQR/libs/factorQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
File ‘falcon/libs/falcon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fame/libs/fame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Familias/libs/Familias.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fanc/libs/fanc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘far/libs/far.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   3.5Mb
File ‘fAsianOptions/libs/fAsianOptions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastAdaboost/libs/fastAdaboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FastBandChol/libs/FastBandChol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastclime/libs/fastclime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastcmh/libs/fastcmh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastdigest/libs/fastdigest.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is 40.4Mb
  sub-directories of 1Mb or more:
    libs  40.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
File ‘FastGP/libs/FastGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.5Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.5Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’
File ‘fastmatch/libs/fastmatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      7.7Mb
Note: information on .o files is not available
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fasttime/libs/fasttime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
File ‘fBasics/libs/fBasics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.2Mb
File ‘FBFsearch/libs/FBFsearch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 47.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  44.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.5Mb
Namespaces in Imports field not imported from:
  ‘usethis’ ‘utils’
  All declared Imports should be used.
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FDRreg/libs/FDRreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fdrtool/libs/fdrtool.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘latex_fdt.Rnw’ using Sweave

Attaching package: ‘fdth’

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

    sd, var


Error: processing vignette 'latex_fdt.Rnw' failed with diagnostics:
 chunk 1 (label = tab) 
Error in x[[i]] : subscript out of bounds

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘testthat’
  All declared Imports should be used.
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘prettycode’
  All declared Imports should be used.
File ‘FFD/libs/FFD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ff/libs/ff.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: Extract.ffdf
> ### Title: Reading and writing data.frames (ffdf)
> ### Aliases: Extract.ffdf [.ffdf [<-.ffdf [[.ffdf [[<-.ffdf $.ffdf $<-.ffdf
> ### Keywords: IO data
> 
> ### ** Examples
> 
>    d <- data.frame(a=letters, b=rev(letters), c=1:26)
>    x <- as.ffdf(d)
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered,  : 
  vmode 'character' not implemented
Calls: as.ffdf ... do.call -> as.ff -> as.ff.default -> clone.ff -> assign -> ff
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
File ‘fGarch/libs/fGarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FGSG/libs/FGSG.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
File ‘FIACH/libs/FIACH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘mapproj’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.3Mb
File ‘FisHiCal/libs/FisHiCal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fishMod/libs/fishMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘grid’ ‘png’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘FitARMA/libs/FitARMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FitAR/libs/FitAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   3.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
File ‘flars/libs/flars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘flashClust/libs/flashClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
File ‘FMStable/libs/FMStable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fNonlinear/libs/fNonlinear.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
File ‘fOptions/libs/fOptions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
File ‘forensim/libs/forensim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rgeos’ ‘viridis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
File ‘fpow/libs/fpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘fable’ ‘fabletools’ ‘feasts’ ‘ggplot2’ ‘lubridate’ ‘tibble’
  ‘tidyr’ ‘tsibble’ ‘tsibbledata’
  All declared Imports should be used.
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘base’ ‘pbapply’ ‘stringr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.0Mb
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘rhandsontable’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  ‘shinythemes’
  All declared Imports should be used.
Found the following significant warnings:
  c_hd_mf.cpp:157:12: warning: explicitly assigning value of variable of type 'Eigen::VectorXd' (aka 'Matrix<double, Dynamic, 1>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/FRegSigCom.Rcheck/00install.out’ for details.
installed size is 68.4Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs  66.6Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   7.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: ‘dggrids’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.4Mb
installed size is 61.7Mb
  sub-directories of 1Mb or more:
    libs  61.2Mb
File ‘frontiles/libs/frontiles.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
File ‘ftnonpar/libs/ftnonpar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fts/libs/fts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fugeR/libs/fugeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
File ‘fUnitRoots/libs/fUnitRoots.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
Running ‘run_tests.R’
Running the tests in ‘tests/run_tests.R’ failed.
Complete output:
  > library(testthat)
  > library(futile.any)
  Loading required package: lambda.r
  
  Attaching package: 'lambda.r'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > test_package('futile.any')
  ── 1. Failure: named data.frame has correct type (@test_anytypes.R#19)  ────────
  `x` not equal to `expected`.
  1/3 mismatches
  x[2]: "character"
  y[2]: "factor"
  
  ── 2. Failure: unnamed data.frame has correct type (@test_anytypes.R#28)  ──────
  `x` not equal to `expected`.
  1/3 mismatches
  x[2]: "character"
  y[2]: "factor"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 16 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Failure: named data.frame has correct type (@test_anytypes.R#19) 
  2. Failure: unnamed data.frame has correct type (@test_anytypes.R#28) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
File ‘futureheatwaves/libs/futureheatwaves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    bin  10.0Mb
File ‘gafit/libs/gafit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
File ‘GAMBoost/libs/GAMBoost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.3Mb
installed size is 116.3Mb
  sub-directories of 1Mb or more:
    libs  115.8Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
installed size is 82.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     79.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
File ‘gausscov/libs/gausscov.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  18.7Mb
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gCat/libs/gCat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

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

Error: Vignette re-building failed.
Execution halted
File ‘gconcord/libs/gconcord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GCPM/libs/GCPM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    libs    42.1Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
File ‘gdmp/libs/gdmp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
File ‘gelnet/libs/gelnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
Running ‘testthat.R’ [19s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(genBaRcode)
  > 
  > test_check("genBaRcode")
  ── 1. Failure: helper functions - com_pair (@test_helper_functions.R#72)  ──────
  test_dat$shared not equal to res$shared.
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  
  ── 2. Failure: helper functions - com_pair (@test_helper_functions.R#73)  ──────
  test_dat$unique_sample1 not equal to res$unique_sample1.
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  
  ── 3. Failure: helper functions - com_pair (@test_helper_functions.R#74)  ──────
  test_dat$unique_sample2 not equal to res$unique_sample2.
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 47 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 3 ]
  1. Failure: helper functions - com_pair (@test_helper_functions.R#72) 
  2. Failure: helper functions - com_pair (@test_helper_functions.R#73) 
  3. Failure: helper functions - com_pair (@test_helper_functions.R#74) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘genBaRcode_GUI_Vignette.Rmd’ using rmarkdown
--- finished re-building ‘genBaRcode_GUI_Vignette.Rmd’

--- re-building ‘genBaRcode_Vignette.Rmd’ using rmarkdown
Quitting from lines 155-176 (genBaRcode_Vignette.Rmd) 
Error: processing vignette 'genBaRcode_Vignette.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘genBaRcode_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘NMF’ ‘RColorBrewer’ ‘VennDiagram’ ‘clValid’ ‘data.table’ ‘grid’
  ‘gtools’ ‘pca3d’ ‘rmarkdown’ ‘scales’ ‘shinydashboard’ ‘shinyjs’
  ‘statmod’ ‘stringr’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R  10.2Mb
Namespace in Imports field not imported from: ‘repmis’
  All declared Imports should be used.
File ‘genepi/libs/genepi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  11.8Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
File ‘GenKern/libs/GenKern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘genSurv/libs/genSurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘phonTools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   5.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   7.2Mb
Namespace in Imports field not imported from: ‘jsonify’
  All declared Imports should be used.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         9.0Mb
    extdata   1.6Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  13.2Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘geosample-vignette.Rnw’ using knitr
Loading required package: sf
Linking to GEOS 3.7.1, GDAL 2.3.2, PROJ 5.2.0
Loading required package: sp
Quitting from lines 269-276 (geosample-vignette.Rnw) 
Error: processing vignette 'geosample-vignette.Rnw' failed with diagnostics:
OGR error
--- failed re-building ‘geosample-vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   3.5Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘utils’
  All declared Imports should be used.
Running examples in ‘germanpolls-Ex.R’ failed
The error most likely occurred in:

