Malformed Description field: should contain one or more complete sentences.
sw.plot : <anonymous>: no visible global function definition for
  'median'
sw.plot : <anonymous>: no visible global function definition for 'mad'
sw.plot : my.line: no visible global function definition for 'lines'
sw.plot : island.line: no visible global function definition for
  'lines'
sw.plot: no visible global function definition for 'plot'
sw.plot: no visible global function definition for 'rug'
sw.plot: no visible global function definition for 'axis'
sw.plot: no visible global function definition for 'mtext'
sw.plot: no visible global function definition for 'abline'
sw.plot: no visible global function definition for 'points'
sw.rob : <anonymous>: no visible global function definition for
  'median'
sw.rob : <anonymous>: no visible global function definition for 'mad'
sw.threshold : <anonymous>: no visible global function definition for
  'median'
sw.threshold : <anonymous>: no visible global function definition for
  'mad'
Undefined global functions or variables:
  abline axis lines mad median mtext plot points rug
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "plot",
             "points", "rug")
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
Checking should be performed on sources prepared by 'R CMD build'.
Hartree2Joule: no visible binding for global variable
  'universalConstants'
Hertz2Joule: no visible binding for global variable
  'universalConstants'
Joule2Hartree: no visible binding for global variable
  'universalConstants'
Joule2Hertz: no visible binding for global variable
  'universalConstants'
Joule2Kelvin: no visible binding for global variable
  'universalConstants'
Joule2centimeterMinusOne: no visible binding for global variable
  'universalConstants'
Joule2electronVolt: no visible binding for global variable
  'universalConstants'
Joule2kiloCaloriePerMole: no visible binding for global variable
  'universalConstants'
Joule2kiloJoulePerMole: no visible binding for global variable
  'universalConstants'
KMC: no visible global function definition for 'runif'
Kelvin2Joule: no visible binding for global variable
  'universalConstants'
LandauZener: no visible binding for global variable
  'universalConstants'
LandauZenerProbability: no visible binding for global variable
  'universalConstants'
Marcus: no visible binding for global variable 'universalConstants'
MarcusLevichJortner: no visible binding for global variable
  'universalConstants'
centimeterMinusOne2Joule: no visible binding for global variable
  'universalConstants'
electronVolt2Joule: no visible binding for global variable
  'universalConstants'
kiloCaloriePerMole2Joule: no visible binding for global variable
  'universalConstants'
kiloJoulePerMole2Joule: no visible binding for global variable
  'universalConstants'
Undefined global functions or variables:
  runif universalConstants
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'RCurl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'bitops' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createDataset: no visible global function definition for 'read.csv'
createInventory: no visible global function definition for 'read.csv'
downloadMaster: no visible global function definition for
  'getURLContent'
downloadMaster: no visible global function definition for 'read.csv'
downloadMaster: no visible global function definition for 'write.csv'
getMissingScrape: no visible global function definition for 'read.csv'
readLocalMaster: no visible global function definition for 'read.csv'
readMonthlyCsv: no visible global function definition for 'read.csv'
scrapeToCsv: no visible global function definition for 'download.file'
writeData: no visible global function definition for 'write.csv'
writeGhcn: no visible global function definition for 'write.table'
writeInventory: no visible global function definition for 'write.table'
writeMonthlyStations: no visible global function definition for
  'read.csv'
writeMonthlyStations: no visible global function definition for
  'write.csv'
Undefined global functions or variables:
  download.file getURLContent read.csv write.csv write.table
Consider adding
  importFrom("utils", "download.file", "read.csv", "write.csv",
             "write.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'ChemoSpec2D'
File
  LICENSE
is not mentioned in the DESCRIPTION file.
choicemodelr : drawDelta: no visible global function definition for
  'rnorm'
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for 'rnorm'
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for 'runif'
choicemodelr : rmultireg: no visible global function definition for
  'rnorm'
choicemodelr : rwishart: no visible global function definition for
  'rchisq'
choicemodelr : rwishart: no visible global function definition for
  'rnorm'
choicemodelr : fsh: no visible global function definition for
  'flush.console'
choicemodelr: no visible global function definition for 'matplot'
choicemodelr: no visible global function definition for 'write.table'
Undefined global functions or variables:
  flush.console matplot rchisq rnorm runif write.table
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "rchisq", "rnorm", "runif")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Qh.times.dhyper: no visible global function definition for 'var'
Qh.times.dhyper: no visible global function definition for 'pnorm'
Qh.times.dhyper: no visible global function definition for 'dhyper'
TDiM: no visible global function definition for 'sd'
choplump.default: no visible global function definition for
  'flush.console'
choplump.formula: no visible global function definition for 'terms'
cm.compact: no visible global function definition for 'dhyper'
Undefined global functions or variables:
  dhyper flush.console pnorm sd terms var
Consider adding
  importFrom("stats", "dhyper", "pnorm", "sd", "terms", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Malformed Description field: should contain one or more complete sentences.
parse_counts: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
combineToSingleMatrix: no visible global function definition for
  'read.table'
combineToSingleMatrix: no visible global function definition for
  'write.table'
compareCIM: no visible global function definition for 'sd'
correctData: no visible global function definition for 'wd'
correctData: no visible global function definition for 'threshold'
correctData: no visible binding for global variable 'madmad'
correctData: no visible global function definition for 'wr'
Undefined global functions or variables:
  madmad read.table sd threshold wd wr write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
cin: no visible global function definition for 'pnorm'
gammaHRF: no visible global function definition for 'dgamma'
intertest: no visible global function definition for 'pnorm'
truncSum: no visible global function definition for 'spline'
Undefined global functions or variables:
  dgamma pnorm spline
Consider adding
  importFrom("stats", "dgamma", "pnorm", "spline")
to your NAMESPACE file.
cit.assignBcmst: no visible binding for global variable 'citbcmst'
cit.assignBcmst : <anonymous>: no visible global function definition
  for 'median'
cit.assignBcmst: no visible global function definition for 'prcomp'
cit.assignBcmst: no visible global function definition for 'par'
cit.assignBcmst: no visible global function definition for 'lines'
cit.assignBcmst: no visible global function definition for 'legend'
cit.centroids : <anonymous>: no visible global function definition for
  'median'
cit.centroids : <anonymous>: no visible global function definition for
  'var'
cit.dist: no visible global function definition for 'dist'
cit.dist: no visible global function definition for 'as.dist'
cit.dist: no visible global function definition for 'cor'
cit.distToCentroids: no visible global function definition for
  'quantile'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'median'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'mad'
Undefined global functions or variables:
  as.dist citbcmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
cit.assignCcmst: no visible binding for global variable 'citccmst'
cit.assignCcmst : <anonymous>: no visible global function definition
  for 'median'
cit.assignCcmst : median.na: no visible global function definition for
  'median'
cit.assignCcmst: no visible global function definition for 'prcomp'
cit.assignCcmst: no visible global function definition for 'par'
cit.assignCcmst: no visible global function definition for 'lines'
cit.assignCcmst: no visible global function definition for 'legend'
cit.centroids : <anonymous>: no visible global function definition for
  'median'
cit.centroids : <anonymous>: no visible global function definition for
  'var'
cit.dist: no visible global function definition for 'dist'
cit.dist: no visible global function definition for 'as.dist'
cit.dist: no visible global function definition for 'cor'
cit.distToCentroids: no visible global function definition for
  'quantile'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'median'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'mad'
Undefined global functions or variables:
  as.dist citccmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
CityPlot: no visible global function definition for 'read.table'
CityPlot: no visible global function definition for 'tail'
CityPlot: no visible global function definition for 'pdf'
CityPlot: no visible global function definition for 'split.screen'
CityPlot: no visible global function definition for 'screen'
CityPlot: no visible global function definition for 'par'
CityPlot: no visible global function definition for 'plot'
CityPlot: no visible global function definition for 'rect'
CityPlot: no visible global function definition for 'text'
CityPlot: no visible global function definition for 'lines'
CityPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off lines par pdf plot read.table rect screen split.screen tail
  text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
Package suggested but not available for checking: 'doMC'
'library' or 'require' call to 'rggobi' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
generate_data : <anonymous>: no visible global function definition for
  'runif'
knnf: no visible global function definition for 'terms'
rescaler.default: no visible global function definition for 'sd'
rescaler.default: no visible global function definition for 'median'
rescaler.default: no visible global function definition for 'mad'
simvar.numeric: no visible global function definition for 'runif'
Undefined global functions or variables:
  mad median runif sd terms
Consider adding
  importFrom("stats", "mad", "median", "runif", "sd", "terms")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
classify.bug: no visible global function definition for
  'txtProgressBar'
classify.bug: no visible global function definition for
  'setTxtProgressBar'
plot.scores: no visible binding for global variable 'quantile'
plot.scores: no visible global function definition for 'runif'
plot.scores: no visible binding for global variable 'median'
scores.gpcm.bug: no visible global function definition for
  'txtProgressBar'
scores.gpcm.bug: no visible global function definition for
  'setTxtProgressBar'
across.reps,classification: no visible global function definition for
  'sd'
Undefined global functions or variables:
  median quantile runif sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "median", "quantile", "runif", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
.boxRadial: no visible global function definition for 'predict'
.radialSVM: no visible global function definition for 'predict'
cfPredict: no visible global function definition for 'predict'
getPerm5Num: no visible global function definition for 'median'
getPerm5Num: no visible global function definition for 'quantile'
ggClassPred: no visible global function definition for 'ftable'
ggEnsHist: no visible global function definition for 'sd'
ggPermHist: no visible global function definition for 'sd'
Undefined global functions or variables:
  ftable median predict quantile sd
Consider adding
  importFrom("stats", "ftable", "median", "predict", "quantile", "sd")
to your NAMESPACE file.
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(classyfireR)
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > 
  > test_check('classyfireR')
  -- 1. Error: submit-classification (@test-submission.R#16)  --------------------
  lexical error: invalid char in json text.
                                         <!DOCTYPE html> <html> <head>  
                       (right here) ------^
  1: expect_true(dplyr::is.tbl(retrieve_classification(inchi_sub$query_id))) at testthat/test-submission.R:16
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: dplyr::is.tbl(retrieve_classification(inchi_sub$query_id))
  5: retrieve_classification(inchi_sub$query_id)
  6: jsonlite::fromJSON(text_content)
  7: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  8: parseJSON(txt, bigint_as_char)
  9: parse_string(txt, bigint_as_char)
  