> ### Name: germanpolls
> ### Title: Get data of German polls from wahlrecht.de.
> ### Aliases: germanpolls
> 
> ### ** Examples
> 
> germanpolls(region = "de")
[1] "http://www.wahlrecht.de/umfragen/bundesweite.xml"
 [1] "datum"    "institut" "gebiet"   "cxu"      "spd"      "grn"     
 [7] "fpd"      "lnk"      "afd"      "pir"      "frw"      "son"     
[13] "befragte" "gerundet" "beginn"   "ende"     "methode"  "art_ag"  
[19] "ag_1"     "ag_2"     "status"   "stand"   
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: All columns in a tibble must be vectors.
✖ Column `node` is a `xml_nodeset` object.
Backtrace:
    █
 1. └─germanpolls::germanpolls(region = "de")
 2.   └─germanpolls::get_data_from_xml_de()
 3.     └─tibble::data_frame(row = seq_along(rows), node = rows)
 4.       └─tibble::tibble(!!!quos(...))
 5.         └─tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
 6.           └─tibble:::check_valid_col(res, col_names[[j]], j)
 7.             └─tibble:::check_valid_cols(set_names(list(x), name))
Execution halted
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘lubridate’ ‘readr’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bitops’ ‘data.table’ ‘dplyr’ ‘httr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘scales’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
File ‘gettz/libs/gettz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘ggalluvial.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: ggplot2
Quitting from lines 36-46 (ggalluvial.rmd) 
Error: processing vignette 'ggalluvial.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘ggalluvial.rmd’

--- re-building ‘labels.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 31-40 (labels.rmd) 
Error: processing vignette 'labels.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘labels.rmd’

--- re-building ‘order-rectangles.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 43-46 (order-rectangles.rmd) 
Error: processing vignette 'order-rectangles.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘order-rectangles.rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘corrr’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘grDevices’ ‘scales’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  18.7Mb
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggforce’ ‘webshot’ ‘ztable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘sna’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘colourpicker’ ‘dplyr’ ‘ggpmisc’
  ‘ggpubr’ ‘ggrepel’ ‘ggstance’ ‘grDevices’ ‘grid’ ‘gridExtra’
  ‘lazyeval’ ‘markdown’ ‘plotly’ ‘quantreg’ ‘rlang’ ‘shinyjs’
  ‘survival’ ‘survminer’ ‘table1’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   3.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘rosm’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/ggtern.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.8Mb
File ‘GiRaF/libs/GiRaF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
File ‘GLIDE/libs/GLIDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gllm/libs/gllm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
File ‘GLMaSPU/libs/GLMaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
File ‘glmgraph/libs/glmgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.1Mb
installed size is 46.6Mb
  sub-directories of 1Mb or more:
    libs  45.7Mb
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    doc         1.2Mb
    libs       45.6Mb
    test_data   1.2Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cplm’ ‘ggplot2’ ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cplexAPI’
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/gnmf.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’
File ‘gnmf/libs/gnmf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cluster’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘stats’
  All declared Imports should be used.
Running examples in ‘gpairs-Ex.R’ failed
The error most likely occurred in:

> ### Name: gpairs
> ### Title: Generalized Pairs Plots
> ### Aliases: gpairs corrgram
> ### Keywords: ts multivariate
> 
> ### ** Examples
> 
> 
> allexamples <- FALSE
> 
> y <- data.frame(A=c(rep("red", 100), rep("blue", 100)),
+                 B=c(rnorm(100),round(rnorm(100,5,1),1)), C=runif(200),
+                 D=c(rep("big", 150), rep("small", 50)),
+                 E=rnorm(200))
> gpairs(y)
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in max(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in min(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in max(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in min(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Error in valid.viewport(x, y, width, height, just, gp, clip, xscale, yscale,  : 
  invalid 'xscale' in viewport
Calls: gpairs ... diag.panel -> pushViewport -> viewport -> valid.viewport
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.7Mb
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.5Mb
File ‘GrammR/libs/GrammR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Imap’ ‘Rdpack’ ‘ade4’ ‘doBy’ ‘mclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Running examples in ‘graphicalVAR-Ex.R’ failed
The error most likely occurred in:

> ### Name: graphicalVAR
> ### Title: Estimate the graphical VAR model.
> ### Aliases: graphicalVAR
> 
> ### ** Examples
> 
> # Simulate model:
> Mod <- randomGVARmodel(4,probKappaEdge = 0.8,probBetaEdge = 0.8)
> 
> # Simulate data:
> Data <- graphicalVARsim(100,Mod$beta,Mod$kappa)
> 
> # Estimate model:
> Res <- graphicalVAR(Data, gamma = 0, nLambda = 10)
Error: Column `V1` must be length 100 (the group size) or one, not 400
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   3.5Mb
File ‘graphscan/libs/graphscan.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
File ‘groupRemMap/libs/groupRemMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
File ‘grr/libs/grr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gsDesign/libs/gsDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File ‘gsmoothr/libs/gsmoothr.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gte/libs/gte.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   3.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    help   5.1Mb
File ‘GUILDS/libs/GUILDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GWASExactHW/libs/GWASExactHW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GWEX/libs/GWEX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gwfa/libs/gwfa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.6Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘dplyr’ ‘ggrepel’ ‘kableExtra’ ‘knitr’ ‘nnet’ ‘plotROC’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is 130.6Mb
  sub-directories of 1Mb or more:
    java  128.5Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
File ‘hapassoc/libs/hapassoc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
File ‘hashFunction/libs/hashFunction.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hashr/libs/hashr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hawkes/libs/hawkes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data  10.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.7Mb
    CWrappers_1.10.3   2.6Mb
    CWrappers_1.12.0   3.0Mb
    libs               1.4Mb
File ‘HDGLM/libs/HDGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hdlm/libs/hdlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  37.7Mb
File ‘HDtweedie/libs/HDtweedie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
Running examples in ‘heemod-Ex.R’ failed
The error most likely occurred in:

> ### Name: define_dsa
> ### Title: Define a Sensitivity Analysis
> ### Aliases: define_dsa define_dsa_
> 
> ### ** Examples
> 
> 
> define_dsa(
+   a, 10, 45,
+   b, .5, 1.5
+ )
Error: All columns in a tibble must be vectors.
✖ Column `dots[i]` is a `lazy_dots` object.
Backtrace:
     █
  1. └─heemod::define_dsa(a, 10, 45, b, 0.5, 1.5)
  2.   └─heemod:::define_dsa_(...)
  3.     ├─base::suppressWarnings(...)
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─dplyr::bind_rows(...)
  6.     │ ├─dplyr:::flatten_bindable(dots_values(...))
  7.     │ └─rlang::dots_values(...)
  8.     ├─stats::setNames(tibble::tibble(dots[i]), names(dots)[i])
  9.     └─tibble::tibble(dots[i])
 10.       └─tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
 11.         └─tibble:::check_valid_col(res, col_names[[j]], j)
 12.           └─tibble:::check_valid_cols(set_names(list(x), name))
Execution halted
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  24.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
File ‘HiCseg/libs/HiCseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HiDimDA/libs/HiDimDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
File ‘hierarchicalSets/libs/hierarchicalSets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hierband/libs/hierband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
File ‘highD2pop/libs/highD2pop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
    libs   1.2Mb
Error(s) in re-building vignettes:
--- re-building ‘the_basics.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 118-131 (the_basics.Rmd) 
Error: processing vignette 'the_basics.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘the_basics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        8.7Mb
File ‘hillmakeR/libs/hillmakeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hint/libs/hint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HI/libs/HI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.8Mb
File ‘hit/libs/hit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hkevp/libs/hkevp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HKprocess/libs/HKprocess.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HLMdiag/libs/HLMdiag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘methods’ ‘rgl’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
File ‘hpa/libs/hpa.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘hpaBinary.o’, ‘hpaML.o’, ‘hpaSelection.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   2.5Mb
File ‘hsmm/libs/hsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hsphase/libs/hsphase.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 67.9Mb
  sub-directories of 1Mb or more:
    libs  67.4Mb
File ‘htdp/libs/htdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   1.9Mb
    libs          2.9Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
    doc    2.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
File ‘humaniformat/libs/humaniformat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
File ‘HUM/libs/HUM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘rvest’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
File ‘HybridMC/libs/HybridMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: writeNcdf
> ### Title: Write to NetCDF file using hyfo list file
> ### Aliases: writeNcdf
> 
> ### ** Examples
> 
> # First open the test NETcDF file.
> filePath <- system.file("extdata", "tnc.nc", package = "hyfo")
> 
> 
> # Then if you don't know the variable name, you can use \code{getNcdfVar} to get variable name
> varname <- getNcdfVar(filePath)
> 
> nc <- loadNcdf(filePath, varname)
Loading data...
Processing...
> 
> # Then write to your work directory
> 
> writeNcdf(nc, 'test.nc')
Error in Ops.difftime(x, 1) : '%%' not defined for "difftime" objects
Calls: writeNcdf ... getTimeUnit -> sapply -> lapply -> FUN -> Ops.difftime
Execution halted
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   6.0Mb
File ‘iBATCGH/libs/iBATCGH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ibdreg/libs/ibdreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ibmcraftr/libs/ibmcraftr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ibm/libs/ibm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Iboot/libs/Iboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Registration problems:
  symbol ‘nom1’ in the local frame:
   .C(nom1, as.double(xord), as.integer(length(xord)), as.double(yord), 
       as.double(gridbw), as.integer(length(gridbw)), as.integer(effold), 
       as.integer(neffold), double(length(gridbw)), double(length(gridbw)))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1), double(n))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1), double(length(newdata)))
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
File ‘iBST/libs/iBST.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
Packages unavailable to check Rd xrefs: ‘BSgenome.Hsapiens.1000genomes.hs37d5’, ‘BSgenome.Mmusculus.UCSC.mm10’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘icapca/libs/icapca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/icd.Rcheck/00install.out’ for details.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   8.6Mb
Running ‘testthat.R’ [46s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # this is common code to all the tests, each of which runs test_check with a
  > # different filter:
  > library("icd")
  > library("testthat", warn.conflicts = FALSE, quietly = TRUE)
  > icd:::.show_options()
  $icd.data.who_url
  [1] "https://icd.who.int/browse10"
  
  > # Definitely don't download data on CRAN
  > if (!icd:::.env_var_is_true("NOT_CRAN")) {
  +   old_offline <- options("icd.data.offline" = TRUE)
  +   on.exit(options(old_offline), add = TRUE)
  + } else {
  +   old_offline <- options("icd.data.offline" = FALSE)
  +   on.exit(options(old_offline), add = TRUE)
  + }
  > if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
  +   old_test_slow <- options("icd.test_slow" = TRUE)
  +   on.exit(options(old_test_slow), add = TRUE)
  + }
  > old_interact <- options("icd.data.interact" = FALSE)
  > on.exit(options(old_interact), add = TRUE)
  > icd:::.show_options()
  $icd.data.interact
  [1] FALSE
  
  $icd.data.offline
  [1] TRUE
  
  $icd.data.who_url
  [1] "https://icd.who.int/browse10"
  
  > testthat::test_check("icd")
  loading helper-base.R
  loading helper-icd10.R
  ── 1. Failure: van_walraven comodbidity index and score (@test-score.R#333)  ───
  van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
  Component "id": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: van_walraven comodbidity index and score (@test-score.R#333) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
File ‘icemelt/libs/icemelt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
File ‘icensmis/libs/icensmis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ICE/libs/ICE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  25.2Mb
File ‘identity/libs/identity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘ieeeround/libs/ieeeround.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testit’
  All declared Imports should be used.
File ‘ifa/libs/ifa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ifctools/libs/ifctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘IFP/libs/IFP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ifs/libs/ifs.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.4Mb
File ‘IHSEP/libs/IHSEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘spelling.R’
  Running ‘testthat.R’ [9s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ijtiff)
  > 
  > test_check("ijtiff")
  ── 1. Error: text-image-io works (@test-io.R#321)  ─────────────────────────────
  No common type for `col2` <double> and `col2` <character>.
  Backtrace:
    1. dplyr::tribble(~col1, ~col2, 1, 5, 8, "y")
    8. vctrs:::vec_ptype2.double.default(...)
    9. vctrs::vec_default_ptype2(x, y, x_arg = x_arg, y_arg = y_arg)
   10. vctrs::stop_incompatible_type(x, y, x_arg = x_arg, y_arg = y_arg)
   11. vctrs:::stop_incompatible(...)
   12. vctrs:::stop_vctrs(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 96 | SKIPPED: 0 | WARNINGS: 98 | FAILED: 1 ]
  1. Error: text-image-io works (@test-io.R#321) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.1Mb
    include   3.0Mb
    libs     44.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Found the following significant warnings:
  ImmigrateCpp.cpp:22:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:32:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/Immigrate.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
File ‘imputeMDR/libs/imputeMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
File ‘imputeMulti/libs/imputeMulti.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘IM/libs/IM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘V8’ ‘assertive’ ‘shinydashboard’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
File ‘IndependenceTests/libs/IndependenceTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    help   1.6Mb
Running examples in ‘INDperform-Ex.R’ failed
The error most likely occurred in:

> ### Name: merge_models
> ### Title: Merging two model output tibbles.
> ### Aliases: merge_models
> 
> ### ** Examples
> 
> # Using some models of the Baltic Sea demo data:
> # Merging GAM and GAMM tibbles
> test_ids <- 47:50 # choose subset
> gam_tbl <- model_gam_ex[test_ids,]
> gamm_tbl <- model_gamm(ind_init_ex[test_ids,], filter= gam_tbl$tac)
Error in model_gamm(ind_init_ex[test_ids, ], filter = gam_tbl$tac) : 
  No IND~pressure GAMM could be fitted! Check if you chose the correct error distribution (default is gaussian()).
Execution halted
File ‘influenceR/libs/influenceR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘infotheo/libs/infotheo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ca’
  All declared Imports should be used.
File ‘INSPIRE/libs/INSPIRE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [4m/14m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(interactions)
  > 
  > test_check("interactions")
  Failed with error:  'there is no package called 'brms''
  ── 1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157)  
  `print(p)` produced messages.
  
  ── 2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162)  
  `print(p)` produced messages.
  
  Failed with error:  'there is no package called 'brms''
  Failed with error:  'there is no package called 'rstanarm''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 161 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157) 
  2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘Interact/libs/Interact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
File ‘intervals/libs/intervals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EValue’ ‘tidyverse’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
Namespaces in Imports field not imported from:
  ‘chron’ ‘zoo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘kableExtra’ ‘markdown’ ‘reshape2’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   7.5Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GlobalOptions’ ‘dplyr’ ‘testthat’
  All declared Imports should be used.
File ‘ipfp/libs/ipfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
File ‘iRafNet/libs/iRafNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  rf.c:492:17: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/iRF.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘irr’
  All declared Imports should be used.
File ‘ISBF/libs/ISBF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
File ‘isingLenzMC/libs/isingLenzMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.2Mb
File ‘isocir/libs/isocir.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
File ‘ISR3/libs/ISR3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘pangaear’ ‘rcrossref’ ‘rgdal’ ‘stringr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘acf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘acf.Rmd’

--- re-building ‘inspect.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 101-106 (inspect.Rmd) 
Error: processing vignette 'inspect.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘inspect.Rmd’

--- re-building ‘test.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 187-200 (test.Rmd) 
Error: processing vignette 'test.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘test.Rmd’

SUMMARY: processing the following files failed:
  ‘inspect.Rmd’ ‘test.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          21.0Mb
Running examples in ‘janitor-Ex.R’ failed
The error most likely occurred in:

> ### Name: adorn_percentages
> ### Title: Convert a data.frame of counts to percentages.
> ### Aliases: adorn_percentages
> 
> ### ** Examples
> 
> 
> mtcars %>%
+   tabyl(am, cyl) %>%
+   adorn_percentages("col")
 am         4         6         8
  0 0.2727273 0.5714286 0.8571429
  1 0.7272727 0.4285714 0.1428571
> 
> # calculates correctly even with totals column and/or row:
> mtcars %>%
+   tabyl(am, cyl) %>%
+   adorn_totals("row") %>%
+   adorn_percentages()
Error: Assigned data `name` must be compatible with existing data.
ℹ Error occurred for column `am`.
✖ No common type for `value` <character> and `x` <double>.
Backtrace:
     █
  1. └─mtcars %>% tabyl(am, cyl) %>% adorn_totals("row") %>% adorn_percentages()
  2.   ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3.   └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       └─`_fseq`(`_lhs`)
  6.         └─magrittr::freduce(value, `_function_list`)
  7.           └─function_list[[i]](value)
  8.             └─janitor::adorn_totals(., "row")
  9.               ├─base::`[<-`(`*tmp*`, 1, 1, value = "Total")
 10.               └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 1, value = "Total")
 11.                 └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 12.                   └─tibble:::tbl_subassign_row(xj, i, value, value_arg)
 13.            
Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘ggExtra’ ‘ggplot2’ ‘grid’ ‘gridExtra’ ‘mcmcplots’
  All declared Imports should be used.
File ‘JASPAR/libs/JASPAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/JavaGD.Rcheck/00install.out’ for details.
File ‘JavaGD/libs/JavaGD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BurStFin’ ‘MASS’ ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’
  ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   5.0Mb
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/jomo.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
File ‘jpeg/libs/jpeg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘JRF/libs/JRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘survC1’
  All declared Imports should be used.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   6.1Mb
Running ‘testthat.R’ [13s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jstor)
  > 
  > test_check("jstor")
  ── 1. Failure: authors are correct (@test-books.R#117)  ────────────────────────
  chap_auth[[5, "authors"]] not identical to `correct_authors`.
  names for current but not for target
  Attributes: < target is NULL, current is list >
  Length mismatch: comparison on first 1 components
  Component 1: Cols in y but not x: `c(NA_character_, NA_character_)`. 
  Component 1: Cols in x but not y: `author_number`, `suffix`, `surname`, `given_name`, `string_name`, `prefix`. 
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 251 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: authors are correct (@test-books.R#117) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
File ‘kappalab/libs/kappalab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kaps/libs/kaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stinepack’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  16.6Mb
File ‘Kendall/libs/Kendall.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
File ‘KERE/libs/KERE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
File ‘KernSmoothIRT/libs/KernSmoothIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘KFKSDS/libs/KFKSDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kissmig/libs/kissmig.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kknn/libs/kknn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kml/libs/kml.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kmlShape/libs/kmlShape.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
File ‘kolmim/libs/kolmim.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mice’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
File ‘kriging/libs/kriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ktspair/libs/ktspair.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  17.7Mb
File ‘labdsv/libs/labdsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.4Mb
File ‘LakeMetabolizer/libs/LakeMetabolizer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘run_tests.R’
Running the tests in ‘tests/run_tests.R’ failed.
Complete output:
  > library(testthat)
  > library(lambda.r)
  
  Attaching package: 'lambda.r'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > library(lambda.tools)
  > test_package('lambda.tools')
  ── 1. Failure: A named data.frame has the correct types (@test_any.R#47)  ──────
  `ts` not equal to c("numeric", "factor", "logical").
  1/3 mismatches
  x[2]: "character"
  y[2]: "factor"
  
  ── 2. Failure: An unnamed data.frame has the correct types (@test_any.R#56)  ───
  `ts` not equal to c("numeric", "factor", "logical").
  1/3 mismatches
  x[2]: "character"
  y[2]: "factor"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 110 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: A named data.frame has the correct types (@test_any.R#47) 
  2. Failure: An unnamed data.frame has the correct types (@test_any.R#56) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/LambertW.Rcheck/00install.out’ for details.
File ‘LambertW/libs/LambertW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LANDD/libs/LANDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘callr’ ‘collections’ ‘repr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.0Mb
    help   1.1Mb
File ‘lars/libs/lars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LassoNet/libs/LassoNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lassoshooting/libs/lassoshooting.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespaces in Imports field not imported from:
  ‘ReinforcementLearning’ ‘ggplot2’ ‘grDevices’ ‘h2o’ ‘lubridate’
  ‘magrittr’ ‘openssl’ ‘readr’ ‘stringr’
  All declared Imports should be used.
File ‘lbfgsb3/libs/lbfgsb3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lbfgs/libs/lbfgs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lbiassurv/libs/lbiassurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lda/libs/lda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ./lda_svi.h:1:9: warning: '_lda_svi_guard' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/data/gannet/ripley/R/packages/tests-clang/lda.svi.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘tm’
  All declared Imports should be used.
File ‘leaderCluster/libs/leaderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
File ‘leaps/libs/leaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LearningRlab/libs/LearningRlab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: annotate_y_axis
> ### Title: Annotations in the axis
> ### Aliases: annotate_y_axis annotate_x_axis
> 
> ### ** Examples
> 
> library(ggplot2)

Attaching package: ‘ggplot2’

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

    element_render

> 
> p <- ggplot(mtcars, aes(mpg, hp, colour=disp)) + geom_point()
> 
> l <- p + annotate_y_axis('mark at', y=200, tick=TRUE)
> l
Error in upgradeUnit.default(list(0, NULL, 1L)) : Not a unit object
Calls: <Anonymous> ... <Anonymous> -> pSummary -> <Anonymous> -> upgradeUnit.default
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lemon)
  > 
  > 
  > if (TRUE) {
  +   test_check("lemon")
  + } #else {
  ── 1. Failure: ggplot2 does not break lemon_plot by altering class (@test_lemon_
  `l + 1` threw an error with unexpected message.
  Expected match: "Don't know how to add 1 to a plot"
  Actual message: "Can't add `1` to a ggplot object."
  Backtrace:
   1. testthat::expect_error(...)
   6. ggplot2:::`+.gg`(l, 1)
   7. ggplot2:::add_ggplot(e1, e2, e2name)
   9. ggplot2:::ggplot_add.default(object, p, objectname)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 137 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: ggplot2 does not break lemon_plot by altering class (@test_lemon_plot.r#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘capped-axes.Rmd’ using rmarkdown
--- finished re-building ‘capped-axes.Rmd’