  == testthat results  ===========================================================
  OK: 10 SKIPPED: 0 FAILED: 1
  1. Error: submit-classification (@test-submission.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
clime: no visible global function definition for 'cov'
cv.clime: no visible global function definition for 'cov'
cv.clime: no visible binding for global variable 'sd'
Undefined global functions or variables:
  cov sd
Consider adding
  importFrom("stats", "cov", "sd")
to your NAMESPACE file.
gxe.cc: no visible global function definition for 'qnorm'
gxe.coh: no visible global function definition for 'qnorm'
utility.cc: no visible global function definition for 'qnorm'
utility.coh: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
socp: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ClusteredMutations.Rcheck/00install.out' for details.
'library' or 'require' call to 'ggplot2' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
hopkins: no visible global function definition for 'runif'
hopkins: no visible global function definition for 'dist'
Undefined global functions or variables:
  dist runif
Consider adding
  importFrom("stats", "dist", "runif")
to your NAMESPACE file.
clustomit: no visible binding for global variable 'weighted.mean'
sim_unif : multivariate_unif: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif weighted.mean
Consider adding
  importFrom("stats", "runif", "weighted.mean")
to your NAMESPACE file.
braycurtis: no visible global function definition for 'as.dist'
czekanowski: no visible global function definition for 'as.dist'
findComplementaryIndices: no visible global function definition for
  'na.omit'
genSimilarityProfile: no visible global function definition for 'dist'
simprof: no visible global function definition for 'dist'
simprof: no visible global function definition for 'hclust'
simprof.plot : <local> : colorizer: no visible global function
  definition for 'is.leaf'
simprof.plot: no visible global function definition for 'rainbow'
simprof.plot: no visible global function definition for 'dendrapply'
simprof.plot: no visible global function definition for 'as.dendrogram'
Undefined global functions or variables:
  as.dendrogram as.dist dendrapply dist hclust is.leaf na.omit rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.dist", "dendrapply", "dist",
             "hclust", "is.leaf", "na.omit")
to your NAMESPACE file.
Package suggested but not available for checking: 'moe430a.db'
'library' or 'require' calls in package code:
  'Biobase' 'GO.db' 'annotate' 'kohonen' 'mclust'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cma_es: no visible global function definition for 'rnorm'
f_rand: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
alpha.cronbach: no visible global function definition for 'cov'
alpha.curve: no visible global function definition for 'plot'
alpha.curve: no visible global function definition for 'text'
Undefined global functions or variables:
  cov plot text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
CMF: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
ComputeLambdaAndNuHat.shiftCMPest: no visible global function
  definition for 'nlminb'
ControlCharts: no visible global function definition for
  'com.log.density'
ControlCharts: no visible global function definition for 'plot'
ControlCharts: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline com.log.density nlminb plot
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "nlminb")
to your NAMESPACE file.
crr: no visible binding for global variable 'na.omit'
crr: no visible global function definition for 'approx'
cuminc: no visible binding for global variable 'na.omit'
cuminc: no visible global function definition for 'pchisq'
plot.cuminc: no visible global function definition for 'par'
plot.cuminc: no visible global function definition for 'plot'
plot.cuminc: no visible binding for global variable 'legend'
plot.cuminc: no visible global function definition for 'lines'
plot.predict.crr: no visible global function definition for 'plot'
plot.predict.crr: no visible global function definition for 'lines'
print.crr: no visible global function definition for 'pnorm'
summary.crr: no visible global function definition for 'pnorm'
summary.crr: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  approx legend lines na.omit par pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("stats", "approx", "na.omit", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
copynumberBootstrap: no visible global function definition for
  'txtProgressBar'
copynumberBootstrap: no visible global function definition for
  'quantile'
copynumberBootstrap: no visible global function definition for
  'setTxtProgressBar'
gethits: no visible global function definition for 'read.table'
normalizeGC: no visible global function definition for 'median'
plotCNOGpro: no visible global function definition for 'par'
plotCNOGpro: no visible global function definition for 'plot'
plotCNOGpro: no visible global function definition for 'rainbow'
plotCNOGpro: no visible global function definition for 'density'
plotCNOGpro: no visible global function definition for 'polygon'
plotCNOGpro: no visible global function definition for 'lines'
plotCNOGpro: no visible global function definition for 'legend'
plotCNOGpro: no visible global function definition for 'boxplot'
sampleChromosome: no visible global function definition for 'median'
sampleChromosome: no visible binding for global variable 'var'
setupEmissionMatrix: no visible global function definition for 'dgeom'
store: no visible global function definition for 'write.table'
Undefined global functions or variables:
  boxplot density dgeom legend lines median par plot polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "plot",
             "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
CNclusterNcenter: no visible global function definition for 'median'
CNclusterNcenter: no visible binding for global variable 'var'
breakIntoGaps: no visible global function definition for 'runif'
centerprob: no visible global function definition for 'pnorm'
getz: no visible global function definition for 'predict'
smad: no visible global function definition for 'mad'
smedian: no visible global function definition for 'median'
smedian.sample: no visible global function definition for 'median'
smedmad: no visible global function definition for 'median'
smedmad: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median pnorm predict runif var
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "predict", "runif",
             "var")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data     3.5Mb
    exdata   5.5Mb
coalescentMCMC: no visible global function definition for
  'packageVersion'
coalescentMCMC : getparams: no visible global function definition for
  'nlminb'
sim.coalescent: no visible global function definition for 'plot'
sim.coalescent: no visible global function definition for 'segments'
sim.coalescent: no visible global function definition for 'points'
Undefined global functions or variables:
  nlminb packageVersion plot points segments
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'lars' 'randomForest' 'ridge' 'snowfall' 'tree'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
Package in Depends field not imported from: 'coda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
Quitting from lines 150-170 (nih-enrollment-html.Rmd) 
Error: processing vignette 'nih-enrollment-html.Rmd' failed with diagnostics:
OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 10054
Execution halted
Malformed Description field: should contain one or more complete sentences.
BMDE: no visible global function definition for 'quantile'
BMDU: no visible global function definition for 'runif'
BMDU: no visible global function definition for 'quantile'
FS: no visible global function definition for 'qnorm'
GM: no visible global function definition for 'qchisq'
QH: no visible global function definition for 'qchisq'
SG : sgp: no visible global function definition for 'ppois'
SG : sgp: no visible global function definition for 'dpois'
WALD: no visible global function definition for 'qchisq'
WALDCC: no visible global function definition for 'qchisq'
WS: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  dpois ppois qchisq qnorm quantile runif
Consider adding
  importFrom("stats", "dpois", "ppois", "qchisq", "qnorm", "quantile",
             "runif")
to your NAMESPACE file.
cICA: no visible global function definition for 'mvfft'
cICA: no visible global function definition for 'ar.yw'
cICA: no visible global function definition for 'rnorm'
scICA: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  ar.yw mvfft rnorm
Consider adding
  importFrom("stats", "ar.yw", "mvfft", "rnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotVenn2d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn2d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn2d: no visible global function definition for 'grid.text'
plotVenn2d: no visible global function definition for 'gpar'
plotVenn2d: no visible global function definition for 'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn3d: no visible global function definition for 'grid.text'
plotVenn3d: no visible global function definition for 'gpar'
plotVenn3d: no visible global function definition for 'grid.polygon'
plotVenn4d : getCommonEllipse: no visible global function definition
  for 'aggregate'
plotVenn4d : region.polygon: no visible global function definition for
  'head'
plotVenn4d : region.polygon: no visible global function definition for
  'grid.polygon'
plotVenn4d : region.polygon: no visible global function definition for
  'gpar'
plotVenn4d: no visible global function definition for 'grid.text'
plotVenn4d: no visible global function definition for 'gpar'
plotVenn4d: no visible global function definition for 'pushViewport'
plotVenn4d: no visible global function definition for 'viewport'
plotVenn4d: no visible global function definition for 'grid.polygon'
plotVenn4d: no visible global function definition for 'upViewport'
resizeCircles: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  aggregate gpar grid.polygon grid.text head pushViewport uniroot
  upViewport viewport
Consider adding
  importFrom("stats", "aggregate", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
generateMonochromaticColors: no visible global function definition for
  'col2rgb'
generateMonochromaticColors: no visible global function definition for
  'rgb'
generateMonochromaticColors: no visible global function definition for
  'tail'
hsv2rgb: no visible global function definition for 'rgb'
rotational_dispersion: no visible global function definition for
  'col2rgb'
rotational_dispersion: no visible global function definition for
  'rgb2hsv'
tetradicColors: no visible global function definition for 'head'
triadicColors: no visible global function definition for 'head'
Undefined global functions or variables:
  col2rgb head rgb rgb2hsv tail
Consider adding
  importFrom("grDevices", "col2rgb", "rgb", "rgb2hsv")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
primary.colors: no visible global function definition for 'rgb'
rgb.tables: no visible global function definition for 'rgb'
ygobb: no visible global function definition for 'approx'
ygobb: no visible global function definition for 'rgb'
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   2.0Mb
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
competitive.test: no visible global function definition for 'runif'
selfcontained.test : fun2: no visible global function definition for
  'qchisq'
selfcontained.test: no visible global function definition for 'cov'
selfcontained.test: no visible global function definition for 'qchisq'
selfcontained.test: no visible global function definition for 'cor'
selfcontained.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor cov pchisq qchisq runif
Consider adding
  importFrom("stats", "cor", "cov", "pchisq", "qchisq", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'lattice' 'rgl'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
p.Johansen: no visible global function definition for 'pgamma'
plotComT: no visible global function definition for 'axis'
plotComT: no visible global function definition for 'title'
plotComT: no visible global function definition for 'lines'
plotComT: no visible global function definition for 'box'
q.Johansen: no visible global function definition for 'qgamma'
Undefined global functions or variables:
  axis box lines pgamma qgamma title
Consider adding
  importFrom("graphics", "axis", "box", "lines", "title")
  importFrom("stats", "pgamma", "qgamma")
to your NAMESPACE file.
addxaxis: no visible global function definition for 'par'
addxaxis: no visible global function definition for 'axis'
addxaxis: no visible global function definition for 'mtext'
eplot: no visible global function definition for 'plot'
eplot: no visible global function definition for 'par'
eplot: no visible global function definition for 'axis'
eplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis mtext par plot
Consider adding
  importFrom("graphics", "axis", "mtext", "par", "plot")
to your NAMESPACE file.
compareC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    app   2.7Mb
    doc   2.3Mb
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'XML' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
compareODM: no visible global function definition for 'xmlRoot'
compareODM: no visible global function definition for 'xmlTreeParse'
compareODM: no visible global function definition for 'xmlChildren'
compareODM: no visible global function definition for 'xmlAttrs'
compareODM: no visible global function definition for 'xmlValue'
Undefined global functions or variables:
  xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
Malformed Description field: should contain one or more complete sentences.
two.level.comparison.items: no visible global function definition for
  'complete.cases'
two.level.components: no visible global function definition for
  'complete.cases'
plot,ece: no visible global function definition for 'par'
plot,ece: no visible global function definition for 'points'
plot,ece: no visible global function definition for 'mtext'
plot,ece: no visible global function definition for 'legend'
plot,ece: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline complete.cases legend mtext par points
Consider adding
  importFrom("graphics", "abline", "legend", "mtext", "par", "points")
  importFrom("stats", "complete.cases")
to your NAMESPACE file.
CIFplot: no visible global function definition for 'plot'
CIFplot: no visible global function definition for 'gray'
CIFplot: no visible global function definition for 'lines'
iprop: no visible global function definition for 'qnorm'
irates: no visible global function definition for 'qnorm'
irates.ratio: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  gray lines plot qnorm
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'inSilicoDb'
Package in Depends field not imported from: 'numDeriv'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dcomplnorm: no visible global function definition for 'grad'
dcomplnorm : f1: no visible global function definition for 'dlnorm'
dcomplnorm : F1: no visible global function definition for 'plnorm'
dcomplnorm : f1L: no visible global function definition for 'dlnorm'
dcomplnorm : F1L: no visible global function definition for 'plnorm'
pcomplnorm: no visible global function definition for 'grad'
pcomplnorm : f1: no visible global function definition for 'dlnorm'
pcomplnorm : F1: no visible global function definition for 'plnorm'
pcomplnorm : F1L: no visible global function definition for 'plnorm'
qcomplnorm: no visible global function definition for 'grad'
qcomplnorm : f1: no visible global function definition for 'dlnorm'
qcomplnorm : F1q: no visible global function definition for 'qlnorm'
qcomplnorm : F1: no visible global function definition for 'plnorm'
rcomplnorm: no visible global function definition for 'runif'
Undefined global functions or variables:
  dlnorm grad plnorm qlnorm runif
Consider adding
  importFrom("stats", "dlnorm", "plnorm", "qlnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'hypergeo' which was already attached by Depends.
  Please remove these calls from your code.
momentCompound: no visible global function definition for 'integrate'
pgfIhypergeometric: no visible global function definition for 'uniroot'
pgfIhyperpoisson: no visible global function definition for 'uniroot'
pgfIkattitypeh1: no visible global function definition for 'uniroot'
pgfIkattitypeh2: no visible global function definition for 'uniroot'
pgfIneymantypeb: no visible global function definition for 'uniroot'
pgfIneymantypec: no visible global function definition for 'uniroot'
pgfIpoissonlindley: no visible global function definition for 'uniroot'
pgfIthomas: no visible global function definition for 'uniroot'
pgfIwaring: no visible global function definition for 'uniroot'
pgfIyule: no visible global function definition for 'uniroot'
rCompound: no visible global function definition for 'runif'
Undefined global functions or variables:
  integrate runif uniroot
Consider adding
  importFrom("stats", "integrate", "runif", "uniroot")
to your NAMESPACE file.
kef: no visible global function definition for 'dgamma'
kef: no visible global function definition for 'dlnorm'
simp_int: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx dgamma dlnorm
Consider adding
  importFrom("stats", "approx", "dgamma", "dlnorm")
to your NAMESPACE file.
prepare_Rd: concor.Rd:4: Dropping empty section \keyword
prepare_Rd: concor.Rd:5: Dropping empty section \keyword
prepare_Rd: concorcano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorcano.Rd:5: Dropping empty section \keyword
prepare_Rd: concoreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concoreg.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgm.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgm.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgmcano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgmcano.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgmreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgmreg.Rd:5: Dropping empty section \keyword
prepare_Rd: concors.Rd:4: Dropping empty section \keyword
prepare_Rd: concors.Rd:5: Dropping empty section \keyword
prepare_Rd: concorscano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorscano.Rd:5: Dropping empty section \keyword
prepare_Rd: concorsreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concorsreg.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbip.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbip.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbip2.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbip2.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbips.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbips.Rd:5: Dropping empty section \keyword
prepare_Rd: svdcp.Rd:4: Dropping empty section \keyword
prepare_Rd: svdcp.Rd:5: Dropping empty section \keyword
K1.norm: no visible global function definition for 'dnorm'
K1.norm: no visible global function definition for 'pnorm'
K1.t3: no visible global function definition for 'pt'
K2.norm: no visible global function definition for 'dnorm'
K2.norm: no visible global function definition for 'pnorm'
K2.t3: no visible global function definition for 'pt'
Undefined global functions or variables:
  dnorm pnorm pt
Consider adding
  importFrom("stats", "dnorm", "pnorm", "pt")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'evd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
Malformed Description field: should contain one or more complete sentences.
ml_solver: no visible global function definition for 'approx'
select_kmax: no visible global function definition for 'median'
Undefined global functions or variables:
  approx median
Consider adding
  importFrom("stats", "approx", "median")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
conicPlot: no visible global function definition for 'palette'
conicPlotAsymptotes: no visible global function definition for
  'palette'
conicPlotAsymptotes: no visible global function definition for 'abline'
conicPlotAxes: no visible global function definition for 'palette'
conicPlotAxes: no visible global function definition for 'abline'
plotDegenerateConic: no visible global function definition for 'plot'
plotDegenerateConic: no visible global function definition for 'points'
plotDegenerateConic: no visible global function definition for 'abline'
plotEllipsis: no visible global function definition for 'lines'
plotEllipsis: no visible global function definition for 'plot'
plotEllipsis: no visible global function definition for 'points'
plotHyperbola: no visible global function definition for 'lines'
plotHyperbola: no visible global function definition for 'plot'
plotHyperbola: no visible global function definition for 'points'
plotParabola: no visible global function definition for 'lines'
plotParabola: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline lines palette plot points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "plot", "points")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to 'parallel' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Rmpi' 'snow'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ConjointChecks: no visible global function definition for 'makeCluster'
ConjointChecks: no visible global function definition for
  'clusterSetRNGStream'
ConjointChecks: no visible global function definition for
  'clusterApply'
ConjointChecks: no visible global function definition for 'stopCluster'
omni.check: no visible global function definition for 'runif'
omni.check: no visible global function definition for 'quantile'
plot.checks: no visible global function definition for 'mtext'
plot.checks: no visible global function definition for 'text'
Undefined global functions or variables:
  clusterApply clusterSetRNGStream makeCluster mtext quantile runif
  stopCluster text
Consider adding
  importFrom("graphics", "mtext", "text")
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/conStruct.Rcheck/00install.out' for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
GNU make is a SystemRequirements.
maCooperative: no visible global function definition for 'points'
maCooperative: no visible global function definition for 'legend'
maPessimistic: no visible global function definition for 'combn'
maRules: no visible global function definition for 'capture.output'
mstCooperative: no visible global function definition for 'points'
mstCooperative: no visible global function definition for 'legend'
mstOptimistic: no visible global function definition for 'combn'
mstPessimistic: no visible global function definition for 'combn'
mstRules: no visible global function definition for 'capture.output'
plotCoreSet: no visible global function definition for 'points'
plotCoreSet: no visible global function definition for 'polygon'
plotImputationSet: no visible global function definition for 'par'
plotImputationSet: no visible global function definition for 'plot'
plotImputationSet: no visible global function definition for 'box'
plotImputationSet: no visible global function definition for 'polygon'
plotImputationSet: no visible global function definition for 'text'
shapleyValue: no visible global function definition for 'combn'
Undefined global functions or variables:
  box capture.output combn legend par plot points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "plot", "points",
             "polygon", "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
density_conditional: no visible global function definition for 'ppois'
density_joint: no visible global function definition for 'ppois'
dgam: no visible global function definition for 'dgamma'
dpolicy_loss: no visible global function definition for 'ppois'
dztp: no visible global function definition for 'dpois'
epolicy_loss: no visible global function definition for 'integrate'
mle_joint: no visible global function definition for 'optim'
mle_marginal: no visible global function definition for 'glm'
mle_marginal: no visible global function definition for 'Gamma'
mle_marginal: no visible global function definition for 'vcov'
mle_marginal: no visible global function definition for 'poisson'
mle_marginal: no visible global function definition for 'coef'
mle_marginal: no visible global function definition for 'ppois'
mle_marginal: no visible global function definition for 'optim'
pgam: no visible global function definition for 'pgamma'
ppolicy_loss: no visible global function definition for 'integrate'
pztp: no visible global function definition for 'ppois'
qpolicy_loss: no visible global function definition for 'uniroot'
rgam: no visible global function definition for 'rgamma'
vuongtest: no visible global function definition for 'sd'
ztp.glm: no visible global function definition for 'coef'
ztp.glm: no visible global function definition for 'glm'
ztp.glm: no visible binding for global variable 'poisson'
ztp.glm: no visible global function definition for 'optim'
Undefined global functions or variables:
  Gamma coef dgamma dpois glm integrate optim pgamma poisson ppois
  rgamma sd uniroot vcov
Consider adding
  importFrom("stats", "Gamma", "coef", "dgamma", "dpois", "glm",
             "integrate", "optim", "pgamma", "poisson", "ppois",
             "rgamma", "sd", "uniroot", "vcov")
to your NAMESPACE file.
advanceRNG: no visible global function definition for 'runif'
randomEventMoves: no visible global function definition for 'runif'
randomRescaledEventMoves: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
coreTDT_geneset: no visible global function definition for
  'write.table'
pvalue_calculator: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  dbinom write.table
Consider adding
  importFrom("stats", "dbinom")
  importFrom("utils", "write.table")
to your NAMESPACE file.
compute.llh: no visible global function definition for 'dnorm'
compute.u.hat.simple: no visible global function definition for 'dnorm'
fit.CLM.1u.simple.start: no visible global function definition for
  'kmeans'
fit.CLMM.simple.start: no visible global function definition for
  'kmeans'
fit.CLMM.simple.start.NA: no visible global function definition for
  'kmeans'
Undefined global functions or variables:
  dnorm kmeans
Consider adding
  importFrom("stats", "dnorm", "kmeans")
to your NAMESPACE file.
CBData: no visible global function definition for 'aggregate'
CMData: no visible global function definition for 'aggregate'
GEE.trend.test: no visible binding for global variable 'binomial'
GEE.trend.test: no visible global function definition for 'pnorm'
RS.trend.test: no visible global function definition for 'pnorm'
SO.mc.est: no visible global function definition for 'xtabs'
SO.trend.test : boot.LRT.fun: no visible global function definition for
  'aggregate'
jointprobs: no visible global function definition for 'xtabs'
mc.test.chisq.CBData: no visible global function definition for
  'pchisq'
mc.test.chisq.CMData : get.T: no visible global function definition for
  'weighted.mean'
mc.test.chisq.CMData: no visible global function definition for
  'pchisq'
mg.DirMult : <anonymous>: no visible global function definition for
  'rmultinom'
mg.LogitNorm : <anonymous>: no visible global function definition for
  'rmultinom'
mg.MixMult : <anonymous>: no visible global function definition for
  'rmultinom'
mg.Resample: no visible global function definition for 'rmultinom'
ran.CBData : ran.gen: no visible global function definition for
  'rmultinom'
read.CBData: no visible global function definition for 'read.table'
read.CBData: no visible global function definition for 'aggregate'
read.CMData: no visible global function definition for 'read.table'
trend.test : boot.LRT.fun: no visible global function definition for
  'aggregate'
unwrap.CMData: no visible global function definition for 'reshape'
Undefined global functions or variables:
  aggregate binomial pchisq pnorm read.table reshape rmultinom
  weighted.mean xtabs
Consider adding
  importFrom("stats", "aggregate", "binomial", "pchisq", "pnorm",
             "reshape", "rmultinom", "weighted.mean", "xtabs")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package suggested but not available for checking: 'ProData'
Package in Depends field not imported from: 'calibrate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
correlogram: no visible global function definition for 'par'
correlogram: no visible global function definition for 'plot'
correlogram: no visible global function definition for 'points'
correlogram: no visible global function definition for 'textxy'
correlogram: no visible global function definition for 'arrows'
correlogram: no visible global function definition for 'circle'
fit_angles: no visible global function definition for 'runif'
fit_angles: no visible global function definition for 'nlminb'
linangplot: no visible global function definition for 'cor'
linangplot: no visible global function definition for 'rad2degree'
linangplot: no visible global function definition for 'ginv'
linangplot: no visible global function definition for 'par'
linangplot: no visible global function definition for 'plot'
linangplot: no visible global function definition for 'calibrate'
linangplot: no visible global function definition for 'var'
pfa: no visible global function definition for 'cor'
Undefined global functions or variables:
  arrows calibrate circle cor ginv nlminb par plot points rad2degree
  runif textxy var
Consider adding
  importFrom("graphics", "arrows", "par", "plot", "points")
  importFrom("stats", "cor", "nlminb", "runif", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/corrgram.Rcheck/00install.out' for details.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
corr.Qmatrix: no visible global function definition for 'cor'
corr.Qmatrix: no visible global function definition for 'cor.test'
summarise.Fst: no visible global function definition for 'cor'
summarise.Fst: no visible global function definition for 'sd'
summarise.lnPD: no visible global function definition for 'sd'
Undefined global functions or variables:
  cor cor.test sd
Consider adding
  importFrom("stats", "cor", "cor.test", "sd")
to your NAMESPACE file.
dist: no visible global function definition for 'quantile'
edgecount: no visible global function definition for 'reshape'
edgecutoff: no visible global function definition for 'boxplot'
edgecutoff: no visible global function definition for 'sd'
edgecutoff: no visible global function definition for 'median'
edgecutoff: no visible global function definition for 'IQR'
Undefined global functions or variables:
  IQR boxplot median quantile reshape sd
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "IQR", "median", "quantile", "reshape", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
GA_search : subset_score: no visible global function definition for
  'combn'
choose_lambda : subset_score: no visible global function definition for
  'combn'
cond.fyx: no visible global function definition for 'var'
cond.fyx: no visible global function definition for 'cor'
diff_gen_PPI: no visible global function definition for 'cov'
diff_gen_PPI: no visible global function definition for 'sd'
f.test: no visible binding for global variable 'var'
get_quantiles : node_edge: no visible global function definition for
  'combn'
score_scaling: no visible global function definition for 'hist'
score_scaling: no visible global function definition for 'sd'
Undefined global functions or variables:
  combn cor cov hist sd var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "cov", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
cosinor.lm: no visible binding for global variable 'na.omit'
cosinor.lm: no visible global function definition for 'terms'
cosinor.lm: no visible global function definition for 'as.formula'
cosinor.lm: no visible global function definition for 'lm'
cosinor_analyzer: no visible binding for global variable 'vitamind'
cosinor_analyzer : <anonymous>: no visible global function definition
  for 'as.formula'
ggplot.cosinor.lm: no visible global function definition for 'predict'
predict.cosinor.lm: no visible global function definition for 'fitted'
predict.cosinor.lm: no visible global function definition for 'predict'
simulate_cosinor: no visible global function definition for 'runif'
simulate_cosinor: no visible global function definition for 'rbinom'
simulate_cosinor: no visible global function definition for 'rnorm'
summary.cosinor.lm: no visible global function definition for 'vcov'
summary.cosinor.lm: no visible global function definition for 'qnorm'
summary.cosinor.lm: no visible global function definition for 'pnorm'
test_cosinor: no visible global function definition for 'pchisq'
test_cosinor: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm
  runif terms vcov vitamind
Consider adding
  importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif",
             "terms", "vcov")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
D.M: no visible global function definition for 'integrate'
lookbackTime: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'Rglpk' 'glmnet' 'parallel' 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
'library' or 'require' calls to packages already attached by Depends:
  'Matrix' 'mlogit' 'poLCA'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Matrix' 'mlogit' 'poLCA'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
covLCA: no visible global function definition for 'model.response'
covLCA: no visible global function definition for 'model.frame'
covLCA: no visible global function definition for 'model.matrix'
covLCA: no visible global function definition for 'rnorm'
covLCA: no visible global function definition for 'flush.console'
covLCA: no visible global function definition for 'ginv'
covLCA.initialAlphaGamma: no visible global function definition for
  'as.formula'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit.data'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit'
covLCA.initialBeta: no visible global function definition for
  'as.formula'
covLCA.initialBeta: no visible global function definition for 'poLCA'
covLCA.initialBeta: no visible global function definition for
  'mlogit.data'
covLCA.initialBeta: no visible global function definition for 'mlogit'
covLCA.paramVariance: no visible global function definition for 'ginv'
covLCA.varianceFirst: no visible global function definition for 'bdiag'
Undefined global functions or variables:
  as.formula bdiag flush.console ginv mlogit mlogit.data model.frame
  model.matrix model.response poLCA rnorm
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response", "rnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
covreg.mcmc: no visible global function definition for 'model.frame'
covreg.mcmc: no visible global function definition for 'model.matrix'
covreg.mcmc: no visible global function definition for 'model.response'
covreg.mcmc: no visible global function definition for 'lm'
covreg.mcmc: no visible global function definition for 'rnorm'
covreg.mcmc: no visible global function definition for 'cov'
rmn: no visible global function definition for 'rnorm'
rwish: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  cov lm model.frame model.matrix model.response rnorm
Consider adding
  importFrom("stats", "cov", "lm", "model.frame", "model.matrix",
             "model.response", "rnorm")
to your NAMESPACE file.
calcz02: no visible global function definition for 'coxph'
calcz02: no visible global function definition for 'residuals'
covTest: no visible global function definition for 'Surv'
covTest: no visible global function definition for 'predict'
covTest: no visible global function definition for 'update'
covTest: no visible global function definition for 'lsfit'
covTest: no visible global function definition for 'pexp'
covTest: no visible global function definition for 'pf'
lars.en: no visible binding for global variable 'var'
predict.lars.en: no visible global function definition for 'predict'
Undefined global functions or variables:
  Surv coxph lsfit pexp pf predict residuals update var
Consider adding
  importFrom("stats", "lsfit", "pexp", "pf", "predict", "residuals",
             "update", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  'parallel' 'snowfall'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Matrix' 'prodlim'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CoxBoost: no visible global function definition for 'Matrix'
CoxBoost: no visible binding for global variable 'sd'
CoxBoost: no visible global function definition for 'predict'
cv.CoxBoost : eval.fold: no visible global function definition for
  'predict'
cv.CoxBoost: no visible global function definition for 'mclapply'
cv.CoxBoost: no visible binding for global variable 'sd'
estimPVal: no visible global function definition for 'mclapply'
iCoxBoost: no visible global function definition for 'terms'
iCoxBoost: no visible global function definition for 'model.response'
iCoxBoost: no visible global function definition for 'model.frame'
iCoxBoost: no visible global function definition for 'model.matrix'
iCoxBoost: no visible global function definition for 'Matrix'
plot.CoxBoost: no visible global function definition for 'plot'
plot.CoxBoost: no visible global function definition for 'lines'
plot.CoxBoost: no visible global function definition for 'text'
predict.iCoxBoost: no visible global function definition for
  'model.response'
predict.iCoxBoost: no visible global function definition for
  'model.frame'
predict.iCoxBoost: no visible global function definition for
  'model.matrix'
Undefined global functions or variables:
  Matrix lines mclapply model.frame model.matrix model.response plot
  predict sd terms text
Consider adding
  importFrom("graphics", "lines", "plot", "text")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "predict", "sd", "terms")
to your NAMESPACE file.
coxaalen: no visible global function definition for 'terms'
coxaalen: no visible global function definition for 'model.matrix'
coxaalen: no visible binding for global variable 'frame'
coxaalen: no visible global function definition for 'update.formula'
coxaalen: no visible global function definition for 'capture.output'
coxdual: no visible global function definition for 'terms'
coxdual: no visible global function definition for 'model.matrix'
coxdual: no visible binding for global variable 'frame'
coxdual: no visible global function definition for 'update.formula'
coxdual: no visible global function definition for 'as.formula'
coxdual: no visible global function definition for 'capture.output'
frame.assign: no visible global function definition for 'model.matrix'
linapprox: no visible global function definition for 'approx'
print.coxinterval: no visible global function definition for 'pchisq'
print.summary.coxinterval : f: no visible global function definition
  for 'printCoefmat'
step2stepfun : f: no visible global function definition for 'stepfun'
summary.coxinterval : f: no visible global function definition for
  'pchisq'
summary.coxinterval : f: no visible global function definition for
  'qnorm'
Undefined global functions or variables:
  approx as.formula capture.output frame model.matrix pchisq
  printCoefmat qnorm stepfun terms update.formula
Consider adding
  importFrom("graphics", "frame")
  importFrom("stats", "approx", "as.formula", "model.matrix", "pchisq",
             "printCoefmat", "qnorm", "stepfun", "terms",
             "update.formula")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
GNU make is a SystemRequirements.
comp.graph: no visible global function definition for 'qnorm'
comp.graph: no visible global function definition for 'plot'
comp.graph: no visible global function definition for 'polygon'
comp.graph: no visible global function definition for 'lines'
cox.ridge: no visible global function definition for 'terms'
cox.ridge: no visible global function definition for 'model.extract'
cox.ridge: no visible global function definition for 'model.matrix'
cox.ridge: no visible binding for global variable 'hat'
Undefined global functions or variables:
  hat lines model.extract model.matrix plot polygon qnorm terms
Consider adding
  importFrom("graphics", "lines", "plot", "polygon")
  importFrom("stats", "hat", "model.extract", "model.matrix", "qnorm",
             "terms")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
coxr: no visible global function definition for 'model.extract'
coxr: no visible global function definition for 'model.matrix'
coxr.draw: no visible global function definition for 'plot'
coxr.draw: no visible global function definition for 'lines'
coxr.draw: no visible global function definition for 'points'
coxr.fit: no visible global function definition for 'quantile'
gen_data: no visible global function definition for 'rnorm'
gen_data: no visible global function definition for 'rexp'
plot.coxr: no visible global function definition for 'quantile'
plot.coxr: no visible global function definition for 'par'
plot.coxr: no visible global function definition for 'mtext'
plot.coxr: no visible global function definition for 'title'
plot.coxr: no visible global function definition for 'split.screen'
plot.coxr: no visible global function definition for 'screen'
plot.coxr: no visible global function definition for 'close.screen'
print.coxr: no visible global function definition for 'pnorm'
print.coxr: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq plot
  pnorm points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par", "plot",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
CumInt : fn: no visible global function definition for 'integrate'
RND0: no visible global function definition for 'runif'
coxseiInt: no visible global function definition for 'approxfun'
coxseiInt : js: no visible global function definition for 'tail'
coxseiest: no visible global function definition for 'approxfun'
coxseiest : loglik : ll: no visible global function definition for
  'tail'
coxseiest: no visible global function definition for 'optim'
coxseiest2: no visible global function definition for 'approxfun'
coxseiest2: no visible global function definition for 'optim'
coxseiest3: no visible global function definition for 'approxfun'
coxseiest3: no visible global function definition for 'optim'
coxseiexp: no visible global function definition for 'approxfun'
coxseiexp: no visible global function definition for 'optim'
coxseiexp : js: no visible global function definition for 'tail'
coxseiexp: no visible global function definition for 'pnorm'
coxseiexp: no visible global function definition for 'stepfun'
coxseifit.ex: no visible global function definition for 'approxfun'
coxseifit.ex: no visible global function definition for 'optim'
coxseifit.ex : js: no visible global function definition for 'tail'
coxseifit.ex: no visible global function definition for 'pnorm'
coxseifit.ex: no visible global function definition for 'stepfun'
coxseisim : int.at.lasttm: no visible global function definition for
  'tail'
plot.coxsei: no visible global function definition for 'plot'
print.summary.coxsei: no visible global function definition for
  'printCoefmat'
summary.coxsei: no visible global function definition for 'coef'
Undefined global functions or variables:
  approxfun coef integrate optim plot pnorm printCoefmat runif stepfun
  tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "approxfun", "coef", "integrate", "optim", "pnorm",
             "printCoefmat", "runif", "stepfun")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cplexAPI.Rcheck/00install.out' for details.
QR.cd: no visible global function definition for 'quantile'
QR.lasso.cd: no visible global function definition for 'quantile'
cqr.cd: no visible global function definition for 'quantile'
cqr.lasso.cd: no visible global function definition for 'quantile'
cqr.lasso.mm: no visible global function definition for 'quantile'
cqr.mm: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
distance.comoving: no visible global function definition for
  'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
.cramer.kritwertfft: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
Malformed Description field: should contain one or more complete sentences.
crantastic.submitInstalledPackages: no visible global function
  definition for 'installed.packages'
postData: no visible global function definition for 'make.socket'
postData: no visible global function definition for 'write.socket'
postData: no visible global function definition for 'read.socket'
postData: no visible global function definition for 'close.socket'
Undefined global functions or variables:
  close.socket installed.packages make.socket read.socket write.socket
Consider adding
  importFrom("utils", "close.socket", "installed.packages",
             "make.socket", "read.socket", "write.socket")
to your NAMESPACE file.
catrandpvalue: no visible global function definition for 'read.table'
catrandpvalue: no visible global function definition for 'rmultinom'
catrandpvaluepermute: no visible global function definition for
  'read.table'
catrandstat: no visible global function definition for 'stack'
catrandstat: no visible global function definition for 'pchisq'
catrandstat: no visible binding for global variable 'var'
Undefined global functions or variables:
  pchisq read.table rmultinom stack var
Consider adding
  importFrom("stats", "pchisq", "rmultinom", "var")
  importFrom("utils", "read.table", "stack")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
cm.CVaR: no visible global function definition for 'quantile'
cm.hist: no visible global function definition for 'hist'
cm.quantile: no visible global function definition for 'qnorm'
cm.rnorm: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  hist qnorm quantile rnorm
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
GNU make is a SystemRequirements.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
makeX_eset: no visible global function definition for 'model.matrix'
normFit: no visible binding for global variable 'lm'
normFit: no visible binding for global variable 'sd'
normFit: no visible global function definition for 'lm'
normPred: no visible binding for global variable 'predict'
normPred: no visible global function definition for 'predict'
normPred: no visible binding for global variable 'median'
plot.nFit: no visible global function definition for 'par'
plot.nFit: no visible global function definition for 'barplot'
plot.nFit: no visible global function definition for 'legend'
show_nfit: no visible global function definition for 'anova'
show_nfit: no visible global function definition for 'residuals'
show_nfit: no visible global function definition for 'fitted'
standardsFit: no visible binding for global variable 'lm'
standardsFit: no visible global function definition for 'resid'
standardsFit: no visible global function definition for
  'compareVersion'
standardsPred: no visible global function definition for 'predict'
makeX,ExpressionSet-character: no visible global function definition
  for 'model.matrix'
plot,nFit: no visible global function definition for 'par'
plot,nFit: no visible global function definition for 'barplot'
plot,nFit: no visible global function definition for 'legend'
show,nFit: no visible global function definition for 'anova'
show,nFit: no visible global function definition for 'residuals'
show,nFit: no visible global function definition for 'fitted'
Undefined global functions or variables:
  anova barplot compareVersion fitted legend lm median model.matrix par
  predict resid residuals sd
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "anova", "fitted", "lm", "median", "model.matrix",
             "predict", "resid", "residuals", "sd")
  importFrom("utils", "compareVersion")
to your NAMESPACE file.
'library' or 'require' call to 'RCurl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'chron'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
collateDaily: no visible global function definition for 'read.table'
collateDaily: no visible global function definition for 'write.table'
collateHourly: no visible global function definition for 'read.table'
collateHourly: no visible global function definition for 'write.table'
downloadCRN: no visible global function definition for 'download.file'
getUrlsCRN: no visible global function definition for 'getURL'
writeDataset: no visible global function definition for 'read.table'
writeDataset: no visible global function definition for 'write.table'
Undefined global functions or variables:
  download.file getURL read.table write.table
Consider adding
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
get.plan: no visible global function definition for 'menu'
Undefined global functions or variables:
  menu
Consider adding
  importFrom("utils", "menu")
to your NAMESPACE file.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
crossmatchtest: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
BootC : BSs: no visible global function definition for 'lm'
BootC : BSs: no visible global function definition for 'vcov'
BootC: no visible global function definition for 'boot'
BootC: no visible global function definition for 'boot.ci'
DeltaC: no visible global function definition for 'lm'
DeltaC: no visible global function definition for 'vcov'
FiellerC: no visible global function definition for 'lm'
FiellerC: no visible global function definition for 'vcov'
nonLinearC: no visible global function definition for 'nls'
Undefined global functions or variables:
  boot boot.ci lm nls vcov
Consider adding
  importFrom("stats", "lm", "nls", "vcov")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'CR' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
curerate : cr: no visible global function definition for 'rbinom'
curerate : cr: no visible global function definition for 'rexp'
curerate : cr: no visible global function definition for 'runif'
curerate: no visible global function definition for 'new'
showcr: no visible global function definition for 'show'
Undefined global functions or variables:
  new rbinom rexp runif show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "rbinom", "rexp", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
crrp: no visible global function definition for 'approx'
gcrrp: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx
Consider adding
  importFrom("stats", "approx")
to your NAMESPACE file.
crrc: no visible binding for global variable 'na.omit'
crrs: no visible binding for global variable 'na.omit'
mycrr: no visible binding for global variable 'na.omit'
mycrr.test: no visible binding for global variable 'na.omit'
print.crrs: no visible global function definition for 'pnorm'
psh.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  na.omit pchisq pnorm
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pnorm")
to your NAMESPACE file.
crrstep : crr.makecov1: no visible global function definition for
  'model.matrix'
crrstep : crr.dropterm: no visible global function definition for
  'terms'
crrstep : crr.dropterm: no visible global function definition for
  'as.formula'
crrstep : crr.addterm: no visible global function definition for
  'terms'
crrstep : crr.addterm: no visible global function definition for
  'as.formula'
crrstep: no visible global function definition for 'as.formula'
crrstep: no visible global function definition for 'terms'
crrstep: no visible global function definition for 'model.frame'
crrstep: no visible binding for global variable 'na.pass'
crrstep: no visible global function definition for 'update'
crrstep: no visible global function definition for 'drop.terms'
Undefined global functions or variables:
  as.formula drop.terms model.frame model.matrix na.pass terms update
Consider adding
  importFrom("stats", "as.formula", "drop.terms", "model.frame",
             "model.matrix", "na.pass", "terms", "update")
to your NAMESPACE file.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
pielou: 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: 'compiler'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
csSAM: no visible binding for global variable 'quantile'
csSAM: no visible global function definition for 'median'
csfit: no visible global function definition for 'lsfit'
csfit: no visible global function definition for 'ls.diag'
plotCsSAM: no visible global function definition for 'pdf'
plotCsSAM: no visible global function definition for 'par'
plotCsSAM: no visible global function definition for 'plot'
plotCsSAM: no visible global function definition for 'title'
plotCsSAM: no visible global function definition for 'dev.off'
runSAM: no visible binding for global variable 'median'
runSAM: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf plot quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
cstar: no visible global function definition for 'vcov'
cstar : utility: no visible global function definition for 'dt'
cstar : maximand: no visible global function definition for 'integrate'
cstar: no visible global function definition for 'uniroot'
cstari : utility: no visible global function definition for 'dt'
cstari : maximand: no visible global function definition for
  'integrate'
cstari: no visible global function definition for 'uniroot'
cstarme : utility: no visible global function definition for 'density'
cstarme : maximand: no visible global function definition for
  'integrate'
cstarme : maximand: no visible global function definition for 'sd'
cstarme: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  density dt integrate sd uniroot vcov
Consider adding
  importFrom("stats", "density", "dt", "integrate", "sd", "uniroot",
             "vcov")
to your NAMESPACE file.
map.coltypes: 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.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    4.0Mb
    libs   7.8Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    extdata  31.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cudaBayesreg.Rcheck/00install.out' for details.
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
'library' or 'require' call to 'lars' which was already attached by Depends.
  Please remove these calls from your code.
jumpoints : seg.lm.fit0: no visible global function definition for
  'lm.fit'
jumpoints : seg.lm.fit0: no visible global function definition for
  'coef'
jumpoints: no visible global function definition for 'quantile'
jumpoints: no visible global function definition for 'coef'
plot.aCGHsegmented: no visible global function definition for 'plot'
plot.aCGHsegmented: no visible global function definition for 'grey'
plot.aCGHsegmented: no visible global function definition for 'abline'
plot.aCGHsegmented: no visible global function definition for 'points'
plot.aCGHsegmented: no visible global function definition for
  'segments'
plot.aCGHsegmented: no visible global function definition for 'par'
Undefined global functions or variables:
  abline coef grey lm.fit par plot points quantile segments
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
  importFrom("stats", "coef", "lm.fit", "quantile")
to your NAMESPACE file.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File 'curl/libs/i386/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
cci.nostrat: no visible global function definition for 'quantile'
cci.nostrat: no visible global function definition for 'plot'
cci.nostrat: no visible global function definition for 'axis'
cci.nostrat: no visible global function definition for 'lines'
cci.nostrat: no visible global function definition for 'legend'
cci.strat: no visible global function definition for 'plot'
cci.strat: no visible global function definition for 'axis'
cci.strat: no visible global function definition for 'lines'
cci.strat: no visible global function definition for 'legend'
clfs.nostrat: no visible global function definition for 'quantile'
clfs.nostrat: no visible global function definition for 'plot'
clfs.nostrat: no visible global function definition for 'axis'
clfs.nostrat: no visible global function definition for 'lines'
clfs.nostrat: no visible global function definition for 'legend'
clfs.strat: no visible global function definition for 'plot'
clfs.strat: no visible global function definition for 'axis'
clfs.strat: no visible global function definition for 'lines'
clfs.strat: no visible global function definition for 'legend'
pvals.2cat: no visible global function definition for 'pchisq'
pvals.cat: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  axis legend lines pchisq plot quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
Cut: no visible global function definition for 'cor'
MissSimulation: no visible global function definition for 'rbinom'
cutoff: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor rbinom
Consider adding
  importFrom("stats", "cor", "rbinom")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
delta.glm: no visible global function definition for 'glm'
delta.glm: no visible global function definition for 'residuals'
delta.glm: no visible global function definition for 'fitted'
delta.glm: no visible global function definition for 'predict.glm'
two.stage.model.outputs: no visible global function definition for 'sd'
Undefined global functions or variables:
  fitted glm predict.glm residuals sd
Consider adding
  importFrom("stats", "fitted", "glm", "predict.glm", "residuals", "sd")
to your NAMESPACE file.
ci.cvAUC: no visible global function definition for 'qnorm'
ci.pooled.cvAUC: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
calfun: no visible global function definition for 'optim'
calfun: no visible global function definition for 'cov'
calfun: no visible global function definition for 'var'
Undefined global functions or variables:
  cov optim var
Consider adding
  importFrom("stats", "cov", "optim", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
func.constructRegressionFormula: no visible global function definition
  for 'as.formula'
func.crossValidationAnalysis: no visible global function definition for
  'glm'
func.crossValidationAnalysis: no visible global function definition for
  'predict'
func.crossValidationAnalysis: no visible global function definition for
  'write.table'
func.externalValidationAnalysis: no visible global function definition
  for 'predict'
func.externalValidationAnalysis: no visible global function definition
  for 'write.table'
func.linearRegressionAnalysis: no visible global function definition
  for 'glm'
func.linearRegressionAnalysis: no visible global function definition
  for 'predict'
func.linearRegressionAnalysis: no visible global function definition
  for 'write.table'
func.sortDataColumns: no visible global function definition for
  'write.table'
mainfunc.q2: no visible global function definition for 'write.table'
mainfunc.q2: no visible global function definition for 'new'
mainfunc.stats: no visible global function definition for 'write.table'
mainfunc.stats: no visible global function definition for 'new'
Undefined global functions or variables:
  as.formula glm new predict write.table
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.formula", "glm", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cvimpute.by.wavelet: no visible global function definition for 'sd'
cvimpute.by.wavelet: no visible global function definition for 'mad'
cvimpute.image.by.wavelet: no visible global function definition for
  'sd'
cvimpute.image.by.wavelet: no visible global function definition for
  'mad'
cvwavelet.image.after.impute: no visible global function definition for
  'sd'
cvwavelet.image.after.impute: no visible global function definition for
  'mad'
Undefined global functions or variables:
  mad sd
Consider adding
  importFrom("stats", "mad", "sd")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'robustbase'
A package should be listed in only one of these fields.
random.CV: no visible global function definition for 'var'
regular.CV: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
create_clustering_problem: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some 'make' programs ignore lines not ending in LF.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   1.9Mb
.mixgauss_init: no visible global function definition for 'cov'
.mixgauss_init: no visible global function definition for 'var'
Undefined global functions or variables:
  cov var
Consider adding
  importFrom("stats", "cov", "var")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Malformed Description field: should contain one or more complete sentences.
cxxfun.from.dll: no visible global function definition for 'new'
cxxfun.from.dso.bin: no visible global function definition for 'new'
cxxfunctionplus: no visible global function definition for 'getPlugin'
cxxfunctionplus: no visible global function definition for
  'cxxfunction'
cxxfunctionplus: no visible global function definition for 'new'
show,cxxdso: no visible global function definition for 'object.size'
Undefined global functions or variables:
  cxxfunction getPlugin new object.size
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package in Depends field not imported from: 'fda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.for.sequence.endpoint.breaks: no visible global function
  definition for 'na.omit'
get.breaks.vector: no visible global function definition for 'na.omit'
get.cycle.breaks: no visible global function definition for 'na.omit'
get.cycle.counts: no visible global function definition for 'na.omit'
get.cycle.matrix: no visible global function definition for 'na.omit'
get.cycle.minimums: no visible global function definition for 'na.omit'
get.peaks: no visible global function definition for 'embed'
get.trans: no visible global function definition for
  'create.bspline.basis'
get.trans: no visible global function definition for 'smooth.basis'
get.trans: no visible global function definition for 'deriv.fd'
get.trans: no visible global function definition for 'eval.fd'
get.transition.locations: no visible global function definition for
  'na.omit'
get.transition.locations.FDiff: no visible global function definition
  for 'na.omit'
get.window: no visible global function definition for 'sd'
Undefined global functions or variables:
  create.bspline.basis deriv.fd embed eval.fd na.omit sd smooth.basis
Consider adding
  importFrom("stats", "embed", "na.omit", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
cytoDiv: no visible global function definition for 'colorRampPalette'
cytoDiv: no visible global function definition for 'persp'
Undefined global functions or variables:
  colorRampPalette persp
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "persp")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
compareModels: no visible binding for global variable 'fgl'
compareModels: no visible global function definition for 'rlm'
compareModels: no visible global function definition for 'lm'
compareModels: no visible global function definition for 'predict'
compareModels: no visible global function definition for 'resid'
plotSampDist: no visible global function definition for 'par'
plotSampDist: no visible global function definition for 'density'
plotSampDist: no visible global function definition for 'plot'
plotSampDist: no visible global function definition for 'lines'
plotSampDist: no visible global function definition for 'legend'
plotSampDist: no visible global function definition for 'qqnorm'
plotSampDist: no visible global function definition for 'points'
plotSampDist: no visible global function definition for 'mtext'
simulateSampDist: no visible binding for global variable 'rnorm'
Undefined global functions or variables:
  density fgl legend lines lm mtext par plot points predict qqnorm
  resid rlm rnorm
Consider adding
  importFrom("graphics", "legend", "lines", "mtext", "par", "plot",
             "points")
  importFrom("stats", "density", "lm", "predict", "qqnorm", "resid",
             "rnorm")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 's20x'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
allCombs: no visible global function definition for 'combn'
brute.search: no visible global function definition for 'na.omit'
dag.draw: no visible global function definition for 'plot'
dag.draw: no visible global function definition for 'text'
dag.init: no visible global function definition for
  'installed.packages'
dag.legend: no visible global function definition for 'text'
dag.letter: no visible global function definition for 'text'
dag.move: no visible global function definition for 'identify'
dag.move: no visible global function definition for 'locator'
dag.sim: no visible global function definition for 'rnorm'
dag.sim: no visible global function definition for 'rbinom'
dag.sim : <anonymous>: no visible global function definition for
  'rbinom'
garrows: no visible global function definition for 'arrows'
smoothArc: no visible global function definition for 'points'
summary_dagRdag: no visible global function definition for 'na.omit'
viv: no visible global function definition for 'na.omit'
write.paths: no visible global function definition for 'text'
Undefined global functions or variables:
  arrows combn identify installed.packages locator na.omit plot points
  rbinom rnorm text
Consider adding
  importFrom("graphics", "arrows", "identify", "locator", "plot",
             "points", "text")
  importFrom("stats", "na.omit", "rbinom", "rnorm")
  importFrom("utils", "combn", "installed.packages")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DAMOCLES_ML: no visible global function definition for 'flush.console'
DAMOCLES_bootstrap: no visible global function definition for
  'cophenetic'
DAMOCLES_bootstrap: no visible global function definition for 'sd'
DAMOCLES_bootstrap: no visible global function definition for
  'quantile'
DAMOCLES_sim: no visible global function definition for 'na.omit'
DAMOCLES_sim: no visible global function definition for 'runif'
DAMOCLES_sim: no visible global function definition for 'lines'
DAMOCLES_sim: no visible global function definition for 'rnorm'
DAMOCLES_sim: no visible global function definition for 'dexp'
DAMOCLES_sim: no visible global function definition for 'dist'
DAMOCLES_simplex: no visible global function definition for
  'flush.console'
Undefined global functions or variables:
  cophenetic dexp dist flush.console lines na.omit quantile rnorm runif
  sd
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "cophenetic", "dexp", "dist", "na.omit",
             "quantile", "rnorm", "runif", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
drawAimSpot: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'par'
drawBoard: no visible global function definition for 'plot'
drawBoard: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'text'
drawHeatmap: no visible global function definition for 'heat.colors'
drawHeatmap: no visible global function definition for 'par'
drawHeatmap: no visible global function definition for 'image'
drawHeatmap: no visible global function definition for 'rect'
generalExpScores: no visible global function definition for 'fft'
simpleExpScores: no visible global function definition for 'mvfft'
simpleExpScores: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft heat.colors image mvfft par plot points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "points", "rect",
             "text")
  importFrom("stats", "fft", "mvfft")
to your NAMESPACE file.
dashboard_open: no visible global function definition for 'write.csv'
dashboard_open: no visible global function definition for
  'capture.output'
dctable: no visible global function definition for 'capture.output'
Undefined global functions or variables:
  capture.output write.csv
Consider adding
  importFrom("utils", "capture.output", "write.csv")
to your NAMESPACE file.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    java  15.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    4.5Mb
    libs   1.9Mb
datadict.profile: no visible global function definition for
  'txtProgressBar'
datadict.profile: no visible global function definition for
  'setTxtProgressBar'
datadict_profile: no visible global function definition for
  'txtProgressBar'
datadict_profile: no visible global function definition for
  'setTxtProgressBar'
heatmap.quality: no visible global function definition for
  'colorRampPalette'
heatmap.quality: no visible global function definition for 'heatmap'
heatmap_quality: no visible global function definition for
  'colorRampPalette'
heatmap_quality: no visible global function definition for 'heatmap'
is.oneOf: no visible global function definition for 'read.csv'
is_one_of: no visible global function definition for 'read.csv'
pkg.version: no visible global function definition for 'citation'
pkg_version: no visible global function definition for 'citation'
ruleCoverage: no visible global function definition for 'dotchart'
ruleCoverage: no visible global function definition for 'abline'
rule_coverage: no visible global function definition for 'dotchart'
rule_coverage: no visible global function definition for 'abline'
scoreSum: no visible global function definition for 'plot'
score_sum: no visible global function definition for 'plot'
shortSummary: no visible global function definition for 'sd'
short_summary: no visible global function definition for 'sd'
Undefined global functions or variables:
  abline citation colorRampPalette dotchart heatmap plot read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart", "plot")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Package has no Sweave vignette sources and no VignetteBuilder field.
Package suggested but not available for checking: 'Rhipe'
Package in Depends field not imported from: 'DBI'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onLoad : <anonymous>: no visible global function definition for
  'read.table'
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
checkDataQuality: no visible binding for global variable 'quantile'
checkDataQuality: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  quantile write.csv
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.0Mb
browse: no visible global function definition for 'slot'
browse: no visible global function definition for 'page'
default.options: no visible binding for global variable 'object.size'
heat.view: no visible global function definition for 'head'
heat.view: no visible global function definition for 'tail'
whos: no visible global function definition for 'slotNames'
whos : <anonymous> : <anonymous>: no visible global function definition
  for 'slot'
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Depends: includes the non-default packages:
  'xtable' 'akima' 'R.oo' 'R.methodsS3' 'matlab' 'lattice' 'locfit'
  'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'R.methodsS3' 'R.oo' 'akima' 'graphics' 'grid' 'lattice' 'locfit'
  'matlab' 'xtable'
  Please remove these calls from your code.
'library' or 'require' call to 'R.matlab' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'R.methodsS3' 'R.oo' 'akima' 'grid' 'lattice' 'locfit' 'matlab'
  'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DAT : DATrun : calch: no visible global function definition for
  'preplot'
DAT : DATrun: no visible global function definition for 'rot90'
DAT : DATrun: no visible global function definition for 'median'
DAT : DATrun: no visible global function definition for 'locfit.robust'
DAT : DATrun: no visible global function definition for 'preplot'
DAT : DATrun: no visible global function definition for 'dev.new'
DAT : DATrun: no visible global function definition for 'image'
DAT : DATrun: no visible global function definition for 'palette'
DAT : DATrun: no visible global function definition for
  'colorRampPalette'
DAT : DATrun: no visible global function definition for 'text'
DAT : DATrun: no visible global function definition for 'dev.set'
DAT : DATrun: no visible global function definition for 'locator'
DAT : DATrun: no visible global function definition for 'graphics.off'
DAT : DATrun: no visible global function definition for 'pdf'
DAT : DATrun: no visible global function definition for 'layout'
DAT : DATrun: no visible global function definition for 'par'
DAT : DATrun: no visible global function definition for 'plot'
DAT : DATrun: no visible global function definition for 'frame'
DAT : DATrun: no visible global function definition for 'lines'
DAT : DATrun: no visible global function definition for 'dev.off'
DAT : DATrun: no visible global function definition for 'writeMat'
DAT: no visible binding for global variable 'DAT.simData'
Undefined global functions or variables:
  DAT.simData colorRampPalette dev.new dev.off dev.set frame
  graphics.off image layout lines locator locfit.robust median palette
  par pdf plot preplot rot90 text writeMat
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "dev.set", "graphics.off", "palette", "pdf")
  importFrom("graphics", "frame", "image", "layout", "lines", "locator",
             "par", "plot", "text")
  importFrom("stats", "median", "preplot")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' calls to packages already attached by Depends:
  'RMySQL' 'gWidgets'
  Please remove these calls from your code.
Malformed Description field: should contain one or more complete sentences.
dbEmpLikeGOF: no visible global function definition for 'runif'
dbEmpLikeGOF: no visible global function definition for 'var'
dbEmpLikeGOF: no visible global function definition for 'rnorm'
emplikeGOFinternal: no visible global function definition for 'var'
getCutoff: no visible binding for global variable 'unifCut'
getCutoff: no visible binding for global variable 'normCut'
getCutoff: no visible global function definition for 'lm'
getCutoff: no visible binding for global variable 'distEqCut'
getPval: no visible binding for global variable 'unifCut'
getPval: no visible binding for global variable 'normCut'
getPval: no visible global function definition for 'lm'
getPval: no visible binding for global variable 'distEqCut'
helperPval: no visible global function definition for 'lm'
returnCutoff: no visible global function definition for 'quantile'
testfun2: no visible global function definition for 'runif'
testfun2: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  distEqCut lm normCut quantile rnorm runif unifCut var
Consider adding
  importFrom("stats", "lm", "quantile", "rnorm", "runif", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
computePval: no visible global function definition for 'lm'
computeQhat: no visible global function definition for 'pnorm'
dbELnorm: no visible global function definition for 'rnorm'
getCutoffTableThree: no visible global function definition for 'lm'
getCutoffTableTwo: no visible global function definition for 'lm'
getCutoffValue: no visible global function definition for 'lm'
helperGetTstat: no visible global function definition for 'rnorm'
returnCutoffValue: no visible global function definition for 'rnorm'
returnCutoffValue: no visible global function definition for 'quantile'
varianceEstimator: no visible global function definition for 'density'
varianceEstimator: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  density ecdf lm pnorm quantile rnorm
Consider adding
  importFrom("stats", "density", "ecdf", "lm", "pnorm", "quantile",
             "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'doMC'
Malformed Title field: should not end in a period.
'library' or 'require' call to 'fdrtool' which was already attached by Depends.
  Please remove these calls from your code.
avelinkdis: no visible global function definition for 'sd'
avelinkdis: no visible global function definition for 'dist'
centdis: no visible global function definition for 'sd'
centdis: no visible global function definition for 'dist'
distable: no visible global function definition for 'write.table'
functionall: no visible global function definition for 'read.table'
randdis: no visible global function definition for 'write.table'
valuep: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  dist read.table sd write.csv write.table
Consider adding
  importFrom("stats", "dist", "sd")
  importFrom("utils", "read.table", "write.csv", "write.table")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.3Mb
.CA.fast2: no visible global function definition for 'lsfit'
.T2.fast: no visible global function definition for 'txtProgressBar'
.T2.fast: no visible global function definition for 'setTxtProgressBar'
.dcemri.bayes: no visible global function definition for 'median'
.dcemri.bayes: no visible global function definition for 'sd'
.dcemri.map : posterior: no visible global function definition for
  'dnorm'
.dcemri.map : posterior: no visible global function definition for
  'dgamma'
.dcemri.map : posterior: no visible global function definition for
  'dbeta'
.dcemri.map.single: no visible global function definition for 'optim'
.dcemri.spline: no visible binding for global variable 'median'
.dcemri.spline: no visible global function definition for 'median'
.dcemri.spline.single: no visible binding for global variable
  'quantile'
.dcemri.spline.single: no visible binding for global variable 'median'
.dcemri.spline.single: no visible global function definition for
  'median'
.ftm: no visible global function definition for 'fft'
.ftm: no visible global function definition for 'matplot'
.ftm: no visible global function definition for 'legend'
compartmentalModel : <anonymous>: no visible global function definition
  for 'approx'
convFFT: no visible global function definition for 'fft'
extractAIF : c.start: no visible global function definition for 'sd'
extractAIF : c.start: no visible global function definition for 'cor'
Undefined global functions or variables:
  approx cor dbeta dgamma dnorm fft legend lsfit matplot median optim
  quantile sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cor", "dbeta", "dgamma", "dnorm", "fft",
             "lsfit", "median", "optim", "quantile", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package suggested but not available for checking: 'doMC'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Packages in Depends field not imported from:
  'lattice' 'latticeExtra'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.LM: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
getDelimiter: no visible global function definition for 'read.csv'
setupfile: no visible global function definition for 'read.csv'
treatPath: no visible global function definition for 'file_test'
Undefined global functions or variables:
  file_test read.csv
Consider adding
  importFrom("utils", "file_test", "read.csv")
to your NAMESPACE file.
ifft: no visible global function definition for 'fft'
lines.deamer: no visible global function definition for 'lines'
plot.deamer: no visible global function definition for 'plot'
rlaplace: no visible global function definition for 'runif'
Undefined global functions or variables:
  fft lines plot runif
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
compare.relimp: no visible global function definition for 'qchisq'
compare.relimp: no visible global function definition for 'pchisq'
plot_transition: no visible global function definition for 'dnorm'
plot_transition: no visible global function definition for 'par'
plot_transition: no visible global function definition for 'plot'
plot_transition: no visible global function definition for 'lines'
plot_transition: no visible global function definition for 'plogis'
plot_transition: no visible global function definition for 'axis'
plot_transition: no visible global function definition for 'mtext'
relative.importance: no visible global function definition for 'glm'
relative.importance: no visible global function definition for 'sd'
relative.importance : tr.pr: no visible global function definition for
  'pnorm'
relative.importance: no visible global function definition for 'vcov'
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis plot pnorm qchisq sd
  vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
DeconCPdf: no visible global function definition for 'bw.nrd0'
DeconCPdf: no visible global function definition for 'bw.nrd'
DeconCPdf: no visible global function definition for 'bw.ucv'
DeconCPdf: no visible global function definition for 'bw.bcv'
DeconCPdf: no visible global function definition for 'bw.SJ'
DeconCPdf: no visible global function definition for 'density'
DeconCPdf: no visible global function definition for 'dnorm'
bw.dboot2 : suppL2: no visible global function definition for 'density'
bw.dboot2 : suppL2: no visible global function definition for 'rnorm'
bw.dboot2 : gaussL2: no visible global function definition for
  'density'
bw.dboot2 : gaussL2: no visible global function definition for 'rnorm'
bw.dmise: no visible global function definition for 'var'
plot.Decon: no visible global function definition for 'plot.default'
plot.Decon: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm plot.default
  rnorm var
Consider adding
  importFrom("graphics", "abline", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "rnorm", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DeducerExtras.Rcheck/00install.out' for details.
'library' or 'require' call to 'irr' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.make3dScatterPlotDialog: no visible global function definition for
  'install.packages'
.makePackageDataDialog: no visible global function definition for
  'data'
.makeVignetteDialog: no visible global function definition for
  'vignette'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible binding for global variable 'winMenuAddItem'
.onLoad: no visible binding for global variable 'jgr.addMenuItem'
.onLoad : gui.addSeperator: no visible global function definition for
  'jgr.addMenuSeparator'
applyModel: no visible global function definition for 'predict'
predict.kmeans : <anonymous>: no visible global function definition for
  'dist'
Undefined global functions or variables:
  data dist install.packages jgr.addMenuItem jgr.addMenuSeparator
  predict vignette winMenuAdd winMenuAddItem
Consider adding
  importFrom("stats", "dist", "predict")
  importFrom("utils", "data", "install.packages", "vignette",
             "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DeducerPlugInExample.Rcheck/00install.out' for details.
Package in Depends field not imported from: 'Deducer'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'Deducer' 'psych' 'GPArotation' 'mvnormtest' 'irr' 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to 'klaR' which was already attached by Depends.
  Please remove these calls from your code.
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/Deducer.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'JavaGD' 'Deducer' 'sp' 'maptools' 'OpenStreetMap' 'scales' 'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'UScensus2010'
A package should be listed in only one of these fields.
'library' or 'require' call to 'UScensus2010' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'JavaGD' 'OpenStreetMap' 'maptools' 'rgdal' 'scales' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DeducerSurvival.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'Deducer'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DeducerText.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
.makeQuickWordcloud: no visible global function definition for 'J'
.makeQuickWordcloud: no visible global function definition for 'new'
.makeQuickWordcloud: no visible global function definition for '.jnull'
.makeTextPlot: no visible global function definition for 'J'
.makeTextPlot: no visible global function definition for 'new'
.makeTextPlot: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.jnew'
.onLoad: no visible global function definition for 'J'
make.color.scale: no visible global function definition for 'rgb'
Undefined global functions or variables:
  .jnew .jnull .jpackage J new rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
binary.state: no visible global function definition for 'runif'
dbn.dnn.train: no visible global function definition for 'runif'
dropout.mask: no visible global function definition for 'runif'
nn.train: no visible global function definition for 'runif'
rbm.train: no visible global function definition for 'runif'
sae.dnn.train: no visible global function definition for 'runif'
show.digit: no visible global function definition for 'gray'
show.digit: no visible global function definition for 'image'
Undefined global functions or variables:
  gray image runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
DEEPR : perm_function: no visible global function definition for 'head'
DEEPR : perm_function: no visible global function definition for 'tail'
simCophy: no visible global function definition for 'rpois'
simCophy: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  head rmultinom rpois tail
Consider adding
  importFrom("stats", "rmultinom", "rpois")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
kern: no visible global function definition for 'var'
kern: no visible global function definition for 'dnorm'
pdeg: no visible global function definition for 'var'
pdeg: no visible global function definition for 'dnorm'
z.b: no visible binding for global variable 'var'
z.s: no visible binding for global variable 'var'
Undefined global functions or variables:
  dnorm var
Consider adding
  importFrom("stats", "dnorm", "var")
to your NAMESPACE file.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
bootbagg: no visible global function definition for 'runif'
bootworpl: no visible global function definition for 'runif'
des12: no visible global function definition for 'rnorm'
des12: no visible global function definition for 'runif'
eval.stage.gauss: no visible global function definition for 'var'
plotparti: no visible global function definition for 'plot'
plotparti: no visible global function definition for 'lines'
plotpartilev: no visible global function definition for 'plot'
plotpartilev: no visible global function definition for 'polygon'
plotpartilev: no visible global function definition for 'points'
simesi: no visible global function definition for 'runif'
simesi3d: no visible global function definition for 'runif'
simfssk: no visible global function definition for 'rnorm'
simfssk: no visible global function definition for 'runif'
simmix.delt: no visible global function definition for 'rnorm'
simmix.delt: no visible global function definition for 'runif'
simpp: no visible global function definition for 'rnorm'
simpp: no visible global function definition for 'runif'
simutree: no visible global function definition for 'runif'
stage.gaussR: no visible global function definition for 'var'
unidis: no visible global function definition for 'runif'
Undefined global functions or variables:
  lines plot points polygon rnorm runif var
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Bootstrapping.CI: no visible global function definition for 'quantile'
D.Jost: no visible global function definition for 'read.table'
D.Jost: no visible global function definition for 'write.table'
Dv.locis.corrected.calc: no visible global function definition for
  'p.adjust'
Gst.Nei: no visible global function definition for 'read.table'
Gst.Nei: no visible global function definition for 'write.table'
H.out: no visible global function definition for 'write.table'
Hardy.calc: no visible global function definition for 'chisq.test'
critical.ci.values: no visible global function definition for
  'quantile'
inputformat: no visible global function definition for 'read.table'
inputformat: no visible global function definition for 'write.table'
over.all.pops: no visible global function definition for 'write.table'
p.value.correcture: no visible global function definition for
  'p.adjust'
pair.pops: no visible global function definition for 'write.table'
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
DEMIPathway: no visible global function definition for 'dhyper'
DEMIPathway: no visible global function definition for 'p.adjust'
calcHypergeoExon: no visible global function definition for 'dhyper'
calcHypergeoProb: no visible global function definition for 'dhyper'
demi: no visible global function definition for 'write.table'
demi.t.test: no visible global function definition for 't.test'
demi.wilcox.test: no visible global function definition for
  'wilcox.test'
demi.wilcox.test.fast: no visible global function definition for
  'wilcox.test'
demiequal: no visible global function definition for 'wilcox.test'
wprob: no visible global function definition for 'combn'
diffexp,DEMIDiff: no visible global function definition for 'median'
diffexp,DEMIDiff: no visible global function definition for 'p.adjust'
loadAnnotation,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadBlat,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadCytoband,DEMIExperiment-environment: no visible global function
  definition for 'data'
loadPathway,DEMIExperiment-environment: no visible global function
  definition for 'data'
Undefined global functions or variables:
  combn data dhyper median p.adjust t.test wilcox.test write.table
Consider adding
  importFrom("stats", "dhyper", "median", "p.adjust", "t.test",
             "wilcox.test")
  importFrom("utils", "combn", "data", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/demu.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DendSer.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
DendSer: no visible global function definition for 'getFromNamespace'
crit2cost : <anonymous>: no visible global function definition for
  'as.dist'
dser.dist: no visible global function definition for 'hclust'
dser.matrix: no visible global function definition for 'dist'
plotAsColor: no visible global function definition for 'image'
plotAsColor: no visible global function definition for 'box'
plotAsColor: no visible global function definition for 'axis'
seriation_method_dist_dser: no visible global function definition for
  'hclust'
seriation_method_dist_dser: no visible global function definition for
  'modifyList'
seriation_method_leafsort: no visible global function definition for
  'modifyList'
Undefined global functions or variables:
  as.dist axis box dist getFromNamespace hclust image modifyList
Consider adding
  importFrom("graphics", "axis", "box", "image")
  importFrom("stats", "as.dist", "dist", "hclust")
  importFrom("utils", "getFromNamespace", "modifyList")
to your NAMESPACE file.
Package suggested but not available for checking: 'Rdonlp2'
Package suggested but not available for checking: 'Rdonlp2'
MBD: no visible global function definition for 'par'
MBD: no visible global function definition for 'gray'
MBD: no visible global function definition for 'matplot'
MBD: no visible global function definition for 'polygon'
MBD: no visible global function definition for 'lines'
MBD: no visible global function definition for 'legend'
MBD: no visible global function definition for 'matlines'
R.test: no visible global function definition for 'runif'
R.test: no visible global function definition for 'wilcox.test'
centralPlot: no visible global function definition for 'par'
centralPlot: no visible global function definition for
  'colorRampPalette'
centralPlot: no visible global function definition for 'matplot'
centralPlot: no visible global function definition for 'matlines'
centralPlot: no visible global function definition for 'legend'
scalecurve: no visible global function definition for 'plot'
scalecurve: no visible global function definition for 'lines'
scalecurve: no visible global function definition for 'legend'
tmean: no visible global function definition for 'matplot'
tmean: no visible global function definition for 'matlines'
tmean: no visible global function definition for 'lines'
tmean: no visible global function definition for 'legend'
tmean: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette gray legend lines matlines matplot par plot polygon
  runif wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "legend", "lines", "matlines", "matplot", "par",
             "plot", "polygon")
  importFrom("stats", "runif", "wilcox.test")
to your NAMESPACE file.
Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.6Mb
    help   1.4Mb
    libs   1.7Mb
ds: no visible global function definition for 'is.ts'
ds: no visible global function definition for 'frequency'
getds: no visible global function definition for 'resid'
getds: no visible global function definition for 'lm.fit'
getds: no visible global function definition for 'sd'
getds: no visible global function definition for 'var'
getds: no visible global function definition for 'fitted'
Undefined global functions or variables:
  fitted frequency is.ts lm.fit resid sd var
Consider adding
  importFrom("stats", "fitted", "frequency", "is.ts", "lm.fit", "resid",
             "sd", "var")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
arrayUpdate : pairUpdate: no visible global function definition for
  'runif'
conditionUpdate: no visible global function definition for 'runif'
designGG: no visible global function definition for 'runif'
experimentDesignTable: no visible global function definition for
  'write.csv'
plotAllScores: no visible global function definition for 'png'
plotAllScores: no visible global function definition for 'par'
plotAllScores: no visible global function definition for 'plot'
plotAllScores: no visible global function definition for 'text'
plotAllScores: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off par plot png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  'gurobi' 'Rcplex' 'Rmosek'
Malformed Description field: should contain one or more complete sentences.
fs.agreement.part: no visible global function definition for 'as.dist'
fs.agreement.part: no visible global function definition for 'cor'
fs.leave.k.out.combn: no visible global function definition for 'sd'
fs.leave.k.out.sample: no visible global function definition for 'sd'
fs.rd: no visible global function definition for 'pchisq'
fs.selection: no visible global function definition for 'p.adjust'
plot.FIT: no visible global function definition for 'qchisq'
plot.FIT: no visible global function definition for 'ppoints'
plot.FIT: no visible global function definition for 'plot'
plot.FIT: no visible global function definition for 'points'
plot.FIT: no visible global function definition for 'abline'
plotJn: no visible global function definition for 'plot'
plotJn: no visible global function definition for 'points'
robust.distance.signed: no visible global function definition for
  'mahalanobis'
snowball: no visible global function definition for 'is'
snowball: no visible global function definition for 'median'
weight.sd: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq plot points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package in Depends field not imported from: 'dplR'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.get' 'InteractiveDetrending' 'RemoveTrend'
GNU make is a SystemRequirements.
Package in Depends field not imported from: 'ash'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'dexter:::get_resp_data' 'dexter:::qcolors'
  See the note in ?`:::` about the use of this operator.
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for 'rbinom'
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for 'rnorm'
simulate_dataframe : generate_initial: no visible global function
  definition for 'rbinom'
simulate_dataframe: no visible binding for global variable 'randu'
simulate_dataframe: no visible global function definition for 'rbinom'
simulate_dataframe: no visible global function definition for 'rnorm'
simulate_dataframe: no visible global function definition for 'rpois'
simulate_dataframe : add_NAs: no visible global function definition for
  'rbinom'
Undefined global functions or variables:
  randu rbinom rnorm rpois
Consider adding
  importFrom("datasets", "randu")
  importFrom("stats", "rbinom", "rnorm", "rpois")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
makeAdjMatrix: no visible global function definition for 'combn'
plotPosteriorN: no visible global function definition for 'plot'
plotPosteriorN: no visible global function definition for 'title'
plotPosteriorN: no visible global function definition for 'lines'
plotPosteriorN: no visible global function definition for 'legend'
venn3: no visible global function definition for 'plot'
venn3: no visible global function definition for 'runif'
venn3: no visible global function definition for 'points'
venn3: no visible global function definition for 'lines'
venn3: no visible global function definition for 'text'
venn4: no visible global function definition for 'plot'
venn4: no visible global function definition for 'lines'
venn4: no visible global function definition for 'runif'
venn4: no visible global function definition for 'points'
Undefined global functions or variables:
  combn legend lines plot points runif text title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text",
             "title")
  importFrom("stats", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: 'doMC'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
Running examples in 'dgmb-Ex.R' failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "table".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
cvm.test : cvm.pval.disc: no visible global function definition for
  'integrate'
cvm.test : cvm.pval.disc: no visible global function definition for
  'dchisq'
cvm.test : cvm.pval.disc: no visible global function definition for
  'nlm'
cvm.test : cvm.stat.disc: no visible global function definition for
  'knots'
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  'knots'
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  'runif'
cvm.test: no visible global function definition for 'is.stepfun'
cvm.test: no visible global function definition for 'knots'
ks.test : exact.pval : ts.pval: no visible global function definition
  for 'ecdf'
ks.test : sim.pval: no visible global function definition for 'runif'
ks.test : sim.pval : getks: no visible global function definition for
  'ecdf'
ks.test: no visible global function definition for 'is.stepfun'
ks.test: no visible global function definition for 'knots'
ks.test: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  dchisq ecdf integrate is.stepfun knots nlm runif
Consider adding
  importFrom("stats", "dchisq", "ecdf", "integrate", "is.stepfun",
             "knots", "nlm", "runif")
to your NAMESPACE file.
dichromat: no visible global function definition for 'col2rgb'
dichromat: no visible global function definition for 'predict'
dichromat: no visible global function definition for 'rgb'
Undefined global functions or variables:
  col2rgb predict rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("stats", "predict")
to your NAMESPACE file.
le.pesquisa: no visible global function definition for 'txtProgressBar'
le.pesquisa: no visible global function definition for 'type.convert'
le.pesquisa: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar type.convert
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "type.convert")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
L2eV: no visible binding for global variable 'constants'
L2w: no visible binding for global variable 'constants'
dielectric: no visible global function definition for 'new'
dielectric2plot: no visible global function definition for 'reshape'
eV2L: no visible binding for global variable 'constants'
t2eV: no visible binding for global variable 'constants'
Undefined global functions or variables:
  constants new reshape
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "reshape")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  'PropCIs' 'gee' 'rootSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
diffpci: no visible global function definition for 'diffpropci.Wald.mp'
diffpci: no visible global function definition for 'diffpropci.mp'
diffpci: no visible global function definition for 'scoreci.mp'
exact.cond : exactci: no visible global function definition for 'qf'
exact.midp : binom.midp : f.low: no visible global function definition
  for 'dbinom'
exact.midp : binom.midp : f.low: no visible global function definition
  for 'pbinom'
exact.midp : binom.midp : f.up: no visible global function definition
  for 'dbinom'
exact.midp : binom.midp : f.up: no visible global function definition
  for 'pbinom'
exact.midp : binom.midp : one.ci: no visible global function definition
  for 'uniroot'
np.nv: no visible global function definition for 'qnorm'
np.t: no visible global function definition for 'qt'
uncond: no visible global function definition for 'qnorm'
wald.cc: no visible global function definition for 'qnorm'
wilson: no visible global function definition for 'qnorm'
wilson: no visible global function definition for 'uniroot.all'
wilson.cc: no visible global function definition for 'qnorm'
wilson.cc: no visible global function definition for 'uniroot.all'
wilson.phi: no visible global function definition for 'qnorm'
wilson.phi: no visible global function definition for 'uniroot.all'
Undefined global functions or variables:
  dbinom diffpropci.Wald.mp diffpropci.mp pbinom qf qnorm qt scoreci.mp
  uniroot uniroot.all
Consider adding
  importFrom("stats", "dbinom", "pbinom", "qf", "qnorm", "qt", "uniroot")
to your NAMESPACE file.
rkMethodPlot: no visible global function definition for 'par'
rkMethodPlot: no visible global function definition for 'axis'
rkMethodPlot: no visible global function definition for 'points'
rkMethodPlot: no visible global function definition for 'text'
rkMethodPlot: no visible global function definition for 'segments'
rkimp: no visible global function definition for 'runif'
stability.bruteforce: no visible global function definition for 'plot'
stability.bruteforce: no visible global function definition for
  'points'
stability.bruteforce: no visible global function definition for
  'abline'
stability.multistep: no visible global function definition for 'plot'
stability.multistep: no visible global function definition for 'lines'
stability.multistep: no visible global function definition for
  'polygon'
stability.multistep: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis lines par plot points polygon runif segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "polygon", "segments", "text")
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
'library' or 'require' calls to packages already attached by Depends:
  'maptools' 'spatstat' 'spdep'
  Please remove these calls from your code.
fAssocmatrix : fAssocmatrix1: no visible global function definition for
  'coordinates<-'
fAssocplot: no visible global function definition for 'plot'
fAssocplot: no visible global function definition for 'coordinates'
fAssocplot: no visible global function definition for 'text'
fAssocplot: no visible global function definition for 'box'
fDrawfigure: no visible global function definition for 'slot'
fDrawfigure : <anonymous>: no visible global function definition for
  'slot'
fDrawfigure: no visible global function definition for
  'SpatialPolygons'
fDrawfigure: no visible global function definition for 'spsample'
fDrawfigure: no visible global function definition for 'plot'
fDrawfigure: no visible global function definition for 'image'
fDrawfigure: no visible global function definition for
  'colorRampPalette'
fDrawfigure: no visible global function definition for 'points'
fRanXY : <anonymous>: no visible global function definition for 'slot'
fRanXY : <anonymous>: no visible global function definition for
  'spsample'
Undefined global functions or variables:
  SpatialPolygons box colorRampPalette coordinates coordinates<- image
  plot points slot spsample text
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "box", "image", "plot", "points", "text")
  importFrom("methods", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'Rcpp' 'igraph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aLine: no visible global function definition for 'lines'
aLine: no visible global function definition for 'ecdf'
dip.test: no visible global function definition for 'complete.cases'
dip.test: no visible global function definition for 'runif'
dip.test: no visible global function definition for 'approx'
plot.dip: no visible global function definition for 'par'
plot.dip: no visible global function definition for 'ecdf'
plot.dip: no visible global function definition for 'plot'
plot.dip: no visible global function definition for 'title'
plot.dip: no visible global function definition for 'abline'
plot.dip: no visible global function definition for 'axis'
plot.dip: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline approx axis complete.cases ecdf legend lines par plot runif
  title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "approx", "complete.cases", "ecdf", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
nullTest: no visible global function definition for 'rmultinom'
rdirichlet: no visible global function definition for 'rgamma'
simPop: no visible global function definition for 'rnorm'
simPop: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  rgamma rmultinom rnorm
Consider adding
  importFrom("stats", "rgamma", "rmultinom", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
rdisclap: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
p.discrete.adjust : <anonymous>: no visible global function definition
  for 'stepfun'
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
value: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'RUnit' 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mix.distlist.facing.gamma : <anonymous>: no visible global function
  definition for 'dgamma'
mix.distlist.norm: no visible binding for global variable 'dnorm'
mix.mle: no visible global function definition for 'sd'
mix.mle: no visible global function definition for 'quantile'
mix.mle: no visible global function definition for 'median'
mix.mle: no visible global function definition for 'optim'
mix.synthetic.facing.gamma: no visible global function definition for
  'runif'
mix.synthetic.facing.gamma: no visible global function definition for
  'rgamma'
mix.synthetic.normal: no visible global function definition for 'runif'
mix.synthetic.normal: no visible global function definition for 'rnorm'
plot.discrimARTs: no visible global function definition for 'hist'
plot.discrimARTs: no visible global function definition for 'points'
plot.discrimARTs: no visible global function definition for 'lines'
plot.discrimARTs: no visible global function definition for 'grid.text'
plot.discrimARTs: no visible global function definition for 'gpar'
Undefined global functions or variables:
  dgamma dnorm gpar grid.text hist lines median optim points quantile
  rgamma rnorm runif sd
Consider adding
  importFrom("graphics", "hist", "lines", "points")
  importFrom("stats", "dgamma", "dnorm", "median", "optim", "quantile",
             "rgamma", "rnorm", "runif", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
densest: no visible global function definition for 'weighted.mean'
diss: no visible global function definition for 'cov'
neighbors: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov weighted.mean
Consider adding
  importFrom("stats", "cov", "weighted.mean")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'car' 'prettyGraphs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Chi2DistanceFromSort: no visible global function definition for
  'model.matrix'
GraphDistatisAll: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'dataEllipse'
GraphDistatisBoot: no visible global function definition for
  'peeledHull'
GraphDistatisCompromise: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisCompromise: no visible global function definition for
  'prettyPlot'
GraphDistatisPartial: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisPartial: no visible global function definition for
  'points'
GraphDistatisPartial: no visible global function definition for
  'prettyPlot'
GraphDistatisRv: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisRv: no visible global function definition for 'prettyPlot'
Undefined global functions or variables:
  createColorVectorsByDesign dataEllipse model.matrix peeledHull points
  prettyPlot
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "model.matrix")
to your NAMESPACE file.
dist.multiPhylo: no visible global function definition for 'as.dist'
gromov.hyperbolicity: no visible global function definition for
  'as.dist'
mcmc.target.seq: no visible global function definition for 'runif'
phylo.diff: no visible global function definition for 'par'
phylo.diff: no visible global function definition for 'plot'
Undefined global functions or variables:
  as.dist par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.dist", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'RUnit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Title field: should not end in a period.
prepare_Rd: extract.val.Rd:25-26: Dropping empty section \note
prepare_Rd: extract.val.Rd:27: Dropping empty section \seealso
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/diveRsity.Rcheck/00install.out' for details.
'library' or 'require' call to 'glmnet' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'glmnet' 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.3Mb
Package suggested but not available for checking: 'asreml'
'library' or 'require' calls to packages already attached by Depends:
  'nlme' 'wgaim'
  Please remove these calls from your code.
'library' or 'require' call to 'asreml' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'ibdreg' 'mgcv' 'nlme' 'qtl' 'wgaim'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'qtl:::adjust.rf.ri'
  See the note in ?`:::` about the use of this operator.
Foreign function call to a different package:
  .C(cfunc, ..., PACKAGE = "qtl")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   2.1Mb
    libs   2.0Mb
Package suggested but not available for checking: 'rPython'
Warning: no function found corresponding to methods exports from 'DMwR' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  'grid' 'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing object imported by a ':::' call: 'rpart:::rpconvert'
Unexported objects imported by ':::' calls:
  'rpart:::rpart.branch' 'rpart:::rpartco'
  'rpart:::string.bounding.box'
  See the note in ?`:::` about the use of this operator.
'library' or 'require' call to 'igraph' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
network.modules: no visible global function definition for
  'graph.empty'
network.modules: no visible global function definition for
  'add.vertices'
network.modules: no visible global function definition for 'add.edges'
network.modules: no visible global function definition for 'tkplot'
network.modules: no visible global function definition for 'V'
Undefined global functions or variables:
  V add.edges add.vertices graph.empty tkplot
DNMF: no visible global function definition for 'runif'
NMFpval: no visible global function definition for 'p.adjust'
ndNMF: no visible global function definition for 'runif'
rnk: no visible global function definition for 'write.table'
Undefined global functions or variables:
  p.adjust runif write.table
Consider adding
  importFrom("stats", "p.adjust", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
ppert: no visible global function definition for 'pbeta'
prepare8pkg: no visible global function definition for 'glob2rx'
qpert: no visible global function definition for 'qbeta'
rpert: no visible global function definition for 'rbeta'
Undefined global functions or variables:
  glob2rx pbeta qbeta rbeta
Consider adding
  importFrom("stats", "pbeta", "qbeta", "rbeta")
  importFrom("utils", "glob2rx")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.2Mb
GNU make is a SystemRequirements.
Packages which this enhances but not available for checking:
  'gurobi' 'Rmosek'
Malformed Description field: should contain one or more complete sentences.
.info: no visible global function definition for 'packageDescription'
redisWorker: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console packageDescription
Consider adding
  importFrom("utils", "flush.console", "packageDescription")
to your NAMESPACE file.
dostats: no visible binding for global variable 'na.fail'
first: no visible global function definition for 'head'
last: no visible global function definition for 'tail'
pval.default: no visible global function definition for '.hasSlot'
pval.lm: no visible global function definition for 'anova'
Undefined global functions or variables:
  .hasSlot anova head na.fail tail
Consider adding
  importFrom("methods", ".hasSlot")
  importFrom("stats", "anova", "na.fail")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.3Mb
File 'DPpackage/libs/i386/DPpackage.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
File 'DPpackage/libs/x64/DPpackage.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'