--- re-building ‘facet-rep-labels.Rmd’ using rmarkdown
--- finished re-building ‘facet-rep-labels.Rmd’

--- re-building ‘geoms.Rmd’ using rmarkdown
Quitting from lines 30-41 (geoms.Rmd) 
Error: processing vignette 'geoms.Rmd' failed with diagnostics:
invalid line type
--- failed re-building ‘geoms.Rmd’

--- re-building ‘gtable_show_lemonade.Rmd’ using rmarkdown
Quitting from lines 42-61 (gtable_show_lemonade.Rmd) 
Error: processing vignette 'gtable_show_lemonade.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘gtable_show_lemonade.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘geoms.Rmd’ ‘gtable_show_lemonade.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘lgarch/libs/lgarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Error(s) in re-building vignettes:
--- re-building ‘liayson.Rnw’ using Sweave

Error: processing vignette 'liayson.Rnw' failed with diagnostics:
 chunk 1 
Error in bmRequest(request = request, verbose = verbose) : 
  Service Unavailable (HTTP 503).

--- failed re-building ‘liayson.Rnw’

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

Error: Vignette re-building failed.
Execution halted
File ‘LiblineaR.ACF/libs/LiblineaR.ACF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LiblineaR/libs/LiblineaR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  clang-10: warning: -lOPF: 'linker' input unused [-Wunused-command-line-argument]
  clang-10: warning: -lm: 'linker' input unused [-Wunused-command-line-argument]
See ‘/data/gannet/ripley/R/packages/tests-clang/LibOPF.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    extdata   1.2Mb
    libs      7.8Mb
Running ‘testthat.R’ [102s/107s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  ── 1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalo
  projection(req2) not equal to "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clrk66 +units=m +no_defs".
  1/1 mismatches
  x[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  x[1]: k66 +units=m +no_defs "
  y[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  y[1]: k66 +units=m +no_defs"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 971 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalog_apply-automerge.R#171) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    extdata   1.1Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘devtools’ ‘e1071’ ‘glmnet’ ‘hash’ ‘pamr’ ‘randomForest’
  All declared Imports should be used.
Running examples in ‘lilikoi-Ex.R’ failed
The error most likely occurred in:

> ### Name: lilikoi.get_pd_scores
> ### Title: A lilikoi.get_pd_scores Function
> ### Aliases: lilikoi.get_pd_scores
> 
> ### ** Examples
> 
> filename <- system.file("extdata", "plasma_breast_cancer.csv", package = "lilikoi")
> data <- read.csv(file = filename, check.names = FALSE, row.names = 1)[, 1:20]
> metaboliteNames <- colnames(data)[-1]
> matches <- lilikoi.metab_to_pathway(metaboliteNames, "name")
[1] "18 out of 19 Matched metabolites 90 %"
[1] "1 out of 19 UnMatched metabolites 0 %"
> PDSmatrix <- lilikoi.get_pd_scores(data, matches, lilikoi::data.smpdb[1:23,], maxit = 1)
Warning in function_list[[i]](value) : NAs introduced by coercion
robust_score_bydist. min_exp= 0 , min_std= 0 
Error in matrix(0, attempts, m) : invalid 'ncol' value (too large or NA)
Calls: lilikoi.get_pd_scores -> .quantify_pathways_deregulation -> matrix
Execution halted
Running ‘testthat.R’ [16s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lilikoi)
  > 
  > test_check("lilikoi")
  [1] "18 out of 19 Matched metabolites 90 %"
  [1] "1 out of 19 UnMatched metabolites 0 %"
  robust_score_bydist. min_exp= 0 , min_std= 0 
  ── 1. Error: full pipeline works (@test-all.r#12)  ─────────────────────────────
  invalid 'ncol' value (too large or NA)
  Backtrace:
   1. lilikoi::lilikoi.get_pd_scores(...)
   2. lilikoi:::.quantify_pathways_deregulation(...)
   3. base::matrix(0, attempts, m)
  
  [1] "5 out of 5 Matched metabolites 100 %"
  [1] "0 out of 5 UnMatched metabolites 0 %"
  [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
  [1] "1 out of 4 Matched metabolites 60 %"
  [1] "3 out of 4 UnMatched metabolites 40 %"
  [1] "5 out of 5 Matched metabolites 100 %"
  [1] "0 out of 5 UnMatched metabolites 0 %"
  [1] "4 out of 5 Matched metabolites 80 %"
  [1] "1 out of 5 UnMatched metabolites 20 %"
  [1] "1 out of 1 Matched metabolites 100 %"
  [1] "0 out of 1 UnMatched metabolites 0 %"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: full pipeline works (@test-all.r#12) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘ddpcr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
File ‘linERR/libs/linERR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  10.4Mb
File ‘listdtr/libs/listdtr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
File ‘ljr/libs/ljr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs      20.7Mb
    testdata   1.6Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
File ‘lmeNBBayes/libs/lmeNBBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lmeNB/libs/lmeNB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
File ‘lmPerm/libs/lmPerm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘localgauss/libs/localgauss.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘locits/libs/locits.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
File ‘loe/libs/loe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘modules’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘logisticPCA/libs/logisticPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘logisticRR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 162-169 (logisticRR.Rmd) 
Error: processing vignette 'logisticRR.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘logisticRR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘LogitNet/libs/LogitNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘loglognorm/libs/loglognorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lokern/libs/lokern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
Namespace in Imports field not imported from: ‘futile.options’
  All declared Imports should be used.
File ‘lorec/libs/lorec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lowmemtkmeans/libs/lowmemtkmeans.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
File ‘LPStimeSeries/libs/LPStimeSeries.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LRcontrast/libs/LRcontrast.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
installed size is 52.0Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  49.4Mb
Namespace in Imports field not imported from: ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
File ‘ltbayes/libs/ltbayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ltsa/libs/ltsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Running ‘testthat.R’ [25s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)  
  +   test_check("lubridate")
  + }
  Loading required package: lubridate
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  ── 1. Failure: difftime comparison with periods works (@test-ops-compare.R#63)  
  days(1) == (t + days(1)) - t isn't true.
  
  ── 2. Failure: difftime comparison with periods works (@test-ops-compare.R#64)  
  (t + days(1)) - t == days(1) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2451 | SKIPPED: 4 | WARNINGS: 115 | FAILED: 2 ]
  1. Failure: difftime comparison with periods works (@test-ops-compare.R#63) 
  2. Failure: difftime comparison with periods works (@test-ops-compare.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   2.0Mb
File ‘lxb/libs/lxb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘etm’
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’
  ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   7.5Mb
File ‘magree/libs/magree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  19.5Mb
File ‘MAMSE/libs/MAMSE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.2Mb
    htmlwidgets   1.9Mb
    libs         42.0Mb
File ‘mapfit/libs/mapfit.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgdal’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘brew’ ‘svglite’ ‘uuid’
  All declared Imports should be used.
Running examples in ‘mapview-Ex.R’ failed
The error most likely occurred in:

> ### Name: +
> ### Title: mapview + mapview adds data from the second map to the first
> ### Aliases: + +,mapview,mapview-method +,mapview,ANY-method
> ###   +,mapview,NULL-method +,mapview,character-method
> 
> ### ** Examples
> 
> m1 <- mapView(franconia, col.regions = "red")
> m2 <- mapView(breweries)
> 
> ### add two mapview objects
> m1 + m2
Error in if (!is.na(getProjection(lst[[i]]))) { : 
  argument is of length zero
Calls: + -> + -> combineExtent -> do.call -> lapply -> FUN
Execution halted
Running ‘testthat.R’ [7s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mapview)
  > 
  > test_check("mapview")
  ── 1. Failure: getProjection() runs without issues (@test-mapviewControls.R#108)
  getProjection(franconia) has type `NULL`, not `character`.
  