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.
The following files look like leftovers:
  'drawExpression/visualRefCard/svn-commit.tmp'
Please remove them from your package.
.drawTree: no visible global function definition for 'pdf'
.drawTree: no visible global function definition for 'dev.off'
drawExpression: no visible global function definition for 'plot.new'
Undefined global functions or variables:
  dev.off pdf plot.new
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "plot.new")
to your NAMESPACE file.
DRaWR: no visible global function definition for 'write.table'
DRaWR: no visible global function definition for 'read.table'
DRaWR: no visible global function definition for 'aggregate'
DRaWR: no visible global function definition for 'slot'
Undefined global functions or variables:
  aggregate read.table slot write.table
Consider adding
  importFrom("methods", "slot")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cdfDRM: no visible global function definition for 'tail'
densityDRM: no visible binding for global variable 'density'
drmdel: no visible binding for global variable 'optim'
drmdel: no visible global function definition for 'pchisq'
quantEst: no visible global function definition for 'tail'
quantileCompWald: no visible global function definition for 'pchisq'
quantileCompWald: no visible global function definition for 'p.adjust'
quantileDRM: no visible global function definition for 'tail'
quantileDRM: no visible global function definition for 'density'
Undefined global functions or variables:
  density optim p.adjust pchisq tail
Consider adding
  importFrom("stats", "density", "optim", "p.adjust", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
compute_xsq: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  chisq.test
Consider adding
  importFrom("stats", "chisq.test")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    media       2.2Mb
    shinyapps   2.6Mb
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
DSBayes: no visible global function definition for 'qnorm'
DSBayes: no visible global function definition for 'coef'
DSBayes: no visible global function definition for 'vcov'
DSBayes : MLE: no visible global function definition for 'qnorm'
DSBayes: no visible global function definition for 'integrate'
DSBayes : qfunc.numer : <anonymous>: no visible global function
  definition for 'dnorm'
DSBayes : ds.numer: no visible global function definition for
  'integrate'
DSBayes : lower: no visible global function definition for 'qlogis'
DSBayes : lower: no visible global function definition for 'integrate'
DSBayes : upper: no visible global function definition for 'qlogis'
DSBayes : upper: no visible global function definition for 'integrate'
DSBayes: no visible global function definition for 'optimize'
DSBayes: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  coef dnorm integrate optimize qlogis qnorm uniroot vcov
Consider adding
  importFrom("stats", "coef", "dnorm", "integrate", "optimize", "qlogis",
             "qnorm", "uniroot", "vcov")
to your NAMESPACE file.
AIC.dspat: no visible global function definition for 'coef'
LTDataFrame: no visible global function definition for 'as.formula'
coef.dspat: no visible global function definition for 'coef'
integrate.intensity: no visible global function definition for 'coef'
integrate.intensity: no visible global function definition for
  'predict'
integrate.intensity: no visible global function definition for
  'model.matrix'
integrate.intensity: no visible global function definition for 'vcov'
integrate.intensity: no visible global function definition for 'fitted'
lgcp.correction: no visible global function definition for 'predict'
lgcp.correction: no visible global function definition for
  'model.matrix'
lgcp.correction: no visible global function definition for 'fitted'
lgcp.correction: no visible global function definition for 'var'
lines_to_strips : line_to_strip: no visible global function definition
  for 'as'
owin.gpc.poly: no visible global function definition for 'as'
sample.points : sample.points.from.line: no visible global function
  definition for 'runif'
sample.points: no visible global function definition for 'model.matrix'
simCovariates: no visible global function definition for 'quantile'
simPts: no visible global function definition for 'model.matrix'
transect.intensity: no visible global function definition for 'predict'
transect.intensity: no visible global function definition for 'hist'
Undefined global functions or variables:
  as as.formula coef fitted hist model.matrix predict quantile runif
  var vcov
Consider adding
  importFrom("graphics", "hist")
  importFrom("methods", "as")
  importFrom("stats", "as.formula", "coef", "fitted", "model.matrix",
             "predict", "quantile", "runif", "var", "vcov")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
X: no visible global function definition for 'read.table'
dplot: no visible global function definition for 'matplot'
dplot: no visible global function definition for 'legend'
dscor : <anonymous>: no visible global function definition for 'combn'
dscor : <anonymous> : <anonymous>: no visible global function
  definition for 'cor.test'
gds: no visible binding for global variable 'na.omit'
gds : medi: no visible global function definition for 'median'
gds : quant: no visible global function definition for 'quantile'
gds: no visible binding for global variable 'shapiro.test'
tables: no visible binding for global variable 'chisq.test'
tables: no visible binding for global variable 'fisher.test'
Undefined global functions or variables:
  chisq.test combn cor.test fisher.test legend matplot median na.omit
  quantile read.table shapiro.test
Consider adding
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "chisq.test", "cor.test", "fisher.test", "median",
             "na.omit", "quantile", "shapiro.test")
  importFrom("utils", "combn", "read.table")
to your NAMESPACE file.
NeedsCompilation field should likely be 'yes'
DStree: no visible global function definition for 'model.frame'
DStree: no visible global function definition for 'model.matrix'
DStree: no visible global function definition for 'model.response'
DStree: no visible global function definition for 'as.formula'
bag: no visible global function definition for 'model.frame'
bag: no visible global function definition for 'model.response'
plot.DStree: no visible global function definition for 'par'
plot.DStree: no visible global function definition for 'plot'
plot.DStree: no visible global function definition for 'rainbow'
plot.DStree: no visible global function definition for 'lines'
plot.DStree: no visible global function definition for 'legend'
predict.DStree: no visible global function definition for 'predict'
print.DStree: no visible global function definition for 'naprint'
prune.DStree: no visible global function definition for 'median'
prune.DStree: no visible global function definition for 'predict'
prune.DStree: no visible binding for global variable 'var'
summ.MAE: no visible global function definition for 'predict'
summary.DStree: no visible global function definition for 'naprint'
Undefined global functions or variables:
  as.formula legend lines median model.frame model.matrix
  model.response naprint par plot predict rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("stats", "as.formula", "median", "model.frame",
             "model.matrix", "model.response", "naprint", "predict",
             "var")
to your NAMESPACE file.
DCEA: no visible global function definition for 'p.adjust'
DS: no visible global function definition for 'p.adjust'
DS: no visible global function definition for 'pdf'
DS: no visible global function definition for 'plot'
DS: no visible global function definition for 'dev.off'
LFC: no visible global function definition for 'glm'
LFC: no visible global function definition for 'predict'
PartialCor: no visible global function definition for 'na.omit'
comDCGLplot: no visible global function definition for 'pdf'
comDCGLplot: no visible global function definition for 'plot'
comDCGLplot: no visible global function definition for 'dev.off'
percentLinkfilter: no visible global function definition for 'cor'
qLinkfilter: no visible global function definition for 'cor'
qLinkfilter: no visible global function definition for 'pt'
qLinkfilter: no visible global function definition for 'p.adjust'
rLinkfilter: no visible global function definition for 'cor'
varianceBasedfilter: no visible binding for global variable 'var'
varianceBasedfilter: no visible global function definition for 'median'
varianceBasedfilter: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor dev.off glm median na.omit p.adjust pchisq pdf plot predict pt
  var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "glm", "median", "na.omit", "p.adjust",
             "pchisq", "predict", "pt", "var")
to your NAMESPACE file.
DLR: no visible global function definition for 'formula'
DLR: no visible global function definition for 'terms'
DLR: no visible global function definition for 'model.matrix'
DLR: no visible global function definition for 'as.formula'
DLR: no visible binding for global variable 'binomial'
DLR: no visible global function definition for 'coef'
DLR: no visible global function definition for 'pnorm'
DLR: no visible global function definition for 'qnorm'
acc.1test: no visible global function definition for 'qnorm'
pv.gs: no visible global function definition for 'pchisq'
pv.rpv: no visible global function definition for 'qnorm'
pv.rpv: no visible global function definition for 'pnorm'
pv.wgs: no visible global function definition for 'pchisq'
sesp.diff.ci: no visible global function definition for 'qnorm'
sesp.mcnemar: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  as.formula binomial coef formula model.matrix pchisq pnorm qnorm
  terms
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "formula",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
efron.petrosian: no visible global function definition for 'dev.new'
efron.petrosian: no visible global function definition for 'par'
efron.petrosian: no visible global function definition for 'plot'
efron.petrosian: no visible global function definition for 'segments'
lynden: no visible global function definition for 'dev.new'
lynden: no visible global function definition for 'par'
lynden: no visible global function definition for 'plot'
lynden: no visible global function definition for 'segments'
shen: no visible global function definition for 'image'
shen: no visible global function definition for 'runif'
shen: no visible global function definition for 'filled.contour'
shen: no visible binding for global variable 'rainbow'
shen: no visible binding for global variable 'topo.colors'
shen: no visible global function definition for 'topo.colors'
shen: no visible global function definition for 'persp'
shen: no visible global function definition for 'dev.new'
shen: no visible global function definition for 'par'
shen: no visible global function definition for 'plot'
shen: no visible global function definition for 'segments'
Undefined global functions or variables:
  dev.new filled.contour image par persp plot rainbow runif segments
  topo.colors
Consider adding
  importFrom("grDevices", "dev.new", "rainbow", "topo.colors")
  importFrom("graphics", "filled.contour", "image", "par", "persp",
             "plot", "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
DTK.plot: no visible global function definition for 'plot'
DTK.plot: no visible global function definition for 'axis'
DTK.plot: no visible global function definition for 'title'
DTK.plot: no visible global function definition for 'lines'
DTK.plot: no visible global function definition for 'points'
DTK.test: no visible binding for global variable 'sd'
DTK.test: no visible global function definition for 'qtukey'
TK.test: no visible global function definition for 'TukeyHSD'
TK.test: no visible global function definition for 'aov'
Undefined global functions or variables:
  TukeyHSD aov axis lines plot points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "plot", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
DTMC: no visible global function definition for 'runif'
DTMC: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.1Mb
GNU make is a SystemRequirements.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
dummy: no visible global function definition for 'model.matrix'
dummy: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  model.frame model.matrix
Consider adding
  importFrom("stats", "model.frame", "model.matrix")
to your NAMESPACE file.
cvSDDT: no visible global function definition for 'qt'
cvSDDT : Cj_SD.fun: no visible global function definition for 'combn'
cvSDDT: no visible global function definition for 'uniroot'
cvSUDT: no visible global function definition for 'rnorm'
cvSUDT: no visible global function definition for 'rchisq'
cvSUDT : psi.fun: no visible global function definition for 'pnorm'
cvSUDT: no visible global function definition for 'qt'
cvSUDT: no visible global function definition for 'uniroot'
cvSUDT: no visible global function definition for 'combn'
nvDT : samplesize: no visible global function definition for 'rnorm'
nvDT : samplesize: no visible global function definition for 'rchisq'
nvDT : samplesize: no visible global function definition for 'pnorm'
nvDT : ssBonf: no visible global function definition for 'qnorm'
nvDT : ssBonf: no visible global function definition for 'qt'
nvDT : ssBonf: no visible global function definition for 'rnorm'
nvDT : ssBonf: no visible global function definition for 'rchisq'
nvDT : ssBonf: no visible global function definition for 'pnorm'
nvDT: no visible global function definition for 'uniroot'
powDT: no visible global function definition for 'rnorm'
powDT: no visible global function definition for 'rchisq'
powDT: no visible global function definition for 'pnorm'
qvSDDT: no visible global function definition for 'pt'
qvSUDT: no visible global function definition for 'rnorm'
qvSUDT: no visible global function definition for 'rchisq'
qvSUDT : psi.fun: no visible global function definition for 'pnorm'
qvSUDT: no visible global function definition for 'pt'
qvSUDT : Pj.fun: no visible global function definition for 'qt'
qvSUDT : Pj.fun: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  combn pnorm pt qnorm qt rchisq rnorm uniroot
Consider adding
  importFrom("stats", "pnorm", "pt", "qnorm", "qt", "rchisq", "rnorm",
             "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
Clough: no visible global function definition for 'dgamma'
computePosterior,Counts: no visible global function definition for
  'dnbinom'
getPosteriorParam,Counts: no visible global function definition for
  'qgamma'
getPosteriorParam,Counts: no visible global function definition for
  'dgamma'
getPosteriorParam,Counts: no visible global function definition for
  'pgamma'
plotPosterior,Counts: no visible global function definition for 'axis'
plotPosterior,Counts: no visible global function definition for
  'abline'
plotPosterior,Counts: no visible global function definition for 'lines'
plotPosterior,Counts: no visible global function definition for 'rect'
plotPosterior,Counts: no visible global function definition for 'curve'
plotPosterior,Counts: no visible global function definition for
  'dgamma'
plotPosterior,Counts: no visible global function definition for
  'legend'
show,Counts: no visible global function definition for 'head'
show,Counts: no visible global function definition for 'tail'
Undefined global functions or variables:
  abline axis curve dgamma dnbinom head legend lines pgamma qgamma rect
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "curve", "legend", "lines",
             "rect")
  importFrom("stats", "dgamma", "dnbinom", "pgamma", "qgamma")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  'ggm' 'tcltk'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'ggm' 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.3Mb
    libs   4.3Mb
MultiTestH0 : MultiTestOneColumn: no visible global function definition
  for 'pchisq'
RunClustering : CheckClusterNew: no visible global function definition
  for 'qchisq'
RunClustering: no visible global function definition for 'qchisq'
RunDenoising: no visible binding for global variable 'var'
RunDenoising: no visible global function definition for 'qchisq'
RunDenoising: no visible binding for global variable 'median'
RunDenoising: no visible global function definition for 'var'
RunDenoising : buildEstimate: no visible global function definition for
  'qchisq'
Undefined global functions or variables:
  median pchisq qchisq var
Consider adding
  importFrom("stats", "median", "pchisq", "qchisq", "var")
to your NAMESPACE file.
GetIntMod: no visible global function definition for 'arima'
GetLikeDI: no visible global function definition for 'arima'
GetLikeDI: no visible global function definition for 'logLik'
GetPV: no visible global function definition for 'optimize'
GetPV: no visible global function definition for 'pchisq'
fitdi: no visible global function definition for 'optimize'
Undefined global functions or variables:
  arima logLik optimize pchisq
Consider adding
  importFrom("stats", "arima", "logLik", "optimize", "pchisq")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(earthtones)
  > 
  > test_check("earthtones")
  -- 1. Error: returns normal (@test-earth.R#5)  ---------------------------------
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=50.759,-125.673&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false'
  1: expect_is(get_earthtones(), "palette") at testthat/test-earth.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: get_earthtones()
  5: ggmap::get_map(location = c(longitude, latitude), maptype = "satellite", zoom = zoom, 
         ...)
  6: get_googlemap(center = location, zoom = zoom, maptype = maptype, scale = scale, messaging = messaging, 
         urlonly = urlonly, force = force, filename = filename, color = color, language = language)
  7: download.file(url, destfile = tmp, quiet = !messaging, mode = "wb")
  