  ── 2. Failure: getProjection() runs without issues (@test-mapviewControls.R#109)
  getProjection(franconia) not equal to "+proj=longlat +datum=WGS84 +no_defs".
  target is NULL, current is character
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 63 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: getProjection() runs without issues (@test-mapviewControls.R#108) 
  2. Failure: getProjection() runs without issues (@test-mapviewControls.R#109) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘betareg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs  11.7Mb
File ‘mateable/libs/mateable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘matie/libs/matie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MAT/libs/MAT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
File ‘MaXact/libs/MaXact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
File ‘mbrglm/libs/mbrglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mcclust/libs/mcclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  12.8Mb
File ‘mcemGLM/libs/mcemGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  51.1Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
File ‘mco/libs/mco.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘bayesplot’ ‘methods’ ‘purrr’
  All declared Imports should be used.
File ‘mcr/libs/mcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘covr’ ‘curl’ ‘devtools’ ‘gh’ ‘git2r’ ‘httr’ ‘knitr’ ‘openssl’
  ‘pkgbuild’ ‘rlang’ ‘rmarkdown’ ‘roxygen2’ ‘spelling’ ‘testthat’
  ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespace in Imports field not imported from: ‘mds’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.3Mb
File ‘meboot/libs/meboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘coxphw’ ‘gmodels’
  All declared Imports should be used.
Found the following significant warnings:
  transpiration.cpp:18:28: warning: result of '10^3' is 9; did you mean '1e3'? [-Wxor-used-as-pow]
  lightextinction.cpp:74:63: warning: explicitly assigning value of variable of type 'Rcpp::String' to itself [-Wself-assign-overloaded]
  lightextinction.cpp:85:64: warning: explicitly assigning value of variable of type 'Rcpp::String' to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/medfate.Rcheck/00install.out’ for details.
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs  31.0Mb
File ‘MediaK/libs/MediaK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RGtk2’ ‘RNifti’ ‘cairoDevice’ ‘gtools’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘foreign’ ‘formattable’ ‘ggplot2’
  ‘haven’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.9Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   6.6Mb
installed size is 123.4Mb
  sub-directories of 1Mb or more:
    libs  122.8Mb
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’ ‘svglite’
  All declared Imports should be used.
Running ‘testthat.R’ [192s/514s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  ── 1. Failure: Summing counts per taxon (@test--calculations.R#103)  ───────────
  sum(x$data$tax_data$`700035949`) not equal to result$`700035949`[1].
  names for current but not for target
  
  ── 2. Failure: Summing counts per taxon (@test--calculations.R#126)  ───────────
  `total_counts` not equal to result$total[1].
  names for current but not for target
  
  ── 3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_write
  result$data$tax_data$unite_seq[5] not equal to "CCAAATCATGTCTCCCGGCCGCAAGGCAGGTGCAGGCGTTTAACCCTTTGTGAACCAAAAAACCTTTCGCTTCGGCAGCAGCTCGGTTGGAGACAGCCTCTGTGTCAGCCTGCCGCTAGCACCAATTATCAAAACTTGCGGTTAGCAACATTGTCTGATTACCAAATTTTCGAATGAAAATCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAACGCGATAGTTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCATTGGTATTCCATTGGGCATGTCTGTTTGAGCGTCATTACAACCCTCGGTCACCACCGGTTTTGAGCGAGCAGGGTCTTCGGATCCAGCTGGCTTTAAAGTTGTAAGCTCTGCTGGCTGCTCGGCCCAACCAGAACATAGTAAAATCATGCTTGTTCAAGGTTCGCGGTCGAAGCGGTACGGCCTGAACAATACCTACCACCTCTTAGG".
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 93 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Summing counts per taxon (@test--calculations.R#103) 
  2. Failure: Summing counts per taxon (@test--calculations.R#126) 
  3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_writers.R#119) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘metafolio/libs/metafolio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MetaheuristicFPA/libs/MetaheuristicFPA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘foreign’ ‘gplots’ ‘httr’ ‘jsonlite’ ‘knitr’ ‘lmerTest’
  ‘magrittr’ ‘mgcv’ ‘repmis’ ‘reshape2’ ‘rmarkdown’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘metan_start.Rmd’ using rmarkdown
[]=====================================================[]
[] Multi-Environment Trial Analysis (metan) v1.4.0     []
[] Author: Tiago Olivoto                               []
[] Type citation('metan') to know how to cite metan    []
[] Type vignette('metan_start') for a short tutorial   []
[] Visit http://bit.ly/2TIq6JE for a complete tutorial []
[]=====================================================[]
No issues detected while inspecting data.
Quitting from lines 133-134 (metan_start.Rmd) 
Error: processing vignette 'metan_start.Rmd' failed with diagnostics:
No common type for `..1$Y` <character> and `..2$Y` <integer>.
--- failed re-building ‘metan_start.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 124.0Mb
  sub-directories of 1Mb or more:
    libs  123.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.5Mb
File ‘MEtest/libs/MEtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs  25.6Mb
    misc   1.1Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
File ‘mewAvg/libs/mewAvg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Namespace in Imports field not imported from: ‘ECoL’
  All declared Imports should be used.
Running examples in ‘mfe-Ex.R’ failed
The error most likely occurred in:

> ### Name: infotheo
> ### Title: Information-theoretic meta-features
> ### Aliases: infotheo infotheo.default infotheo.formula
> 
> ### ** Examples
> 
> ## Extract all metafeatures
> infotheo(Species ~ ., iris)
Error in `[.data.frame`(x, , j) : undefined columns selected
Calls: infotheo ... concentration.coefficient -> table -> [ -> [.data.frame
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘mfe-vignette.Rmd’ using rmarkdown
Quitting from lines 55-66 (mfe-vignette.Rmd) 
Error: processing vignette 'mfe-vignette.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘mfe-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘mgarchBEKK/libs/mgarchBEKK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MGL/libs/MGL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MGSDA/libs/MGSDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  19.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
File ‘mhsmm/libs/mhsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
Running examples in ‘micropan-Ex.R’ failed
The error most likely occurred in:

> ### Name: binomixEstimate
> ### Title: Binomial mixture model estimates
> ### Aliases: binomixEstimate
> 
> ### ** Examples
> 
> # Loading an example pan-matrix
> data(xmpl.panmat)
> 
> # Estimating binomial mixture models
> binmix.lst <- binomixEstimate(xmpl.panmat, K.range = 3:8)
binomixEstimate: Fitting 3 component model...
Error: Assigned data `lst[[1]]` must be compatible with row subscript `i`.
✖ 1 row must be assigned.
✖ Assigned data has 3 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─micropan::binomixEstimate(xmpl.panmat, K.range = 3:8)
 2.   ├─base::`[<-`(...)
 3.   └─tibble:::`[<-.tbl_df`(...)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
Running ‘testthat.R’ [28s/71s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  Loading required package: Rcpp
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 cores── 1. Failure: fastRank schemes , default fixed options identcal results  (@test
  all.equal(getRanking(origExample), getRanking(fastExample)) isn't true.
  
  ── 2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@t
  rankedSetOfSchemesOrig@ranking not equal to rankedSetOfSchemesNew@ranking.
  Component "name": 'current' is not a factor
  
  start Ranking Schemes on cluster with  2 cores── 3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47)  ────────────
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 19 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: fastRank schemes , default fixed options identcal results  (@testRankSetOfSchemes.R#87) 
  2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@testRankSetOfSchemes.R#95) 
  3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘mipfp’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
Running examples in ‘MIMSunit-Ex.R’ failed
The error most likely occurred in:

> ### Name: import_mhealth_csv
> ### Title: Import raw multi-channel accelerometer data stored in mHealth
> ###   Specification
> ### Aliases: import_mhealth_csv
> 
> ### ** Examples
> 
>   default_ops = options()
>   options(digits.secs=3)
>   # Use the sample mhealth csv file provided by the package
>   filepath = system.file('extdata', 'mhealth.csv', package='MIMSunit')
>   filepath
[1] "/data/gannet/ripley/R/packages/tests-clang/MIMSunit.Rcheck/MIMSunit/extdata/mhealth.csv"
> 
>   # Load the file
>   df = import_mhealth_csv(filepath)
Error: Assigned data `as.character(df[, factor_cols])` must be compatible with existing data.
✖ Existing data has 5000 rows.
✖ Assigned data has 0 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─MIMSunit::import_mhealth_csv(filepath)
 2.   ├─base::`[<-`(`*tmp*`, , factor_cols, value = character(0))
 3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, , factor_cols, value = character(0))
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.
File ‘minpack.lm/libs/minpack.lm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   8.1Mb
File ‘MiSPU/libs/MiSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/missDeaths.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  42.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
File ‘mixedMem/libs/mixedMem.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mixexp/libs/mixexp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
File ‘mkde/libs/mkde.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
File ‘mlbench/libs/mlbench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiscriMiner’ ‘MASS’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘klaR’
  ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
File ‘MLEcens/libs/MLEcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
File ‘mlmc/libs/mlmc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlmmm/libs/mlmmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlogitBMA/libs/mlogitBMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [11m/27m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("checkmate")
  > library("testthat")
  > library("mlr3")
  > library("paradox")
  > library("mlr3pipelines")
  > 
  > test_check("mlr3pipelines")
  Training debug.multi with input list(input_1 = 1, input_2 = 1)
  ── 1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12)  ───────────
  <TaskClassif:tsk> has the following unsupported feature types: character
  Backtrace:
   1. lrn$train(tsk)
   2. mlr3::assert_learnable(task, self)
   3. mlr3misc::stopf(...)
  
  ── 2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removecon
  Target column 'target' must have at least two levels
  Backtrace:
   1. mlr3pipelines:::test_dropping(iris, iris, list())
   2. TaskClassif$new(...)
   3. .subset2(public_bind_env, "initialize")(...)
   4. private$.update_class_property()
   5. mlr3misc::stopf(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 7497 | SKIPPED: 44 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12) 
  2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removeconstants.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘e1071’ ‘mlr3’ ‘mlr3learners’ ‘mlr3measures’ ‘plyr’
  ‘purrr’ ‘ranger’ ‘readxl’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stats’ ‘stringr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
File ‘mnormpow/libs/mnormpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mnormt/libs/mnormt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘amap’ ‘fields’ ‘matrixStats’ ‘mco’ ‘miscTools’ ‘plyr’
  ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
File ‘ModelGood/libs/ModelGood.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BioStatR’ ‘ggplot2’
  All declared Imports should be used.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    doc  23.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   4.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
File ‘MonetDB.R/libs/MonetDB.R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
File ‘monreg/libs/monreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   9.9Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   9.0Mb
Running ‘testthat.R’ [121s/299s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library("checkmate")
  > library("testthat")
  > library("ParamHelpers")
  > library("mlr")
  'mlr' is in maintenance mode since July 2019. Future development
  efforts will go into its successor 'mlr3' (<https://mlr3.mlr-org.com>).
  > library("mlrCPO")
  > 
  > test_check("mosmafs")
  Loading required package: mosmafs
  Loading required package: ecr
  Loading required package: BBmisc
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  Loading required package: smoof
  
  Attaching package: 'ecr'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  
  Attaching package: 'mosmafs'
  
  The following objects are masked from 'package:ecr':
  
      getPopulations, getStatistics
  
  ── 1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232)  ─────────
  `slickEcr(...)` threw an error with unexpected message.
  Expected match: "Must be of type 'numeric', not 'factor'"
  Actual message: "Assertion on 'fidelity[[2]]' failed: Must be of type 'numeric', not 'character'."
  Backtrace:
    1. testthat::expect_error(...)
    6. mosmafs::slickEcr(...)
    7. mosmafs::initEcr(...)
    8. mosmafs:::checkFidelity(fidelity)
    9. checkmate::assertNumeric(fidelity[[2]], any.missing = FALSE)
   10. checkmate::makeAssertion(x, res, .var.name, add)
   11. checkmate:::mstop(...)
  
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 458 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.8Mb
File ‘mpbart/libs/mpbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
File ‘mp/libs/mp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
File ‘MRCE/libs/MRCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.2Mb
File ‘mrfse/libs/mrfse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘MRH/libs/MRH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’
File ‘MRwarping/libs/MRwarping.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘msda/libs/msda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  28.4Mb
installed size is 51.6Mb
  sub-directories of 1Mb or more:
    libs  51.2Mb
File ‘MSGLasso/libs/MSGLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘msgps/libs/msgps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  18.6Mb
Namespace in Imports field not imported from: ‘amap’
  All declared Imports should be used.
Running examples in ‘MST-Ex.R’ failed
The error most likely occurred in:

> ### Name: MST
> ### Title: Multivariate Survival Trees
> ### Aliases: MST splitting.stat.MST1 splitting.stat.MST2
> ###   splitting.stat.MST3 splitting.stat.MST4
> ### Keywords: Trees Survival Multivariate Correlated
> 
> ### ** Examples
> 
> set.seed(186117)
> data <- rmultime(N = 200, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> test <- rmultime(N = 100, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> 
> #Construct Multivariate Survival Tree:
> fit <- MST(formula = Surv(time, status) ~ x1 + x2 + x3 + x4 | id, data, test,
+     method = "marginal", minsplit = 100, minevents = 20, selection.method = "test.sample")
Error in plot.window(...) : need finite 'ylim' values
Calls: MST -> plot -> plot.default -> localWindow -> plot.window
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
Execution halted
File ‘MTS/libs/MTS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
File ‘muhaz/libs/muhaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MultiCNVDetect/libs/MultiCNVDetect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cowsay’
  All declared Imports should be used.
installed size is 83.5Mb
  sub-directories of 1Mb or more:
    libs  83.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
File ‘multinomRob/libs/multinomRob.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘multispatialCCM/libs/multispatialCCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
File ‘MVB/libs/MVB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mvcluster/libs/mvcluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mvnmle/libs/mvnmle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘utils’
  All declared Imports should be used.
File ‘mvrtn/libs/mvrtn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
File ‘namespace/libs/namespace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Error(s) in re-building vignettes:
--- re-building ‘exploring-imputed-values.Rmd’ using rmarkdown
Quitting from lines 78-87 (exploring-imputed-values.Rmd) 
Error: processing vignette 'exploring-imputed-values.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘exploring-imputed-values.Rmd’