  == testthat results  ===========================================================
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: returns normal (@test-earth.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 26-28 (earthtones.rmd) 
Error: processing vignette 'earthtones.rmd' failed with diagnostics:
cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=36.094994,-111.837962&zoom=12&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false'
Execution halted
Packages in Depends field not imported from:
  'base64enc' 'knitr' 'markdown'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.file_attachment: no visible global function definition for
  'base64encode'
.plot_attachment: no visible global function definition for 'dev.off'
.update_list: no visible global function definition for 'modifyList'
easyHtmlReport: no visible global function definition for 'knit'
easyHtmlReport: no visible global function definition for
  'markdownToHTML'
mime_part.data.frame: no visible global function definition for
  'write.table'
mime_part.ggplot: no visible binding for global variable 'pdf'
mime_part.matrix: no visible global function definition for
  'write.table'
mime_part.trellis: no visible binding for global variable 'pdf'
simpleHtmlReport : <anonymous>: no visible global function definition
  for 'write.table'
Undefined global functions or variables:
  base64encode dev.off knit markdownToHTML modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
MARK.MCMC : Model.Creator: no visible global function definition for
  'combn'
MARK.MCMC : formula.Maker: no visible global function definition for
  'combn'
Simulate.CH: no visible global function definition for 'rnorm'
Simulate.CH: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  combn rbinom rnorm
Consider adding
  importFrom("stats", "rbinom", "rnorm")
  importFrom("utils", "combn")
to your NAMESPACE file.
eb: no visible global function definition for 'optimize'
ebalance: no visible global function definition for 'var'
Undefined global functions or variables:
  optimize var
Consider adding
  importFrom("stats", "optimize", "var")
to your NAMESPACE file.
ebSNP: no visible global function definition for 'optim'
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
ecipex: no visible binding for global variable 'nistiso'
ecipex : <anonymous>: no visible global function definition for 'nextn'
ecipex : <anonymous>: no visible global function definition for 'fft'
ecipex : <anonymous> : <anonymous>: no visible global function
  definition for 'fft'
Undefined global functions or variables:
  fft nextn nistiso
Consider adding
  importFrom("stats", "fft", "nextn")
to your NAMESPACE file.
Running examples in 'EcoHydRology-Ex.R' failed
The error most likely occurred in:

> ### Name: get_usgs_gage
> ### Title: A function to grab daily stream flow measurements from the USGS
> ###   waterdata.usgs.gov server.
> ### Aliases: get_usgs_gage
> 
> ### ** Examples
> 
> 
> flowgage_id="04216500"
> flowgage=get_usgs_gage(flowgage_id)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: get_usgs_gage -> readLines -> file
Execution halted
dilution: no visible global function definition for 'grey'
dilution: no visible global function definition for 'lines'
dilution: no visible global function definition for 'rect'
dilution: no visible global function definition for 'segments'
dilution: no visible global function definition for 'text'
dilution: no visible global function definition for 'arrows'
pricefit: no visible global function definition for 'runif'
Undefined global functions or variables:
  arrows grey lines rect runif segments text
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "arrows", "lines", "rect", "segments", "text")
  importFrom("stats", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: 'spc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
UCexactTest: no visible global function definition for 'is'
UCexactTest: no visible global function definition for 'new'
pvalue: no visible global function definition for 'dnbinom'
pvalue: no visible global function definition for 'pnbinom'
sup.mu: no visible global function definition for 'predict'
Undefined global functions or variables:
  dnbinom is new pnbinom predict
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "dnbinom", "pnbinom", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.2Mb
geteegdata: no visible global function definition for 'untar'
geteegdata: no visible global function definition for 'read.table'
geteegdata: no visible global function definition for 'write.csv'
geteegdata: no visible global function definition for 'write.table'
Undefined global functions or variables:
  read.table untar write.csv write.table
Consider adding
  importFrom("utils", "read.table", "untar", "write.csv", "write.table")
to your NAMESPACE file.
.gdf : find_loss: no visible global function definition for 'rnorm'
.p.values : <anonymous>: no visible global function definition for
  'pnorm'
.relist.dwt: no visible global function definition for 'relist'
.relist.dwt: no visible global function definition for 'as'
.std.wav.coeff : <anonymous>: no visible global function definition for
  'mad'
regrid: no visible global function definition for 'predict'
regrid: no visible global function definition for 'var'
regrid: no visible global function definition for 'medpolish'
Undefined global functions or variables:
  as mad medpolish pnorm predict relist rnorm var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "mad", "medpolish", "pnorm", "predict", "rnorm",
             "var")
  importFrom("utils", "relist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Title field: should not end in a period.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/EFS.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'eggCountsExtra'
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'sna' which was already attached by Depends.
  Please remove these calls from your code.
read.egonet: 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.
prepare_Rd: index.egonet.Rd:29-31: Dropping empty section \details
prepare_Rd: index.egonet.Rd:32-38: Dropping empty section \value
prepare_Rd: index.egonet.Rd:45-47: Dropping empty section \note
prepare_Rd: index.egonet.Rd:39-41: Dropping empty section \references
prepare_Rd: index.egonet.Rd:51-53: Dropping empty section \seealso
prepare_Rd: read.egonet.Rd:27-29: Dropping empty section \note
eiginv: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
boot_pr_comp: no visible global function definition for 'cov'
boot_pr_comp: no visible global function definition for 'quantile'
boot_pr_comp: no visible global function definition for 'segments'
boot_pr_comp: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cov quantile segments
Consider adding
  importFrom("graphics", "abline", "segments")
  importFrom("stats", "cov", "quantile")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'class' 'quantreg'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cluster.segment: no visible global function definition for 'kmeans'
cluster.segment: no visible global function definition for 'knn'
comp.anc.dist: no visible global function definition for 'wilcox.test'
eila: no visible global function definition for 'hasArg'
get.prob.score: no visible global function definition for 'glm'
get.prob.score: no visible global function definition for 'binomial'
get.prob.score: no visible binding for global variable 'logit'
get.prob.score: no visible global function definition for 'predict'
quantreg.est: no visible global function definition for 'rnorm'
quantreg.est: no visible global function definition for 'rq.fit.fnb'
Undefined global functions or variables:
  binomial glm hasArg kmeans knn logit predict rnorm rq.fit.fnb
  wilcox.test
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "binomial", "glm", "kmeans", "predict", "rnorm",
             "wilcox.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Packages in Depends field not imported from:
  'MASS' 'coda' 'msm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
S3 methods shown with full name in documentation object 'density.plot':
  'density.plot'