--- re-building ‘getting-started-w-naniar.Rmd’ using rmarkdown
Quitting from lines 284-292 (getting-started-w-naniar.Rmd) 
Error: processing vignette 'getting-started-w-naniar.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘getting-started-w-naniar.Rmd’

--- re-building ‘naniar-visualisation.Rmd’ using rmarkdown
--- finished re-building ‘naniar-visualisation.Rmd’

--- re-building ‘replace-with-na.Rmd’ using rmarkdown
Quitting from lines 43-52 (replace-with-na.Rmd) 
Error: processing vignette 'replace-with-na.Rmd' failed with diagnostics:
No common type for `y` <character> and `y` <double>.
--- failed re-building ‘replace-with-na.Rmd’

--- re-building ‘special-missing-values.Rmd’ using rmarkdown
--- finished re-building ‘special-missing-values.Rmd’

SUMMARY: processing the following files failed:
  ‘exploring-imputed-values.Rmd’ ‘getting-started-w-naniar.Rmd’
  ‘replace-with-na.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘nanop/libs/nanop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (!requireNamespace("testthat", quietly=TRUE)) install.packages("testthat", dependencies=TRUE, repos="http://cran.rstudio.com/")
  > library(nbc4va)
  To view the 'nbc4va' package description see: 
  help(nbc4va) 
  
  To view the 'nbc4va' package documentation, see: 
  https://rrwen.github.io/nbc4va 
  
  To cite the original method used in the 'nbc4va' package see: 
  citation("nbc4va")
  > 
  > testthat::test_check("nbc4va")
  ── 1. Failure: (unknown) (@test_nbc4va.R#29)  ──────────────────────────────────
  `results <- nbc(train, test)` did not produce any warnings.
  
  ── 2. Failure: (unknown) (@test_nbc4va.R#32)  ──────────────────────────────────
  `resultsNoCauses <- nbc(train, noCauses, known = FALSE)` did not produce any warnings.
  
  ── 3. Failure: nbc() sets the out$test.known to correctly indicate whether or no
  `expect_equal(...)` did not produce any warnings.
  
  ── 4. Error: nbc() can handle incorrect column data types in the correct positio
  The train data IDs are not unique (duplicates found:)
  Backtrace:
   1. testthat::expect_warning(...)
   6. nbc4va:::internalCheckNBC(trainTypes, testTypes)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 68 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 4 ]
  1. Failure: (unknown) (@test_nbc4va.R#29) 
  2. Failure: (unknown) (@test_nbc4va.R#32) 
  3. Failure: nbc() sets the out$test.known to correctly indicate whether or not the test causes are known (@test_nbc4va.R#46) 
  4. Error: nbc() can handle incorrect column data types in the correct positions (@test_nbc4va.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘nbpMatching/libs/nbpMatching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NBPSeq/libs/NBPSeq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’
File ‘NeatMap/libs/NeatMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
File ‘NetComp/libs/NetComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mvrtn’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespace in Imports field not imported from: ‘clue’
  All declared Imports should be used.
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   7.0Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
File ‘networksis/libs/networksis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘networkTomography/libs/networkTomography.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
File ‘neuRosim/libs/neuRosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              6.1Mb
    classic-bugs   1.6Mb
    include        5.7Mb
    libs          17.2Mb
    tests          1.6Mb
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Namespace in Imports field not imported from: ‘deSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
File ‘nmfgpu4R/libs/nmfgpu4R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘KernelKnn’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘uroot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘multicool’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stars’
  All declared Imports should be used.
File ‘nnls/libs/nnls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
  ‘forcats’ ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘arrow’
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
File ‘nontarget/libs/nontarget.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
File ‘norm/libs/norm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NORMT3/libs/NORMT3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
File ‘NPsimex/libs/NPsimex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘npst/libs/npst.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  20.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.4Mb
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’
File ‘obliclus/libs/obliclus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    doc    2.3Mb
    help   2.7Mb
    libs   4.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
Running examples in ‘ODEnetwork-Ex.R’ failed
The error most likely occurred in:

> ### Name: setEvents
> ### Title: Setting Events
> ### Aliases: setEvents
> 
> ### ** Examples
> 
> masses <- 1
> dampers <- as.matrix(1.5)
> springs <- as.matrix(4)
> odenet <- ODEnetwork(masses, dampers, springs)
> eventdat <- data.frame(  var = c("x.1", "x.1")
+                        , time = c(1, 3)
+                        , value = c(1, 3)
+                        )
> odenet <- setState(odenet, 0, 0)
> odenet <- setEvents(odenet, eventdat)
Error: Assertion failed. One of the following must apply:
 * checkDataFrame(events): May only contain the following types:
 * {factor,numeric,numeric}, but element 1 has type 'character'
 * checkDataFrame(events): Must have exactly 4 cols, but has 3 cols
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ODEnetwork.Rmd’ using rmarkdown
Quitting from lines 168-175 (ODEnetwork.Rmd) 
Error: processing vignette 'ODEnetwork.Rmd' failed with diagnostics:
Assertion failed. One of the following must apply:
 * checkDataFrame(events): May only contain the following types:
 * {factor,numeric,numeric}, but element 1 has type 'character'
 * checkDataFrame(events): Must have exactly 4 cols, but has 3 cols
--- failed re-building ‘ODEnetwork.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  34.0Mb
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.4Mb
File ‘onemap/libs/onemap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘onlinePCA/libs/onlinePCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘digest’ ‘dplyr’ ‘miniUI’ ‘text2vec’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   6.3Mb
Running ‘testthat.R’ [35s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OpenLand)
  > 
  > test_check("OpenLand")
  ── 1. Error: (unknown) (@test_generalfunctions.R#29)  ──────────────────────────
  package 'rgdal' is not available
  Backtrace:
    1. base::lapply(...)
    2. OpenLand:::FUN(X[[i]], ...)
    4. raster::writeRaster(...)
    5. raster:::.local(x, filename, ...)
    6. raster:::.writeGDALall(...)
    7. raster:::.startGDALwriting(...)
    8. raster:::.getGDALtransient(...)
    9. raster:::.isSupportedFormat(gdalfiletype)
   10. raster:::.isSupportedGDALFormat(dname)
   11. raster:::.requireRgdal()
  
  ── 2. Error: (unknown) (@test_inputrasters.R#5)  ───────────────────────────────
  package 'rgdal' is not available
  Backtrace:
    1. base::lapply(...)
    2. OpenLand:::FUN(X[[i]], ...)
    4. raster::writeRaster(...)
    5. raster:::.local(x, filename, ...)
    6. raster:::.writeGDALall(...)
    7. raster:::.startGDALwriting(...)
    8. raster:::.getGDALtransient(...)
    9. raster:::.isSupportedFormat(gdalfiletype)
   10. raster:::.isSupportedGDALFormat(dname)
   11. raster:::.requireRgdal()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 96 | SKIPPED: 0 | WARNINGS: 24 | FAILED: 2 ]
  1. Error: (unknown) (@test_generalfunctions.R#29) 
  2. Error: (unknown) (@test_inputrasters.R#5) 
  
  Error: testthat unit tests failed
  Execution halted