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

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.
comPlot: no visible global function definition for 'plot'
comPlot: no visible global function definition for 'lines'
convertEiData: no visible global function definition for 'model.frame'
plot.eiwild: no visible global function definition for 'plot'
plot.eiwild: no visible global function definition for 'par'
plotResult: no visible global function definition for 'grey'
plotResult: no visible global function definition for
  'colorRampPalette'
plotResult: no visible global function definition for 'plot.new'
plotResult: no visible global function definition for 'plot.window'
prioriPlot: no visible global function definition for 'par'
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for 'rgamma'
prioriPlot : <anonymous>: no visible global function definition for
  'rbeta'
prioriPlot: no visible global function definition for 'hist'
prioriPlot : <anonymous>: no visible global function definition for
  'rgamma'
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for 'rexp'
prioriPlot : <anonymous>: no visible global function definition for
  'rexp'
runMBayes: no visible global function definition for 'runif'
runMBayes: no visible global function definition for 'rgamma'
runMBayes: no visible global function definition for 'rexp'
str0: no visible global function definition for 'str'
tuneVars: no visible global function definition for 'sd'
Undefined global functions or variables:
  colorRampPalette grey hist lines model.frame par plot plot.new
  plot.window rbeta rexp rgamma runif sd str
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey")
  importFrom("graphics", "hist", "lines", "par", "plot", "plot.new",
             "plot.window")
  importFrom("stats", "model.frame", "rbeta", "rexp", "rgamma", "runif",
             "sd")
  importFrom("utils", "str")
to your NAMESPACE file.
CAST.calc.opt.cut: no visible global function definition for 'points'
CAST.calc.opt.cut: no visible global function definition for 'axis'
CAST.calc.sample: no visible global function definition for 'uniroot'
KM.audit: no visible global function definition for 'abline'
KM.audit: no visible global function definition for 'points'
KM.audit: no visible global function definition for 'segments'
KM.audit: no visible global function definition for 'text'
find.stark.SRS.p: no visible global function definition for 'phyper'
make.opt.packed.bad: no visible global function definition for 'runif'
make.random.truth: no visible global function definition for 'runif'
print.elec.data: no visible global function definition for 'head'
simulateIt: no visible global function definition for 'abline'
simulateIt: no visible global function definition for 'points'
simulateIt: no visible global function definition for 'segments'
simulateIt: no visible global function definition for 'text'
stark.test.Z: no visible global function definition for 'pbinom'
tri.audit.sim: no visible global function definition for 'runif'
trinomial.bound: no visible global function definition for 'contour'
trinomial.bound: no visible global function definition for 'segments'
trinomial.bound: no visible global function definition for 'points'
Undefined global functions or variables:
  abline axis contour head pbinom phyper points runif segments text
  uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "contour", "points",
             "segments", "text")
  importFrom("stats", "pbinom", "phyper", "runif", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
Package in Depends field not imported from: 'elec'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BaB: no visible binding for global variable 'calc.pairwise.e_p'
BaB: no visible global function definition for 'weight.function'
BaB: no visible global function definition for 'compute.stark.t'
LKPBound: no visible binding for global variable 'calc.pairwise.e_p'
LKPBound: no visible global function definition for 'weight.function'
LKPBound: no visible global function definition for 'compute.stark.t'
eqValBound: no visible binding for global variable 'calc.pairwise.e_p'
eqValBound: no visible global function definition for 'weight.function'
eqValBound: no visible global function definition for 'compute.stark.t'
getEbsMargin: no visible global function definition for 'is.elec.data'
getEbsMargin: no visible global function definition for
  'maximumMarginBound'
makeStratObj: no visible global function definition for 'is.elec.data'
makeStratObj: no visible global function definition for
  'maximumMarginBound'
strat.elec.data: no visible global function definition for 'elec.data'
takeOutZeroMMB: no visible global function definition for
  'maximumMarginBound'
withReplaceBound: no visible binding for global variable
  'calc.pairwise.e_p'
withReplaceBound: no visible global function definition for
  'weight.function'
withReplaceBound: no visible global function definition for
  'compute.stark.t'
Undefined global functions or variables:
  calc.pairwise.e_p compute.stark.t elec.data is.elec.data
  maximumMarginBound weight.function
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Likelihood: no visible global function definition for
  'makePSOCKcluster'
Likelihood: no visible global function definition for 'clusterExport'
Likelihood: no visible global function definition for 'makeForkCluster'
Likelihood.first.run: no visible global function definition for
  'clusterApply'
Likelihood.next.runs: no visible global function definition for
  'clusterApply'
es.stopCluster: no visible global function definition for 'stopCluster'
plot.es.pedigree: no visible global function definition for 'hasArg'
Undefined global functions or variables:
  clusterApply clusterExport hasArg makeForkCluster makePSOCKcluster
  stopCluster
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'MASS' 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    extdata  10.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    xsd   5.4Mb
'library' or 'require' calls to packages already attached by Depends:
  'clusterSim' 'earth'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'clusterSim' 'earth'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distance: no visible global function definition for
  'data.Normalization'
emmatn: no visible global function definition for 'runif'
estimateModel: no visible global function definition for 'as.formula'
estimateModel: no visible global function definition for 'earth'
estimateModel: no visible global function definition for 'plotmo'
estimateModel: no visible global function definition for 'predict'
mutation: no visible global function definition for 'runif'
plot.emma: no visible global function definition for 'colorRampPalette'
plot.emma: no visible global function definition for 'par'
plot.emma: no visible global function definition for 'persp'
plot.emma: no visible global function definition for 'points'
plot.emma: no visible global function definition for 'trans3d'
Undefined global functions or variables:
  as.formula colorRampPalette data.Normalization earth par persp plotmo
  points predict runif trans3d
Consider adding
  importFrom("grDevices", "colorRampPalette", "trans3d")
  importFrom("graphics", "par", "persp", "points")
  importFrom("stats", "as.formula", "predict", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'reshape' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MFFetch: no visible global function definition for 'melt'
Undefined global functions or variables:
  melt
Package which this enhances but not available for checking: 'glmmADMB'
Found the following significant warnings:
  Warning: S3 methods 'print.sparseSummary', 'print.diagSummary', 'c.abIndex', 'c.sparseVector', 'as.array.Matrix', 'as.array.sparseVector', 'as.matrix.Matrix', 'as.matrix.sparseVector', 'as.vector.Matrix', 'as.vector.sparseVector' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.5/emmeans.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
nondominated_ordering: no visible binding for global variable 'par'
rsbxbeta: no visible global function definition for 'runif'
Undefined global functions or variables:
  par runif
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
empiricalFDR: no visible global function definition for 'axis'
empiricalFDR: no visible global function definition for 'loess'
empiricalFDR: no visible global function definition for 'predict'
empiricalFDR: no visible global function definition for 'lines'
empiricalFDR: no visible global function definition for 'abline'
fdrBiCurve: no visible global function definition for 'plot'
fdrBiCurve: no visible global function definition for 'axis'
fdrBiCurve: no visible global function definition for 'lines'
fdrBiCurve: no visible global function definition for 'abline'
fdrBiCurve: no visible global function definition for 'legend'
simulateCounts: no visible global function definition for
  'txtProgressBar'
simulateCounts: no visible global function definition for
  'setTxtProgressBar'
simulateCounts: no visible global function definition for 'rnorm'
simulateCounts: no visible global function definition for 'hist'
simulateCounts: no visible global function definition for 'colData'
Undefined global functions or variables:
  abline axis colData hist legend lines loess plot predict rnorm
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "plot")
  importFrom("stats", "loess", "predict", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
ExactMultinomialTest: no visible global function definition for
  'dmultinom'
ExactMultinomialTest : <anonymous>: no visible global function
  definition for 'dmultinom'
ExactMultinomialTestChisquare : <anonymous>: no visible global function
  definition for 'dmultinom'
MonteCarloMultinomialTest: no visible global function definition for
  'rmultinom'
MonteCarloMultinomialTest: no visible global function definition for
  'flush.console'
MonteCarloMultinomialTestChisquare: no visible global function
  definition for 'rmultinom'
MonteCarloMultinomialTestChisquare: no visible global function
  definition for 'flush.console'
multinomial.test: no visible global function definition for
  'flush.console'
plotMultinom: no visible global function definition for 'barplot'
plotMultinom: no visible global function definition for 'mtext'
Undefined global functions or variables:
  barplot dmultinom flush.console mtext rmultinom
Consider adding
  importFrom("graphics", "barplot", "mtext")
  importFrom("stats", "dmultinom", "rmultinom")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
'library' or 'require' call to 'RColorBrewer' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Rcmdr' 'gWidgets' 'gWidgetstcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Hmisc' 'RColorBrewer' 'vcd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Checking should be performed on sources prepared by 'R CMD build'.
matplot_enrichment_curve: no visible global function definition for
  'plot'
matplot_enrichment_curve: no visible global function definition for
  'lines'
matplot_enrichment_curve: no visible global function definition for
  'legend'
plot_enrichment_curve: no visible global function definition for 'plot'
plot_enrichment_curve: no visible global function definition for
  'lines'
plot_enrichment_curve: no visible global function definition for
  'plot.xy'
plot_enrichment_curve: no visible global function definition for
  'xy.coords'
plot_enrichment_curve: no visible global function definition for
  'rainbow'
plot_enrichment_curve: no visible global function definition for
  'axTicks'
plot_enrichment_curve: no visible global function definition for 'rect'
plot_enrichment_curve: no visible global function definition for 'axis'
plot_enrichment_curve_xlog: no visible global function definition for
  'plot'
plot_enrichment_curve_xlog: no visible global function definition for
  'lines'
plot_enrichment_curve_xlog: no visible global function definition for
  'plot.xy'
plot_enrichment_curve_xlog: no visible global function definition for
  'xy.coords'
plot_enrichment_curve_xlog: no visible global function definition for
  'rainbow'
plot_enrichment_curve_xlog: no visible global function definition for
  'axTicks'
plot_enrichment_curve_xlog: no visible global function definition for
  'rect'
plot_enrichment_curve_xlog: no visible global function definition for
  'axis'
Undefined global functions or variables:
  axTicks axis legend lines plot plot.xy rainbow rect xy.coords
Consider adding
  importFrom("grDevices", "rainbow", "xy.coords")
  importFrom("graphics", "axTicks", "axis", "legend", "lines", "plot",
             "plot.xy", "rect")
to your NAMESPACE file.
diffcv: no visible global function definition for 'sd'
diffcvall: no visible global function definition for 'sd'
diffcvall: no visible global function definition for 'fligner.test'
diffcvall: no visible global function definition for 'p.adjust'
diffcvpFK: no visible global function definition for 'fligner.test'
diffcvpFK: no visible global function definition for 'p.adjust'
diffexp: no visible global function definition for 'var'
diffexp: no visible global function definition for 't.test'
diffexp: no visible global function definition for 'p.adjust'
diffexp2: no visible global function definition for 'var'
diffexp2: no visible global function definition for 't.test'
diffexp2: no visible global function definition for 'p.adjust'
diffnsepperm: no visible global function definition for 'p.adjust'
diffseall: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  fligner.test p.adjust sd t.test var
Consider adding
  importFrom("stats", "fligner.test", "p.adjust", "sd", "t.test", "var")
to your NAMESPACE file.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    3.3Mb
    help   3.4Mb
'library' or 'require' call to 'plotrix' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Hmisc' 'survival'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'plotrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'a.alpha.ade' 'a.coladd.ade' 'a.getcol.ade' 'a.glc'
plot.eb: no visible global function definition for 'plot'
plot.eb : <anonymous>: no visible global function definition for
  'lines'
plot.ebhistorical: no visible global function definition for 'palette'
plot.ebhistorical: no visible global function definition for 'dev.new'
plot.ebhistorical: no visible global function definition for 'par'
plot.ebhistorical: no visible global function definition for
  'topo.colors'
plot.ebhistorical: no visible global function definition for 'plot'
plot.ebhistorical: no visible global function definition for 'curve'
plot.ebhistorical: no visible global function definition for 'lines'
plot.ebhistoricalsummary: no visible global function definition for
  'topo.colors'
plot.ebhistoricalsummary: no visible global function definition for
  'dev.new'
plot.ebhistoricalsummary: no visible global function definition for
  'plot'
plot.ebhistoricalsummary: no visible global function definition for
  'axis'
plot.ebhistoricalsummary: no visible global function definition for
  'lines'
plot.ebhistoricalsummary: no visible global function definition for
  'legend'
Undefined global functions or variables:
  axis curve dev.new legend lines palette par plot topo.colors
Consider adding
  importFrom("grDevices", "dev.new", "palette", "topo.colors")
  importFrom("graphics", "axis", "curve", "legend", "lines", "par",
             "plot")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
DiscrSI : CDFGamma: no visible global function definition for 'pgamma'
EstimateR : SampleFromPosterior : <anonymous>: no visible global
  function definition for 'rgamma'
EstimateR: no visible global function definition for 'rnorm'
EstimateR: no visible binding for global variable 'sd'
EstimateR: no visible binding for global variable 'quantile'
EstimateR: no visible binding for global variable 'median'
EstimateR: no visible global function definition for 'qgamma'
EstimateR: no visible global function definition for 'par'
EstimateR: no visible global function definition for 'title'
EstimateR: no visible global function definition for 'polygon'
EstimateR: no visible global function definition for 'lines'
EstimateR: no visible global function definition for 'legend'
EstimateR: no visible global function definition for 'hist'
WT : DrawOneSetOfAncestries: no visible global function definition for
  'rmultinom'
WT: no visible binding for global variable 'quantile'
WT: no visible binding for global variable 'sd'
WT: no visible global function definition for 'par'
WT: no visible global function definition for 'segments'
WT: no visible global function definition for 'points'
WT: no visible global function definition for 'lines'
WT: no visible global function definition for 'legend'
Undefined global functions or variables:
  hist legend lines median par pgamma points polygon qgamma quantile
  rgamma rmultinom rnorm sd segments title
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "par", "points",
             "polygon", "segments", "title")
  importFrom("stats", "median", "pgamma", "qgamma", "quantile", "rgamma",
             "rmultinom", "rnorm", "sd")
to your NAMESPACE file.
plot.episplineDensity: no visible global function definition for 'plot'
plot.episplineDensity: no visible global function definition for
  'points'
postproc: no visible global function definition for 'plot'
postproc: no visible global function definition for 'points'
preprocess.data: no visible global function definition for 'sd'
Undefined global functions or variables:
  plot points sd
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "sd")
to your NAMESPACE file.
FCIplot: no visible global function definition for 'na.omit'
FCIplot: no visible global function definition for 'plot'
FCIplot: no visible global function definition for 'tail'
FCIplot: no visible global function definition for 'grid'
FCIplot: no visible global function definition for 'polygon'
FCIplot: no visible global function definition for 'rgb'
linpred: no visible global function definition for 'lm'
mplott: no visible global function definition for 'par'
mplott: no visible global function definition for 'plot'
mplott: no visible global function definition for 'na.omit'
mplott: no visible global function definition for 'lines'
mplott: no visible global function definition for 'legend'
mplott: no visible global function definition for 'grid'
plott: no visible global function definition for 'lines'
plott: no visible global function definition for 'par'
plott: no visible global function definition for 'plot'
plott: no visible global function definition for 'grid'
tsideplot: no visible global function definition for 'par'
tsideplot: no visible global function definition for 'plot'
tsideplot: no visible global function definition for 'axis'
tsideplot: no visible global function definition for 'grid'
Undefined global functions or variables:
  axis grid legend lines lm na.omit par plot polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package suggested but not available for checking: 'RCytoscape'
Malformed Description field: should contain one or more complete sentences.
.getFactor: no visible global function definition for 'integrate'
check.cumulants: no visible global function definition for 'runif'
edgeworth: no visible global function definition for 'dnorm'
eql : getEQL: no visible binding for global variable 'glm'
eql: no visible global function definition for 'splinefun'
eql: no visible binding for global variable 'glm'
eql : <anonymous>: no visible global function definition for 'glm'
plot.approximation: no visible global function definition for 'mtext'
plot.eql: no visible global function definition for 'points'
plot.eql: no visible global function definition for 'par'
plot.eql: no visible global function definition for 'segments'
plot.eql: no visible global function definition for 'qchisq'
plot.eql: no visible global function definition for 'text'
plot.eql: no visible global function definition for 'abline'
plot.eql : eql.panel: no visible global function definition for
  'qchisq'
plot.eql: no visible global function definition for 'colorRampPalette'
plot.eql: no visible global function definition for 'heat.colors'
varianceFamily : devf : <anonymous>: no visible global function
  definition for 'integrate'
varianceFamily: no visible global function definition for 'make.link'
Undefined global functions or variables:
  abline colorRampPalette dnorm glm heat.colors integrate make.link
  mtext par points qchisq runif segments splinefun text
Consider adding
  importFrom("grDevices", "colorRampPalette", "heat.colors")
  importFrom("graphics", "abline", "mtext", "par", "points", "segments",
             "text")
  importFrom("stats", "dnorm", "glm", "integrate", "make.link", "qchisq",
             "runif", "splinefun")
to your NAMESPACE file.
eqs2lavaan: no visible global function definition for 'ignore.case'
eqs2lavaan: no visible global function definition for 'str_join'
eqs2lavaan: no visible binding for global variable 'r'
eqsCorr: no visible global function definition for 'cov2cor'
plotCov: no visible global function definition for 'cov2cor'
plotCov: no visible global function definition for 'par'
plotCov: no visible global function definition for 'image'
plotCov: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis cov2cor ignore.case image par r str_join
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "cov2cor")
to your NAMESPACE file.
'library' or 'require' call to 'qtl' which was already attached by Depends.
  Please remove these calls from your code.
Unexported objects imported by ':::' calls:
  'qtl:::c.scanone' 'qtl:::plot.scanone'
  See the note in ?`:::` about the use of this operator.
The following files contain a license that requires
distribution of original sources:
  'upgreek.sty'
Please ensure that you have complied with it.
ESA: no visible binding for global variable 'var'
plot.esabcv: no visible global function definition for 'plot'
plot.esabcv: no visible global function definition for 'points'
plot.esabcv: no visible global function definition for 'axis'
plot.esabcv: no visible global function definition for 'title'
Undefined global functions or variables:
  axis plot points title var
Consider adding
  importFrom("graphics", "axis", "plot", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
ESEA.Main: no visible global function definition for 'rnorm'
ESEA.Main: no visible global function definition for 'sd'
ESEA.Main: no visible global function definition for 'p.adjust'
PlotGlobEdgeCorProfile: no visible global function definition for
  'plot'
PlotGlobEdgeCorProfile: no visible global function definition for
  'lines'
PlotGlobEdgeCorProfile: no visible global function definition for
  'colors'
PlotGlobEdgeCorProfile: no visible global function definition for
  'points'
PlotGlobEdgeCorProfile: no visible global function definition for
  'legend'
PlotGlobEdgeCorProfile: no visible global function definition for
  'text'
PlotPathwayGraph: no visible global function definition for 'par'
PlotPathwayGraph: no visible global function definition for 'plot'
PlotRunEnrichment: no visible global function definition for 'plot'
PlotRunEnrichment: no visible global function definition for 'lines'
PlotRunEnrichment: no visible global function definition for 'colors'
PlotRunEnrichment: no visible global function definition for 'text'
SavePathway2File: no visible global function definition for 'is'
calEdgeCorScore: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  colors is legend lines na.omit p.adjust par plot points rnorm sd text
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "text")
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "p.adjust", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
rAllRisksFactors: no visible global function definition for 'new'
rAssetDistribution: no visible global function definition for 'new'
rDefaultSpread: no visible global function definition for 'new'
rLiquiditySpread: no visible global function definition for 'new'
rRealEstate: no visible global function definition for 'new'
rShortRate: no visible global function definition for 'new'
rStock: no visible global function definition for 'new'
EuroCall_Stock_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
EuroCall_ZC_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
EuroPut_Stock_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
EuroPut_ZC_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
MartingaleTest,Scenarios: no visible global function definition for
  'plot'
MartingaleTest,Scenarios: no visible global function definition for
  'lines'
MartingaleTest,Scenarios: no visible global function definition for
  'title'
customPathsGeneration,Scenarios: no visible global function definition
  for 'rnorm'
Undefined global functions or variables:
  lines new plot pnorm rnorm title
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
cv.ES: no visible binding for global variable 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'estoutstorage'
descsto: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.Transition: no visible global function definition for 'rnorm'
.Transition.DC: no visible global function definition for 'runif'
CondPdf.CC.interval: no visible global function definition for 'plot'
CondPdf.DC.interval: no visible global function definition for 'plot'
Simu.Cond.HR: no visible global function definition for 'rpois'
Simu.Cond.HR: no visible global function definition for 'runif'
Simu.Cond.HR: no visible global function definition for 'hist'
Simu.Cond.HR: no visible global function definition for 'var'
Simu.HR: no visible global function definition for 'rpois'
Simu.HR: no visible global function definition for 'runif'
Simu.HR: no visible global function definition for 'hist'
Simu.HR: no visible global function definition for 'var'
Simu.PDMP: no visible global function definition for 'plot'
Simu.PDMP.DC: no visible global function definition for 'plot'
plotCHR: no visible global function definition for 'plot'
plotHR: no visible global function definition for 'plot'
Undefined global functions or variables:
  hist plot rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Hmisc' 'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
corr_p_cell: no visible global function definition for 'cov.wt'
iqr_cell: no visible global function definition for 'quantile'
iqr_cell: no visible global function definition for 'wtd.quantile'
mean_sd_cell: no visible global function definition for 'wtd.mean'
mean_sd_cell: no visible global function definition for 'wtd.var'
mode_cell: no visible global function definition for 'wtd.table'
quantile_cell: no visible global function definition for 'wtd.quantile'
quantile_cell: no visible global function definition for 'quantile'
stat_cell: no visible global function definition for 'quantile'
stat_cell: no visible global function definition for 'wtd.quantile'
stat_cell: no visible global function definition for 'wtd.mean'
stat_cell: no visible global function definition for 'wtd.var'
stat_cell: no visible global function definition for 'mad'
stat_cell: no visible global function definition for 'wtd.table'
Undefined global functions or variables:
  cov.wt mad quantile wtd.mean wtd.quantile wtd.table wtd.var
Consider adding
  importFrom("stats", "cov.wt", "mad", "quantile")
to your NAMESPACE file.
etc.diff: no visible global function definition for 'model.frame'
etc.diff: no visible binding for global variable 'sd'
etc.diff: no visible global function definition for 'qt'
etc.diff: no visible global function definition for 'pt'
etc.diff: no visible global function definition for 'wilcox.test'
etc.rat: no visible global function definition for 'model.frame'
etc.rat: no visible binding for global variable 'sd'
etc.rat: no visible global function definition for 'qt'
etc.rat: no visible global function definition for 'pt'
Undefined global functions or variables:
  model.frame pt qt sd wilcox.test
Consider adding
  importFrom("stats", "model.frame", "pt", "qt", "sd", "wilcox.test")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: xml2
trying URL 'https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ft2020_rk310.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 4490 bytes
==================================================
downloaded 4490 bytes

Table t2020_rk310 cached at D:\temp\RtmpY3laaj/eurostat/t2020_rk310_num_code_TF.rds

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

trying URL 'https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ften00081.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 13630 bytes (13 KB)
==================================================
downloaded 13 KB

Table ten00081 cached at D:\temp\RtmpY3laaj/eurostat/ten00081_date_code_TF.rds
trying URL 'https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftgs00026.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 5998 bytes
==================================================
downloaded 5998 bytes

Quitting from lines 291-308 (eurostat_tutorial.Rmd) 
Error: processing vignette 'eurostat_tutorial.Rmd' failed with diagnostics:
Open failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
powerSet : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
mposterior: no visible global function definition for 'optim'
rl.pred: no visible global function definition for 'matplot'
rl.pst: no visible binding for global variable 'quantile'
rl.pst: no visible global function definition for 'matplot'
Undefined global functions or variables:
  matplot optim quantile
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
make_dyads : ff: no visible global function definition for 'aggregate'
make_scale: no visible global function definition for 'read.csv'
plot_dyad: no visible global function definition for 'is'
read_eventdata : read_ed_file: no visible global function definition
  for 'read.csv'
Undefined global functions or variables:
  aggregate is read.csv
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
evolvabilityBetaMCMC : <anonymous>: no visible binding for global
  variable 'median'
evolvabilityBetaMCMC: no visible binding for global variable 'median'
evolvabilityBetaMCMC2: no visible binding for global variable 'median'
evolvabilityMeans: no visible global function definition for 'var'
evolvabilityMeansMCMC : <anonymous>: no visible global function
  definition for 'var'
evolvabilityMeansMCMC: no visible binding for global variable 'median'
randomBeta: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  median rnorm var
Consider adding
  importFrom("stats", "median", "rnorm", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/Evomorph.Rcheck/00install.out' for details.
Package in Depends field not imported from: 'evd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DPOT: no visible global function definition for 'optim'
mop.rho: no visible global function definition for 'median'
Undefined global functions or variables:
  median optim
Consider adding
  importFrom("stats", "median", "optim")
to your NAMESPACE file.
EW : PhiP : Phi: no visible global function definition for 'pnorm'
EWplot: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot pnorm
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
BinomialCIone: no visible global function definition for 'na.omit'
PairedCIone: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
build.mcx.obj: no visible global function definition for 'glm'
build.mcx.obj: no visible binding for global variable 'poisson'
build.mcx.obj: no visible global function definition for 'fitted'
cab: no visible global function definition for 'rbinom'
cab: no visible global function definition for 'runif'
mcexact: no visible global function definition for 'update'
rounded.tprob: no visible global function definition for 'pt'
simtable.cab: no visible global function definition for 'rbinom'
simtable.cab: no visible global function definition for 'runif'
Undefined global functions or variables:
  fitted glm poisson pt rbinom runif update
Consider adding
  importFrom("stats", "fitted", "glm", "poisson", "pt", "rbinom",
             "runif", "update")
to your NAMESPACE file.
plot.pgrid: no visible global function definition for 'image'
statistic.cv: no visible global function definition for 'quantile'
statistic.sim: no visible global function definition for 'contourLines'
Undefined global functions or variables:
  contourLines image quantile
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "image")
  importFrom("stats", "quantile")
to your NAMESPACE file.
countBamInGRanges.exomeDepth: no visible global function definition for
  'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: 'prettyGraphs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
computeConstraints: no visible global function definition for
  'minmaxHelper'
coreCA: no visible global function definition for 'repmat'
coreMDS: no visible global function definition for 'repmat'
corePCA: no visible global function definition for 'repmat'
epGraphs: no visible global function definition for
  'createColorVectorsByDesign'
epGraphs: no visible global function definition for 'prettyPlot'
epGraphs: no visible global function definition for 'contributionBars'
expo.scale: no visible binding for global variable 'sd'
makeDistancesAndWeights: no visible global function definition for
  'cor'
makeDistancesAndWeights: no visible global function definition for
  'dist'
makeNominalData: no visible global function definition for 'repmat'
mca.eigen.fix: no visible global function definition for 'repmat'
pcaSupplementaryColsPreProcessing: no visible global function
  definition for 'repmat'
pcaSupplementaryRowsPreProcessing: no visible global function
  definition for 'repmat'
rowNorms: no visible global function definition for 'repmat'
supplementalProjection: no visible global function definition for
  'repmat'
Undefined global functions or variables:
  contributionBars cor createColorVectorsByDesign dist minmaxHelper
  prettyPlot repmat sd
Consider adding
  importFrom("stats", "cor", "dist", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ape' 'deSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
expoTree.optim: no visible global function definition for 'optim'
node.age: no visible global function definition for 'is.binary.tree'
node.age: no visible global function definition for 'multi2di'
plotLTT: no visible global function definition for 'rgb'
plotLTT: no visible global function definition for 'par'
plotLTT: no visible global function definition for 'lines'
plotLTT: no visible global function definition for 'axis'
plotLTT: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis is.binary.tree lines mtext multi2di optim par rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "lines", "mtext", "par")
  importFrom("stats", "optim")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
index.citations: no visible global function definition for
  'txtProgressBar'
read.exsic: no visible global function definition for 'read.csv'
update.pb: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  read.csv setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package in Depends field not imported from: 'rmeta'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
extfunnel: no visible global function definition for 'qnorm'
extfunnel: no visible global function definition for 'meta.summaries'
extfunnel: no visible global function definition for 'flush.console'
extfunnel: no visible global function definition for 'qt'
extfunnel: no visible global function definition for 'dev.new'
extfunnel: no visible global function definition for 'par'
extfunnel: no visible global function definition for 'plot'
extfunnel: no visible global function definition for 'polygon'
extfunnel: no visible global function definition for 'segments'
extfunnel: no visible global function definition for 'abline'
extfunnel: no visible global function definition for 'axis'
extfunnel: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par plot polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "plot",
             "polygon", "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
bars: no visible global function definition for 'segments'
cv.binomial: no visible binding for global variable 'var'
cv.binomial: no visible global function definition for 'abline'
cv.normal: no visible binding for global variable 'var'
cv.normal: no visible global function definition for 'abline'
cv.poisson: no visible binding for global variable 'var'
cv.poisson: no visible global function definition for 'abline'
plot.extlasso: no visible global function definition for 'matplot'
plot.extlasso: no visible global function definition for 'axis'
Undefined global functions or variables:
  abline axis matplot segments var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments")
  importFrom("stats", "var")
to your NAMESPACE file.
exbio: no visible global function definition for 'as.formula'
exbio: no visible global function definition for 'glm'
exbio: no visible binding for global variable 'gaussian'
exbio: no visible global function definition for 'Gamma'
exbio: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  Gamma as.formula gaussian glm pchisq
Consider adding
  importFrom("stats", "Gamma", "as.formula", "gaussian", "glm", "pchisq")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
font_install: no visible global function definition for
  'installed.packages'
font_install: no visible global function definition for
  'install.packages'
fonttable_add: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  install.packages installed.packages write.csv
Consider adding
  importFrom("utils", "install.packages", "installed.packages",
             "write.csv")
to your NAMESPACE file.
toJavaMatrix2D: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
bootstrapCMLE: no visible global function definition for 'qweibull'
bootstrapCMLE: no visible binding for global variable 'sd'
bootstrapCMLE: no visible global function definition for 'quantile'
bootstrapCenWbMix: no visible binding for global variable 'sd'
bootstrapCenWbMix: no visible global function definition for 'quantile'
cenWeibullMLE: no visible global function definition for 'sd'
expmx.p2.censor: no visible global function definition for 'dweibull'
expmx.p2.censor: no visible global function definition for 'pweibull'
genWbMixIni: no visible global function definition for 'runif'
log.llh.p2.censor: no visible global function definition for 'dweibull'
log.llh.p2.censor: no visible global function definition for 'pweibull'
quanWbMix : t.fun: no visible global function definition for 'pweibull'
quanWbMix: no visible global function definition for 'uniroot'
quanWbMix.int : t.fun: no visible global function definition for
  'pweibull'
quanWbMix.int: no visible global function definition for 'uniroot'
simWbMix: no visible global function definition for 'rbinom'
simWbMix: no visible global function definition for 'rweibull'
Undefined global functions or variables:
  dweibull pweibull quantile qweibull rbinom runif rweibull sd uniroot
Consider adding
  importFrom("stats", "dweibull", "pweibull", "quantile", "qweibull",
             "rbinom", "runif", "rweibull", "sd", "uniroot")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'doMC'
Error in re-building vignettes:
  ...
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning in make_onset_data(response_window_clean, onset_time = 15500, fixation_window_length = 1,  :
  Very few trials have a legitimate first AOI! Possible incorrect onset time?
Warning in max(SwitchAOI) :
  no non-missing arguments to max; returning -Inf
Warning in min(SwitchAOI) :
  no non-missing arguments to min; returning Inf
Warning in max(df_plot$.Time) :
  no non-missing arguments to max; returning -Inf
Quitting from lines 91-93 (onset_contingent_analysis_vignette.Rmd) 
Error: processing vignette 'onset_contingent_analysis_vignette.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
Execution halted
Malformed Title field: should not end in a period.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ez.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
createFormula: no visible global function definition for 'tail'
createFormula: no visible global function definition for 'head'
createFormula: no visible global function definition for 'as.formula'
ezsim: no visible global function definition for 'runif'
plot.ezsim: no visible global function definition for 'quantile'
plot.ezsim: no visible global function definition for 'head'
plot.ezsim: no visible global function definition for 'tail'
plot.ezsim: no visible global function definition for 'plot'
plot.ezsim: no visible binding for global variable 'dnorm'
plot.ezsim: no visible binding for global variable 'pdf'
plot.ezsim: no visible global function definition for 'dev.off'
plot.ezsim : <anonymous>: no visible global function definition for
  'dev.new'
plot.summary.ezsim: no visible global function definition for 'head'
plot.summary.ezsim: no visible global function definition for 'tail'
plot.summary.ezsim: no visible binding for global variable 'pdf'
plot.summary.ezsim: no visible global function definition for 'dev.off'
plot.summary.ezsim : <anonymous>: no visible global function definition
  for 'dev.new'
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf plot quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
gibbs2: no visible global function definition for 'rnorm'
gibbs_sampling: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
fma: no visible global function definition for 'factanal'
fma: no visible global function definition for 'runif'
fma: no visible global function definition for 'kmeans'
fma: no visible global function definition for 'var'
fma.em.alg: no visible global function definition for 'var'
misc : q: no visible global function definition for 'name'
Undefined global functions or variables:
  factanal kmeans name runif var
Consider adding
  importFrom("stats", "factanal", "kmeans", "runif", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RCurl' 'RJSONIO' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createFactualConnection: no visible global function definition for
  'new'
factualGetSchema: no visible global function definition for 'fromJSON'
factualRead: no visible global function definition for 'curlEscape'
factualRead: no visible global function definition for 'fromJSON'
processFactualReadJSON: no visible global function definition for 'new'
processFactualSchemaJSON: no visible global function definition for
  'new'
Undefined global functions or variables:
  curlEscape fromJSON new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
faisalconjoint: no visible global function definition for 'barplot'
faisalconjoint: no visible global function definition for 'text'
faisalconjoint: no visible global function definition for 'jpeg'
faisalconjoint: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  barplot dev.off jpeg text
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "barplot", "text")
to your NAMESPACE file.
File 'fame/R/windows/zzz.R':
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Aggregation : foo: no visible global function definition for
  'weighted.mean'
Aggregation: no visible global function definition for 'txtProgressBar'
Aggregation: no visible global function definition for
  'setTxtProgressBar'
constructSYB: no visible global function definition for 'str'
fillCountryCode: no visible global function definition for 'na.omit'
getFAO: no visible global function definition for 'read.csv'
getWDImetaData: no visible global function definition for 'write.csv'
getWDItoSYB: no visible global function definition for 'na.omit'
lsgr: no visible global function definition for 'na.omit'
lsgr: no visible global function definition for 'coef'
lsgr: no visible global function definition for 'lm'
Undefined global functions or variables:
  coef lm na.omit read.csv setTxtProgressBar str txtProgressBar
  weighted.mean write.csv
Consider adding
  importFrom("stats", "coef", "lm", "na.omit", "weighted.mean")
  importFrom("utils", "read.csv", "setTxtProgressBar", "str",
             "txtProgressBar", "write.csv")
to your NAMESPACE file.
basis_hica: no visible global function definition for 'princomp'
energy_hica: no visible global function definition for 'dev.new'
energy_hica: no visible global function definition for 'points'
energy_hica: no visible global function definition for 'legend'
Undefined global functions or variables:
  dev.new legend points princomp
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "princomp")
to your NAMESPACE file.
Package suggested but not available for checking: 'coxKM'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
File 'fastmatch/libs/i386/fastmatch.dll':
  Found non-API call to R: 'match5'
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
FBN.histogramMaxima: no visible global function definition for 'hist'
FBN.kmeans: no visible global function definition for 'median'
FBN.kmeans: no visible global function definition for 'kmeans'
FBNormalization: no visible global function definition for 'read.table'
FBNormalization: no visible global function definition for 'median'
FBNormalization: no visible global function definition for 'hist'
FBNormalization: no visible global function definition for 'par'
FBNormalization: no visible global function definition for 'dev.print'
FBNormalization: no visible binding for global variable 'bmp'
FBNormalization: no visible global function definition for 'sd'
FBNormalization: no visible global function definition for
  'write.table'
medianFilter: no visible global function definition for 'median'
Undefined global functions or variables:
  bmp dev.print hist kmeans median par read.table sd write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.print")
  importFrom("graphics", "hist", "par")
  importFrom("stats", "kmeans", "median", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'RCurl' 'RJSONIO' 'XML' 'glmnet' 'httr' 'speedglm' 'tcltk' 'xtable'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'MASS' 'combinat' 'glmnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fcd.cluster: no visible global function definition for 'kmeans'
fcd.start: no visible global function definition for 'ginv'
fcd.start: no visible global function definition for 'glmnet'
gen.dcbm: no visible global function definition for 'rbinom'
gen.sbm: no visible global function definition for 'rbinom'
mis.cluster: no visible global function definition for 'permn'
spectral.clustering: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  ginv glmnet kmeans permn rbinom
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
PTSingleAssetBarrierOption2: no visible global function definition for
  'new'
newton: no visible global function definition for 'plot'
newton: no visible global function definition for 'abline'
probInRange: no visible global function definition for 'pnorm'
shortfall_risk: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline new plot pnorm
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
asymp.vcov: no visible global function definition for 'cov'
corFDG: no visible global function definition for 'cor'
g.exponential: no visible global function definition for 'integrate'
rho.exponential: no visible global function definition for 'integrate'
rho.sinus: no visible global function definition for 'integrate'
tau.exponential: no visible global function definition for 'integrate'
tau.sinus: no visible global function definition for 'integrate'
tfun.sinus.rho: no visible global function definition for 'integrate'
wlsdc: no visible global function definition for 'optim'
Undefined global functions or variables:
  cor cov integrate optim
Consider adding
  importFrom("stats", "cor", "cov", "integrate", "optim")
to your NAMESPACE file.
FDRreg: no visible global function definition for 'dnorm'
colnormalize: no visible global function definition for 'sd'
efron: no visible global function definition for 'median'
efron: no visible global function definition for 'hist'
efron: no visible global function definition for 'glm'
efron: no visible binding for global variable 'poisson'
efron: no visible global function definition for 'qchisq'
efron: no visible global function definition for 'predict'
efron: no visible global function definition for 'quantile'
efron: no visible global function definition for 'lm'
efron: no visible global function definition for 'coef'
make.bspline.matrix: no visible global function definition for
  'quantile'
plotFDR: no visible global function definition for 'hist'
plotFDR: no visible global function definition for 'par'
plotFDR: no visible global function definition for 'plot'
plotFDR: no visible global function definition for 'axis'
plotFDR: no visible global function definition for 'lines'
plotFDR: no visible global function definition for 'legend'
plotFDR: no visible global function definition for 'rug'
plotFDR: no visible global function definition for 'title'
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par plot poisson
  predict qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par",
             "plot", "rug", "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(feather)
  > 
  > test_check("feather")
  -- 1. Error: can read/write with utf-8 filename (@test-read.R#19)  -------------
  IO error: Failed to open file: D:\temp\RtmpWO6Vcc\Ã¥.feather
  1: read_feather(path) at testthat/test-read.R:19
  2: feather(path)
  3: openFeather(path)
  
  == testthat results  ===========================================================
  OK: 50 SKIPPED: 0 FAILED: 1
  1. Error: can read/write with utf-8 filename (@test-read.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(feather)
  > 
  > test_check("feather")
  -- 1. Error: can read/write with utf-8 filename (@test-read.R#19)  -------------
  IO error: Failed to open file: D:\temp\RtmpoXRkjK\Ã¥.feather
  1: read_feather(path) at testthat/test-read.R:19
  2: feather(path)
  3: openFeather(path)
  
  == testthat results  ===========================================================
  OK: 50 SKIPPED: 0 FAILED: 1
  1. Error: can read/write with utf-8 filename (@test-read.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  'ggplot2' 'gridExtra'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FFieldPtRepDemo: no visible global function definition for 'ggplot'
FFieldPtRepDemo: no visible binding for global variable 'mtcars'
FFieldPtRepDemo: no visible global function definition for 'aes'
FFieldPtRepDemo: no visible binding for global variable 'mpg'
FFieldPtRepDemo: no visible global function definition for 'geom_point'
FFieldPtRepDemo: no visible global function definition for 'geom_text'
FFieldPtRepDemo: no visible global function definition for 'ggtitle'
FFieldPtRepDemo: no visible global function definition for
  'geom_segment'
FFieldPtRepDemo: no visible global function definition for
  'grid.arrange'
Undefined global functions or variables:
  aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg
  mtcars
Consider adding
  importFrom("datasets", "mtcars")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
ftest: no visible global function definition for 'wilcox.test'
ftest: no visible global function definition for 't.test'
Undefined global functions or variables:
  t.test wilcox.test
Consider adding
  importFrom("stats", "t.test", "wilcox.test")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'mvtnorm' 'numDeriv'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dmymvnorm: no visible global function definition for 'dmvnorm'
dmymvt: no visible global function definition for 'dmvt'
gof.test: no visible global function definition for 'quantile'
gof.test : ecdf: no visible global function definition for 'mecdf'
gof.test: no visible global function definition for 'jacobian'
gof.test: no visible global function definition for 'var'
gradCdfT: no visible global function definition for 'dt'
gradCdfT: no visible global function definition for 'pt'
gradCdfT: no visible global function definition for 'pmvt'
influFun: no visible global function definition for 'jacobian'
mult.sim: no visible global function definition for 'rnorm'
plackettFormula: no visible global function definition for 'pt'
plackettFormula: no visible global function definition for 'pmvt'
pmymvnorm: no visible global function definition for 'GenzBretz'
pmymvnorm: no visible global function definition for 'TVPACK'
pmymvnorm : <anonymous>: no visible global function definition for
  'pmvnorm'
pmymvt: no visible global function definition for 'GenzBretz'
pmymvt: no visible global function definition for 'TVPACK'
pmymvt : <anonymous>: no visible global function definition for 'pmvt'
rmymvnorm: no visible global function definition for 'rmvnorm'
rmymvt: no visible global function definition for 'rmvt'
Undefined global functions or variables:
  GenzBretz TVPACK dmvnorm dmvt dt jacobian mecdf pmvnorm pmvt pt
  quantile rmvnorm rmvt rnorm var
Consider adding
  importFrom("stats", "dt", "pt", "quantile", "rnorm", "var")
to your NAMESPACE file.
fgeasy: no visible global function definition for 'dist'
fgeasy : cor.est: no visible global function definition for 'cor.test'
fgeasy: no visible binding for global variable 'var'
fgperm : runrand: no visible global function definition for 'runif'
fgperm : runrand: no visible global function definition for 'ave'
fgploc : runrand: no visible global function definition for 'runif'
fgploc : runrand: no visible global function definition for 'ave'
fyshuffle: no visible global function definition for 'runif'
plot.fg: no visible global function definition for 'par'
plot.fg: no visible global function definition for 'plot'
plot.fg: no visible global function definition for 'segments'
plot.fg: no visible binding for global variable 'quantile'
plot.fg: no visible global function definition for 'abline'
plot.fg: no visible global function definition for 'axis'
summary.fg: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  abline ave axis cor.test dist par plot quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
fieldsim: no visible global function definition for 'rnorm'
midpoint: no visible global function definition for 'rnorm'
setAtlas_under: no visible global function definition for 'runif'
setCovf_under : Ibeta: no visible global function definition for
  'pbeta'
visualize: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'filehash' 'DBI'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'RSQLite' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createSQLite: no visible global function definition for 'dbDriver'
createSQLite: no visible global function definition for 'dbConnect'
createSQLite: no visible global function definition for
  'dbUnloadDriver'
createSQLite: no visible global function definition for 'dbGetQuery'
initializeSQLite: no visible global function definition for 'dbDriver'
initializeSQLite: no visible global function definition for 'dbConnect'
initializeSQLite: no visible global function definition for 'new'
dbDelete,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbDisconnect,filehashSQLite: no visible global function definition for
  'dbUnloadDriver'
dbFetch,filehashSQLite-character: no visible global function definition
  for 'dbGetQuery'
dbInsert,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbList,filehashSQLite: no visible global function definition for
  'dbGetQuery'
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'testthat.R' [94s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(fingertipscharts)
  > test_check("fingertipscharts")
  -- 1. Failure: area profiles example draws correctly (@test-examples.R#156)  ---
  Figures don't match: area-profiles-example.svg
  
  
  == testthat results  ===========================================================
  OK: 46 SKIPPED: 0 FAILED: 1
  1. Failure: area profiles example draws correctly (@test-examples.R#156) 
  
  Error: testthat unit tests failed
  Execution halted
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'tkrplot' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'methods' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
lsmacof: no visible global function definition for 'cmdscale'
plotInc: no visible global function definition for 'rainbow'
plotInc: no visible global function definition for 'plot'
prepareCalib: no visible global function definition for 'lm'
Undefined global functions or variables:
  cmdscale lm plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "plot")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
fishmove : coefs: no visible global function definition for 'coef'
fishmove : coefs: no visible global function definition for 'pf'
fishmove: no visible global function definition for 'lm'
fishmove: no visible global function definition for 'predict.lm'
fishmove.estimate: no visible global function definition for 'quantile'
fishmove.estimate : ddoublenorm: no visible global function definition
  for 'dnorm'
fishmove.query: no visible global function definition for 'hasArg'
fishmove.query : f: no visible global function definition for 'pnorm'
fishmove.query: no visible global function definition for 'uniroot'
pdk: no visible global function definition for 'hasArg'
pdk : eq: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  coef dnorm hasArg lm pf pnorm predict.lm quantile uniroot
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "coef", "dnorm", "lm", "pf", "pnorm", "predict.lm",
             "quantile", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Depends: includes the non-default packages:
  'gWidgets' 'tcltk' 'tkrplot' 'RGtk2' 'gWidgetsRGtk2' 'cairoDevice'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  'RGtk2' 'cairoDevice' 'gWidgets' 'gWidgetsRGtk2' 'tcltk' 'tkrplot'
  Please remove these calls from your code.
Package in Depends field not imported from: 'FitAR'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
FitARMA: no visible global function definition for 'PacfDL'
FitARMA: no visible global function definition for 'GetARMeanMLE'
FitARMA: no visible global function definition for
  'BackcastResidualsAR'
FitARMA: no visible global function definition for 'acf'
FitARMA: no visible global function definition for 'LjungBoxTest'
FitARMA: no visible global function definition for 'tsp'
GetFitARMA: no visible global function definition for 'LoglikelihoodAR'
GetFitARMA: no visible global function definition for 'ChampernowneD'
GetFitARMA : EntropyARMA: no visible global function definition for
  'PacfToAR'
GetFitARMA : EntropyARMA: no visible global function definition for
  'PacfDL'
GetFitARMA : EntropyARMA: no visible global function definition for
  'FastLoglikelihoodAR'
GetFitARMA: no visible global function definition for 'optim'
GetFitARMA: no visible global function definition for 'PacfToAR'
InformationMatrixARMA: no visible global function definition for
  'InvertibleQ'
InformationMatrixARMA: no visible global function definition for
  'toeplitz'
SimulateGaussianARMA: no visible global function definition for 'rnorm'
SimulateGaussianARMA: no visible global function definition for
  'toeplitz'
TacvfARMA: no visible global function definition for 'InvertibleQ'
Undefined global functions or variables:
  BackcastResidualsAR ChampernowneD FastLoglikelihoodAR GetARMeanMLE
  InvertibleQ LjungBoxTest LoglikelihoodAR PacfDL PacfToAR acf optim
  rnorm toeplitz tsp
Consider adding
  importFrom("stats", "acf", "optim", "rnorm", "toeplitz", "tsp")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'leaps' 'ltsa'
A package should be listed in only one of these fields.
Package in Depends field not imported from: 'bestglm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking: 'doMC' 'RSvgDevice'
'library' or 'require' calls in package code:
  'devEMF' 'doMC' 'foreach' 'grDevices'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'ActuDistns'
Missing or unexported object: 'ggmap::has_goog_key'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R   6.3Mb
RIind: no visible global function definition for 'aggregate'
RIind: no visible binding for global variable 'sd'
RIpop: no visible global function definition for 'aggregate'
RIpop: no visible binding for global variable 'sd'
SI: no visible global function definition for 'sd'
SI2: no visible global function definition for 'sd'
SI3: no visible global function definition for 'aggregate'
SI3: no visible global function definition for 'pairs'
SI3: no visible global function definition for 'cor'
SI4: no visible global function definition for 'aggregate'
SI4: no visible global function definition for 'sd'
fCV: no visible global function definition for 'sd'
Undefined global functions or variables:
  aggregate cor pairs sd
Consider adding
  importFrom("graphics", "pairs")
  importFrom("stats", "aggregate", "cor", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GCV: no visible global function definition for 'lm'
GCV: no visible global function definition for 'resid'
ffplot: no visible global function definition for 'par'
ffplot: no visible global function definition for 'plot'
ffplot: no visible global function definition for 'points'
ffplot: no visible global function definition for 'legend'
flowfield: no visible global function definition for 'write.table'
gpr: no visible global function definition for 'quantile'
gpr: no visible global function definition for 'var'
smoothp: no visible global function definition for 'lm'
smoothp: no visible global function definition for 'predict'
smoothp: no visible global function definition for 'resid'
smoothp: no visible global function definition for 'optimize'
Undefined global functions or variables:
  legend lm optimize par plot points predict quantile resid var
  write.table
Consider adding
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
prepare_Rd: Flury-package.Rd:37-39: Dropping empty section \examples
prepare_Rd: apples.Rd:19-21: Dropping empty section \details
prepare_Rd: basketball.Rd:28-29: Dropping empty section \references
prepare_Rd: challenger.Rd:18-20: Dropping empty section \details
prepare_Rd: computers.Rd:16-18: Dropping empty section \details
prepare_Rd: cork.Rd:19-20: Dropping empty section \details
prepare_Rd: dead.beetles.Rd:17-19: Dropping empty section \details
prepare_Rd: deer.Rd:14-16: Dropping empty section \details
prepare_Rd: dogwood.Rd:22-24: Dropping empty section \details
prepare_Rd: f.twins.Rd:23-25: Dropping empty section \details
prepare_Rd: flea.beetles.Rd:22-24: Dropping empty section \details
prepare_Rd: ghq.Rd:25-27: Dropping empty section \details
prepare_Rd: lookup.Rd:15-17: Dropping empty section \details
prepare_Rd: lookup.Rd:18-20: Dropping empty section \source
prepare_Rd: m.twins.Rd:24-26: Dropping empty section \details
prepare_Rd: mumps.Rd:14-16: Dropping empty section \details
prepare_Rd: pipits.Rd:17-19: Dropping empty section \details
prepare_Rd: pipits2.Rd:18-19: Dropping empty section \details
prepare_Rd: robustus.Rd:17-19: Dropping empty section \details
prepare_Rd: sibling.heads.Rd:18-20: Dropping empty section \details
prepare_Rd: snailsf.Rd:25-27: Dropping empty section \details
prepare_Rd: steve.Rd:19-20: Dropping empty section \details
prepare_Rd: steve.Rd:26-27: Dropping empty section \references
prepare_Rd: turtles.Rd:19: Dropping empty section \details
prepare_Rd: vasoc.Rd:18-20: Dropping empty section \details
prepare_Rd: wine.sugar.Rd:22-24: Dropping empty section \details
export: no visible global function definition for 'write.table'
flux.odae : <anonymous>: no visible global function definition for
  'combn'
mf.flux: no visible global function definition for 'runsd'
plot.fluss: no visible global function definition for 'dev.new'
plot.fluss: no visible global function definition for 'pdf'
plot.fluss: no visible global function definition for 'dev.off'
plot.fluxes: no visible global function definition for 'dev.new'
plot.fluxes: no visible global function definition for 'devAskNewPage'
plot.fluxes: no visible global function definition for 'pdf'
plot.fluxes: no visible global function definition for 'dev.off'
plot.fluxxes: no visible global function definition for 'dev.new'
plot.fluxxes: no visible global function definition for 'devAskNewPage'
plot.fluxxes: no visible global function definition for 'pdf'
plot.fluxxes: no visible global function definition for 'dev.off'
reco.bulk : get.out: no visible global function definition for
  'boxplot.stats'
Undefined global functions or variables:
  boxplot.stats combn dev.new dev.off devAskNewPage pdf runsd
  write.table
Consider adding
  importFrom("grDevices", "boxplot.stats", "dev.new", "dev.off",
             "devAskNewPage", "pdf")
  importFrom("utils", "combn", "write.table")
to your NAMESPACE file.
BSOptionValue: no visible global function definition for 'pnorm'
ImpliedVol: no visible global function definition for 'uniroot'
callFMstable: no visible global function definition for 'integrate'
fitGivenQuantile: no visible global function definition for 'uniroot'
matchQuartiles: no visible global function definition for 'optim'
putFMstable: no visible global function definition for 'integrate'
standardStableQuantile: no visible global function definition for
  'qnorm'
tailsGstable: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate optim pnorm qnorm uniroot
Consider adding
  importFrom("stats", "integrate", "optim", "pnorm", "qnorm", "uniroot")
to your NAMESPACE file.
'library' or 'require' call to 'limma' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fmt.default: no visible global function definition for 'loessFit'
fmt.default: no visible global function definition for
  'trigammaInverse'
plot.fmt: no visible global function definition for 'par'
plot.fmt: no visible global function definition for 'plot'
plot.fmt: no visible global function definition for 'points'
Undefined global functions or variables:
  loessFit par plot points trigammaInverse
Consider adding
  importFrom("graphics", "par", "plot", "points")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'predict.foba':
  'predict.foba'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'library' or 'require' call to 'rgl' which was already attached by Depends.
  Please remove these calls from your code.
Package which this enhances but not available for checking: 'doMC'
Error in re-building vignettes:
  ...
Error: processing vignette 'JSS2008.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  'combinat' 'genetics'
  Please remove these calls from your code.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'forensic/R/zzz.R':
  .First.lib calls:
    cat("## Statistical Methods in Forensic Genetics \n")
    cat("## The work was supported by the project 1M06014 of the Ministry of \n        Education, Youth and Sports of the Czech Republic. \n")
    require(genetics, quietly = TRUE)
    require(combinat, quietly = TRUE)

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
ForImp: no visible global function definition for 'head'
ForImp: no visible global function definition for 'tail'
ForImp: no visible global function definition for 'dist'
medianimp: no visible global function definition for 'quantile'
rancatmat: no visible global function definition for 'runif'
transfmatcat: no visible global function definition for 'qnorm'
transfmatcat: no visible global function definition for 'sd'
Undefined global functions or variables:
  dist head qnorm quantile runif sd tail
Consider adding
  importFrom("stats", "dist", "qnorm", "quantile", "runif", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
INFCvpe: no visible binding for global variable 'INFCstats'
INFCvpe: no visible binding for global variable 'INFCdomain'
Undefined global functions or variables:
  INFCdomain INFCstats
Warning: no function found corresponding to methods exports from 'FormalSeries' for: 'initialize', 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
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.
&,fseries-numeric: no visible global function definition for 'new'
*,fseries-fseries: no visible global function definition for 'new'
*,fseries-numeric: no visible global function definition for 'new'
*,numeric-fseries: no visible global function definition for 'new'
+,fseries-fseries: no visible global function definition for 'new'
+,fseries-numeric: no visible global function definition for 'new'
+,numeric-fseries: no visible global function definition for 'new'
-,fseries-ANY: no visible global function definition for 'new'
-,fseries-numeric: no visible global function definition for 'new'
-,numeric-fseries: no visible global function definition for 'new'
/,fseries-numeric: no visible global function definition for 'new'
[<-,fseries-matrix-missing-matrix: no visible global function
  definition for 'new'
[<-,fseries-numeric-missing-numeric: no visible global function
  definition for 'new'
initialize,fseries: no visible global function definition for
  'validObject'
rfseries,numeric-numeric-numeric: no visible global function definition
  for 'runif'
rfseries,numeric-numeric-numeric: no visible global function definition
  for 'rbinom'
rfseries,numeric-numeric-numeric: no visible global function definition
  for 'new'
Undefined global functions or variables:
  new rbinom runif validObject
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "rbinom", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
ForwardSearch.fit: no visible global function definition for 'glm.fit'
ForwardSearch.plot: no visible global function definition for 'lines'
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for 'qnorm'
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for 'dnorm'
Undefined global functions or variables:
  dnorm glm.fit lines qnorm
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "dnorm", "glm.fit", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to 'shapefiles' which was already attached by Depends.
  Please remove these calls from your code.
dino.dist: no visible global function definition for 'as.dist'
earth.dist: no visible global function definition for 'as.dist'
ecol.dist: no visible global function definition for 'as.dist'
loc.map: no visible global function definition for 'points'
msn.map: no visible global function definition for 'points'
msn.map: no visible global function definition for 'lines'
mstlines: no visible global function definition for 'lines'
nmds.mst: no visible global function definition for 'lines'
rclust.null: no visible global function definition for 'sd'
sim.occ: no visible global function definition for 'rlnorm'
spp.est: no visible global function definition for 'sd'
Undefined global functions or variables:
  as.dist lines points rlnorm sd
Consider adding
  importFrom("graphics", "lines", "points")
  importFrom("stats", "as.dist", "rlnorm", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
GenObs: no visible global function definition for 'rnorm'
GenObs.T: no visible global function definition for 'rt'
MeasL: no visible global function definition for 'rbeta'
OutDet: no visible global function definition for 'median'
RanCur: no visible global function definition for 'rnorm'
init: no visible global function definition for 'prcomp'
Undefined global functions or variables:
  median prcomp rbeta rnorm rt
Consider adding
  importFrom("stats", "median", "prcomp", "rbeta", "rnorm", "rt")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'Rsocp' 'Rnlminb2' 'Rdonlp2'
confint.fracdiff: no visible global function definition for 'coef'
confint.fracdiff: no visible global function definition for 'qnorm'
fdGPH: no visible global function definition for 'na.fail'
fdGPH: no visible global function definition for 'as.ts'
fdGPH: no visible global function definition for 'lm'
fdGPH: no visible global function definition for 'coef'
fdGPH: no visible global function definition for 'resid'
fdSperio: no visible global function definition for 'na.fail'
fdSperio: no visible global function definition for 'as.ts'
fdSperio: no visible global function definition for 'lm'
fdSperio: no visible global function definition for 'coef'
fdSperio: no visible global function definition for 'resid'
fracdiff.sim: no visible binding for global variable 'rnorm'
logLik.fracdiff: no visible global function definition for 'coef'
print.fracdiff: no visible global function definition for 'coef'
print.summary.fracdiff: no visible global function definition for
  'printCoefmat'
print.summary.fracdiff: no visible global function definition for
  'symnum'
summary.fracdiff: no visible global function definition for 'coef'
summary.fracdiff: no visible global function definition for 'pnorm'
summary.fracdiff: no visible global function definition for 'logLik'
summary.fracdiff: no visible global function definition for 'AIC'
Undefined global functions or variables:
  AIC as.ts coef lm logLik na.fail pnorm printCoefmat qnorm resid rnorm
  symnum
Consider adding
  importFrom("stats", "AIC", "as.ts", "coef", "lm", "logLik", "na.fail",
             "pnorm", "printCoefmat", "qnorm", "resid", "rnorm",
             "symnum")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'pcaPP' 'snowFT' 'wavelets'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ComputeDCT2FFT: no visible global function definition for 'fft'
ComputeSemipgramFFT: no visible global function definition for 'fft'
WaveVarFD: no visible global function definition for 'modwt'
do.fd.estimate: no visible global function definition for
  'performParallel'
do.fd.estimate2d.simple: no visible global function definition for
  'median'
fd.Genton: no visible global function definition for 'qn'
fd.estimate.matrix: no visible global function definition for
  'performParallel'
fd.plot.legend: no visible global function definition for 'legend'
fd.plot.loglog: no visible global function definition for 'plot'
fd.plot.loglog: no visible global function definition for 'points'
fd.plot.loglog: no visible global function definition for 'abline'
summary.FractalDim: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline fft legend median modwt performParallel plot points qn sd
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points")
  importFrom("stats", "fft", "median", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'futile.any' 'futile.logger' 'quantmod' 'timeDate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'library' or 'require' calls to packages already attached by Depends:
  'CCP' 'MASS' 'calibrate' 'corpcor'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'CCP' 'MASS' 'calibrate' 'corpcor'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
custom.draw.circle: no visible global function definition for 'lines'
frcc: no visible binding for global variable 'sd'
frcc: no visible global function definition for 'cor.shrink'
frcc: no visible global function definition for 'cor'
frcc: no visible global function definition for 'p.asym'
generate_multivariate_normal_sample: no visible global function
  definition for 'mvrnorm'
plot_units: no visible binding for global variable 'sd'
plot_units: no visible global function definition for 'plot'
plot_units: no visible global function definition for 'points'
plot_units: no visible global function definition for 'textxy'
plot_variables: no visible global function definition for 'plot'
plot_variables: no visible global function definition for 'points'
plot_variables: no visible global function definition for 'textxy'
plot_variables: no visible global function definition for 'segments'
Undefined global functions or variables:
  cor cor.shrink lines mvrnorm p.asym plot points sd segments textxy
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
cv.work: no visible global function definition for 'predict'
fakedata: no visible global function definition for 'runif'
Undefined global functions or variables:
  predict runif
Consider adding
  importFrom("stats", "predict", "runif")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Package in Depends field not imported from: 'FrF2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'dggrids'
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   1.4Mb
Packages in Depends field not imported from:
  'Rmpfr' 'partitions'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Bell : nways: no visible global function definition for 'setparts'
Bell: no visible global function definition for 'restrictedparts'
CalIncLapInt : Deriv: no visible global function definition for 'D'
CalIncLapInt: no visible global function definition for 'is.whole'
CalIncLapInt: no visible global function definition for 'mpfr'
CalIncLapInt: no visible global function definition for 'chooseMpfr'
derivErfc : Deriv: no visible global function definition for 'D'
derivErfc : Erfc: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  D chooseMpfr is.whole mpfr pnorm restrictedparts setparts
Consider adding
  importFrom("stats", "D", "pnorm")
to your NAMESPACE file.
ROCscore: no visible global function definition for 'par'
ROCscore: no visible global function definition for 'axis'
ROCscore: no visible global function definition for 'mtext'
ROCscore: no visible global function definition for 'legend'
alphafrontier.2d: no visible global function definition for 'par'
alphafrontier.2d: no visible global function definition for 'polygon'
alphafrontier.2d: no visible global function definition for 'lines'
alphafrontier.2d: no visible global function definition for 'points'
alphafrontier.3d: no visible global function definition for 'layout'
alphafrontier.3d: no visible global function definition for 'barplot'
alphafrontier.3d: no visible global function definition for 'axis'
alphafrontier.3d: no visible global function definition for 'lines'
alphafrontier.3d: no visible global function definition for 'na.omit'
ordermfrontier.2d: no visible global function definition for 'par'
ordermfrontier.2d: no visible global function definition for 'polygon'
ordermfrontier.2d: no visible global function definition for 'lines'
ordermfrontier.2d: no visible global function definition for 'points'
ordermscore.boot: no visible global function definition for 'sd'
Undefined global functions or variables:
  axis barplot layout legend lines mtext na.omit par points polygon sd
Consider adding
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "points", "polygon")
  importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
prepare_Rd: frt.Rd:21: Dropping empty section \note
prepare_Rd: frt.paired.Rd:23: Dropping empty section \note
prepare_Rd: shoes.Rd:19: Dropping empty section \details
prepare_Rd: shoes.Rd:21-22: Dropping empty section \references
prepare_Rd: tomatoes.Rd:16: Dropping empty section \details
prepare_Rd: tomatoes.Rd:18: Dropping empty section \references
Error in re-building vignettes:
  ...
trying URL 'http://cmic.cs.ucl.ac.uk/camino//uploads/Tutorials/example_dwi.zip'
Content type 'application/zip' length 16129429 bytes (15.4 MB)
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downloaded 15.2 MB

Quitting from lines 39-44 (dti_data.Rmd) 
Error: processing vignette 'dti_data.Rmd' failed with diagnostics:
invalid 'description' argument
Execution halted
GNU make is a SystemRequirements.
'library' or 'require' calls to packages already attached by Depends:
  'Matrix' 'splines'
  Please remove these calls from your code.
prepare_Rd: baseline.Rd:123: Dropping empty section \examples
prepare_Rd: display.tests.Rd:43: Dropping empty section \references
prepare_Rd: display.tests.Rd:57: Dropping empty section \examples
prepare_Rd: extract.pars.Rd:114: Dropping empty section \examples
prepare_Rd: locate.peaks.Rd:72: Dropping empty section \examples
prepare_Rd: make.par.file.Rd:117: Dropping empty section \examples
prepare_Rd: run.all.Rd:76: Dropping empty section \examples
prepare_Rd: run.analysis.Rd:153: Dropping empty section \examples
prepare_Rd: run.baselines.Rd:91: Dropping empty section \examples
prepare_Rd: run.cluster.matrix.Rd:171: Dropping empty section \examples
prepare_Rd: run.lrg.peaks.Rd:95: Dropping empty section \examples
prepare_Rd: run.peaks.Rd:99: Dropping empty section \examples
prepare_Rd: run.strong.peaks.Rd:115: Dropping empty section \examples
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'Rcpp' 'snowfall'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fugeR.evo: no visible global function definition for 'runif'
fugeR.sfRun: no visible global function definition for 'sfInit'
fugeR.sfRun: no visible global function definition for 'sfLibrary'
fugeR.sfRun: no visible global function definition for 'sfExport'
fugeR.sfRun: no visible global function definition for 'sfLapply'
fugeR.sfRun: no visible global function definition for 'sfStop'
Undefined global functions or variables:
  runif sfExport sfInit sfLapply sfLibrary sfStop
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
Malformed Title field: should not end in a period.
mfpcaPlot: no visible global function definition for 'dev.new'
mfpcaPlot: no visible global function definition for 'par'
plotOC: no visible global function definition for 'dev.new'
plotfd: no visible global function definition for 'dev.new'
plotfd: no visible global function definition for 'plot'
Undefined global functions or variables:
  dev.new par plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "par", "plot")
to your NAMESPACE file.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Funclustering/makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
bic.generation: no visible global function definition for 'lm'
bic.generation: no visible global function definition for 'BIC'
bic.generation : <anonymous>: no visible global function definition for
  'lm'
bic.generation : <anonymous>: no visible global function definition for
  'BIC'
data.generation : <anonymous> : <anonymous>: no visible global function
  definition for 'sd'
Undefined global functions or variables:
  BIC lm sd
Consider adding
  importFrom("stats", "BIC", "lm", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
.FunFEM.main: no visible global function definition for 'kmeans'
.FunFEM.main: no visible global function definition for 'rmultinom'
.FunFEM.main: no visible global function definition for 'cutree'
.FunFEM.main: no visible global function definition for 'hclust'
.FunFEM.main: no visible global function definition for 'dist'
.FunFEM.main: no visible global function definition for 'par'
.FunFEM.main: no visible global function definition for 'plot'
.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov cutree dist hclust kmeans par plot rmultinom
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "cov", "cutree", "dist", "hclust", "kmeans",
             "rmultinom")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RUnit' 'futile.options'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.validateGuardExpression: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      1.5Mb
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable 'nn'
Undefined global functions or variables:
  nn
NeedsCompilation field must take value 'yes' or 'no'
'library' or 'require' call to 'splines' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gensurf: no visible global function definition for 'persp'
gensurf: no visible global function definition for 'rainbow'
plotMF: no visible global function definition for 'plot.new'
plotMF: no visible global function definition for 'plot.window'
plotMF: no visible global function definition for 'runif'
plotMF: no visible global function definition for 'predict'
plotMF: no visible global function definition for 'interpSpline'
plotMF: no visible global function definition for 'lines'
plotMF: no visible global function definition for 'text'
plotMF: no visible global function definition for 'title'
plotMF: no visible global function definition for 'axis'
plotMF: no visible global function definition for 'box'
Undefined global functions or variables:
  axis box interpSpline lines persp plot.new plot.window predict
  rainbow runif text title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "persp", "plot.new",
             "plot.window", "text", "title")
  importFrom("stats", "predict", "runif")
to your NAMESPACE file.
alpha: no visible global function definition for 'var'
coefH: no visible global function definition for 'var'
coefZ: no visible global function definition for 'var'
coefZ: no visible binding for global variable 'var'
fs.MSA: no visible global function definition for 'runif'
fs.MSA: no visible global function definition for 'boxplot'
plot.fs.class: no visible global function definition for 'lines'
plot.fs.class: no visible global function definition for 'text'
plot.fs.class: no visible global function definition for 'axis'
plot.fs.class: no visible global function definition for 'segments'
plot.fs.class: no visible global function definition for 'title'
plot.fs.class: no visible global function definition for
  'devAskNewPage'
plot.fs.class : <anonymous>: no visible global function definition for
  'quantile'
plot.fs.n1.class: no visible global function definition for 'segments'
plot.fs.n1.class: no visible global function definition for 'axis'
plot.fs.n1.class: no visible global function definition for 'lines'
plot.fs.n1.class: no visible global function definition for 'legend'
search.normal: no visible global function definition for 'var'
search.normal: no visible binding for global variable 'var'
search.normal: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  axis boxplot devAskNewPage legend lines qnorm quantile runif segments
  text title var
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "axis", "boxplot", "legend", "lines",
             "segments", "text", "title")
  importFrom("stats", "qnorm", "quantile", "runif", "var")
to your NAMESPACE file.
'library' or 'require' call to 'foreach' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fxreturns: no visible binding for global variable 'FXRatesCHF'
fxreturns : <anonymous>: no visible global function definition for
  'tail'
gbreakpoints: no visible global function definition for '%dopar%'
gbreakpoints: no visible global function definition for 'foreach'
Undefined global functions or variables:
  %dopar% FXRatesCHF foreach tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'MASS' 'igraph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DBNScoreStep1: no visible global function definition for 'lm'
DBNScoreStep1: no visible global function definition for 'rlm'
DBNScoreStep1: no visible global function definition for 'pt'
DBNScoreStep2: no visible global function definition for 'lm'
DBNScoreStep2: no visible global function definition for 'rlm'
DBNScoreStep2: no visible global function definition for 'pt'
SimulGeneExpressionAR1: no visible global function definition for
  'rnorm'
SimulGeneExpressionAR1: no visible global function definition for 'ts'
SimulNetworkAdjMatrix: no visible global function definition for
  'runif'
Undefined global functions or variables:
  lm pt rlm rnorm runif ts
Consider adding
  importFrom("stats", "lm", "pt", "rnorm", "runif", "ts")
to your NAMESPACE file.
crossover: no visible global function definition for 'runif'
exchangeSols: no visible global function definition for 'runif'
fps: no visible global function definition for 'runif'
mutation: no visible global function definition for 'runif'
plotBicluster: no visible global function definition for 'gray'
plotBicluster: no visible global function definition for 'heatmap'
reproduction: no visible global function definition for 'runif'
Undefined global functions or variables:
  gray heatmap runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "heatmap", "runif")
to your NAMESPACE file.
FPTsimul: no visible global function definition for 'runif'
histplot: no visible global function definition for 'dev.new'
histplot: no visible global function definition for 'hist'
histplot: no visible global function definition for 'par'
histplot: no visible global function definition for 'plot'
histplot: no visible global function definition for 'legend'
mdt: no visible binding for global variable 'deltat'
plot.FPTdensity: no visible global function definition for 'dev.new'
plot.FPTdensity: no visible global function definition for 'plot'
res_summary: no visible global function definition for 'write.table'
res_summary: no visible global function definition for 'sd'
res_summary: no visible global function definition for 'median'
vdt: no visible binding for global variable 'deltat'
Undefined global functions or variables:
  deltat dev.new hist legend median par plot runif sd write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "legend", "par", "plot")
  importFrom("stats", "deltat", "median", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CI.RMSEA: no visible global function definition for 'qchisq'
CI.RMSEA: no visible global function definition for 'pchisq'
GAIPE.RMSEA: no visible global function definition for 'par'
GAIPE.RMSEA: no visible global function definition for 'plot'
GAIPE.RMSEA: no visible global function definition for 'abline'
GAIPE.RMSEA: no visible global function definition for 'colors'
GAIPE.RMSEA: no visible global function definition for 'text'
GAIPE.RMSEA: no visible global function definition for 'arrows'
GAIPE.RMSEA: no visible global function definition for 'points'
GAIPE.RMSEA: no visible global function definition for 'axis'
GAIPE.RMSEA: no visible global function definition for 'lines'
GAIPE.RMSEA: no visible global function definition for 'legend'
GAIPE.RMSEA: no visible global function definition for 'pchisq'
GAIPE.RMSEA: no visible global function definition for 'qchisq'
GAIPE.RMSEA: no visible global function definition for 'mtext'
GAIPE.RMSEA: no visible global function definition for 'title'
PA.RMSEA: no visible global function definition for 'pchisq'
PA.RMSEA: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  abline arrows axis colors legend lines mtext par pchisq plot points
  qchisq text title
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "par", "plot", "points", "text", "title")
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
cvriskMSM: no visible global function definition for 'predict'
plotcvriskMSM: no visible global function definition for 'plot'
plotcvriskMSM: no visible binding for global variable 'lines'
plotcvriskMSM: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot predict
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  'parallel' 'snowfall'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Matrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GAMBoost: no visible global function definition for 'binomial'
GAMBoost: no visible global function definition for 'gaussian'
GAMBoost: no visible global function definition for 'poisson'
GAMBoost: no visible binding for global variable 'sd'
GAMBoost: no visible global function definition for 'Matrix'
calc.confidence.bands: no visible global function definition for
  'predict'
cv.GAMBoost: no visible global function definition for 'binomial'
cv.GAMBoost : eval.fold: no visible global function definition for
  'predict'
cv.GAMBoost: no visible global function definition for 'mclapply'
cv.GAMBoost: no visible binding for global variable 'var'
estimPVal: no visible global function definition for 'mclapply'
plot.GAMBoost: no visible global function definition for 'plot'
plot.GAMBoost: no visible global function definition for 'lines'
Undefined global functions or variables:
  Matrix binomial gaussian lines mclapply plot poisson predict sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "binomial", "gaussian", "poisson", "predict", "sd",
             "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'gamlss'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'gamlss:::.gamlss.bi.list'
  See the note in ?`:::` about the use of this operator.
finterp.data.frame: no visible global function definition for
  'as.formula'
finterp.data.frame: no visible global function definition for 'terms'
finterp.data.frame: no visible global function definition for
  'model.matrix'
finterp.data.frame: no visible global function definition for
  'model.frame'
finterp.default: no visible global function definition for 'terms'
finterp.default: no visible global function definition for
  'model.matrix'
finterp.default: no visible global function definition for
  'model.frame'
gamlss.nl: no visible global function definition for 'nlm'
nl: no visible global function definition for 'is'
nlgamlss: no visible global function definition for 'NO'
nlgamlss: no visible global function definition for 'as.gamlss.family'
nlgamlss: no visible global function definition for 'nlm'
nlgamlss: no visible global function definition for 'cov2cor'
summary.nlgamlss: no visible global function definition for 'coef'
summary.nlgamlss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
gammahetero1: no visible global function definition for 'terms'
gammahetero1: no visible global function definition for 'model.matrix'
gammahetero1: no visible global function definition for 'glm.fit'
gammahetero1: no visible global function definition for 'Gamma'
gammahetero1: no visible global function definition for 'qt'
gammahetero2: no visible global function definition for 'terms'
gammahetero2: no visible global function definition for 'model.matrix'
gammahetero2: no visible global function definition for 'glm.fit'
gammahetero2: no visible global function definition for 'Gamma'
gammahetero2: no visible global function definition for 'qt'
print.summary.Gammareg: no visible global function definition for
  'printCoefmat'
summary.Gammareg: no visible global function definition for 'coef'
Undefined global functions or variables:
  Gamma coef glm.fit model.matrix printCoefmat qt terms
Consider adding
  importFrom("stats", "Gamma", "coef", "glm.fit", "model.matrix",
             "printCoefmat", "qt", "terms")
to your NAMESPACE file.
Package in Depends field not imported from: 'GANPAdata'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
prepare_Rd: GANPA-package.Rd:30: Dropping empty section \seealso
prepare_Rd: GANPA-package.Rd:31: Dropping empty section \examples
prepare_Rd: GSE.Test.Main.Rd:24: Dropping empty section \details
prepare_Rd: GSE.Test.Main.Rd:32: Dropping empty section \note
prepare_Rd: GSE.Test.Main.Rd:33: Dropping empty section \seealso
prepare_Rd: weight.gsets.test.Rd:14: Dropping empty section \details
prepare_Rd: weight.gsets.test.Rd:25: Dropping empty section \note
prepare_Rd: weight.gsets.with.msprot.Rd:17: Dropping empty section \details
prepare_Rd: weight.gsets.with.msprot.Rd:27: Dropping empty section \note
prepare_Rd: weight.gsets.with.msprot.Rd:31: Dropping empty section \examples
Checking should be performed on sources prepared by 'R CMD build'.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
'library' or 'require' call to 'orthopolynom' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'orthopolynom' 'polynom'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
contindic.gb2: no visible global function definition for 'contour'
contindic.gb2: no visible global function definition for 'box'
contindic.gb2: no visible global function definition for 'mtext'
contprof.gb2: no visible global function definition for 'image'
contprof.gb2: no visible global function definition for 'heat.colors'
contprof.gb2: no visible global function definition for 'contour'
contprof.gb2: no visible global function definition for 'text'
contprof.gb2: no visible global function definition for 'box'
dplot.cavgb2: no visible global function definition for 'par'
dplot.cavgb2: no visible global function definition for 'curve'
dplot.cavgb2: no visible global function definition for 'legend'
dplot.cavgb2: no visible global function definition for 'plot'
dplot.cavgb2: no visible global function definition for 'lines'
dplot.cgb2: no visible global function definition for 'curve'
dplot.cgb2: no visible global function definition for 'lines'
dplot.cgb2: no visible global function definition for 'legend'
plotsML.gb2: no visible global function definition for 'par'
plotsML.gb2: no visible global function definition for 'plot'
plotsML.gb2: no visible global function definition for 'abline'
plotsML.gb2: no visible global function definition for 'curve'
plotsML.gb2: no visible global function definition for 'legend'
saveplot : <local>: no visible global function definition for 'dev.set'
saveplot : <local>: no visible global function definition for
  'dev.print'
saveplot : <local>: no visible binding for global variable 'pdf'
Undefined global functions or variables:
  abline box contour curve dev.print dev.set heat.colors image legend
  lines mtext par pdf plot text
Consider adding
  importFrom("grDevices", "dev.print", "dev.set", "heat.colors", "pdf")
  importFrom("graphics", "abline", "box", "contour", "curve", "image",
             "legend", "lines", "mtext", "par", "plot", "text")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.8Mb
GNU make is a SystemRequirements.
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'tools:::.Rd_get_argument_names' 'tools:::RdTags' 'tools:::fetchRdDB'
  See the note in ?`:::` about the use of this operator.
coeplot: no visible global function definition for 'plot'
coeplot: no visible global function definition for 'axis'
coeplot: no visible global function definition for 'lines'
coeplot: no visible global function definition for 'title'
coeplot: no visible global function definition for 'legend'
corplot: no visible global function definition for 'par'
corplot: no visible global function definition for 'pairs'
corplot: no visible global function definition for 'strwidth'
lm.estimate: no visible global function definition for 'as.formula'
lm.estimate: no visible global function definition for 'glm'
panel.cor: no visible global function definition for 'par'
panel.cor: no visible global function definition for 'cor'
panel.cor: no visible global function definition for 'strwidth'
panel.cor: no visible global function definition for 'text'
panel.smooth.r: no visible global function definition for 'par'
panel.smooth.r: no visible global function definition for 'points'
panel.smooth.r: no visible global function definition for 'lines'
posplot: no visible global function definition for 'par'
posplot: no visible global function definition for 'barplot'
posplot: no visible global function definition for 'plot'
posplot: no visible global function definition for 'points'
Undefined global functions or variables:
  as.formula axis barplot cor glm legend lines pairs par plot points
  strwidth text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "pairs",
             "par", "plot", "points", "strwidth", "text", "title")
  importFrom("stats", "as.formula", "cor", "glm")
to your NAMESPACE file.
gcat.test: no visible global function definition for 'pnorm'
generate_sub: no visible global function definition for 'runif'
pfcn: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm runif
Consider adding
  importFrom("stats", "pnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DownloadGdelt: no visible global function definition for
  'packageVersion'
DownloadGdelt: no visible global function definition for
  'download.file'
GdeltZipToDataframe: no visible global function definition for
  'read.delim'
GdeltZipToDataframe: no visible global function definition for 'unzip'
GetSizeOfGDELT: no visible global function definition for 'read.delim'
IsValidGDELT: no visible global function definition for 'read.delim'
IsValidGDELT: no visible global function definition for 'md5sum'
NormEventCounts: no visible global function definition for
  'download.file'
NormEventCounts: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  download.file md5sum packageVersion read.csv read.delim unzip
Consider adding
  importFrom("utils", "download.file", "packageVersion", "read.csv",
             "read.delim", "unzip")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
plot.rbga: no visible global function definition for 'par'
plot.rbga: no visible global function definition for 'hist'
plot.rbga: no visible global function definition for 'plot'
plot.rbga: no visible global function definition for 'lines'
rbga: no visible global function definition for 'runif'
rbga: no visible global function definition for 'dnorm'
rbga.bin: no visible global function definition for 'dnorm'
rbga.bin: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm hist lines par plot runif
Consider adding
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
clopper.pearson.ci: no visible global function definition for 'qbeta'
cm.clopper.pearson.ci: no visible global function definition for
  'uniroot'
cm.clopper.pearson.ci : <anonymous>: no visible global function
  definition for 'pbeta'
cm.n.clopper.pearson: no visible global function definition for
  'uniroot'
cm.n.clopper.pearson : <anonymous>: no visible global function
  definition for 'pbeta'
n.clopper.pearson: no visible global function definition for 'uniroot'
n.clopper.pearson : <anonymous>: no visible global function definition
  for 'pbeta'
rgbinom: no visible global function definition for 'runif'
Undefined global functions or variables:
  pbeta qbeta runif uniroot
Consider adding
  importFrom("stats", "pbeta", "qbeta", "runif", "uniroot")
to your NAMESPACE file.
genmvnorm: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'genderdata'
File
  LICENSE
is not mentioned in the DESCRIPTION file.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
gPopCreate: no visible global function definition for 'rnorm'
periodogram.freq: no visible global function definition for 'spectrum'
periodogram.freq: no visible global function definition for 'frequency'
periodogram.spec.single: no visible global function definition for
  'spectrum'
periodogram.spec.single: no visible global function definition for
  'fft'
robust.g.test: no visible global function definition for 'read.table'
robust.g.test: no visible global function definition for 'density'
robust.spectrum: no visible global function definition for 'density'
robust.spectrum.single: no visible global function definition for 'fft'
spearman: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor density fft frequency read.table rnorm spectrum
Consider adding
  importFrom("stats", "cor", "density", "fft", "frequency", "rnorm",
             "spectrum")
  importFrom("utils", "read.table")
to your NAMESPACE file.
t1p1: no visible global function definition for 'var'
t1p1: no visible global function definition for 'pt'
t1p2: no visible global function definition for 'pt'
Undefined global functions or variables:
  pt var
Consider adding
  importFrom("stats", "pt", "var")
to your NAMESPACE file.
load.genelist: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
Package suggested but not available for checking: 'RHugin'
fit.dbn: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   1.6Mb
'library' or 'require' calls to packages already attached by Depends:
  'igraph' 'splines'
  Please remove these calls from your code.
timedelay.lm: no visible global function definition for 'lm'
timedelay.lm: no visible global function definition for 'AIC'
timedelay.lm: no visible global function definition for 'pdf'
timedelay.lm: no visible global function definition for 'x11'
timedelay.lm: no visible global function definition for 'rainbow'
timedelay.lm: no visible global function definition for 'title'
timedelay.lm: no visible global function definition for 'lines'
timedelay.lm: no visible global function definition for 'predict'
timedelay.lm: no visible global function definition for 'points'
timedelay.lm: no visible global function definition for 'legend'
timedelay.lm: no visible global function definition for 'dev.off'
timedelay.univariate.lm: no visible global function definition for 'lm'
timedelay.univariate.lm: no visible global function definition for
  'AIC'
ts.bspline: no visible global function definition for 'lm'
ts.bspline: no visible global function definition for 'predict'
Undefined global functions or variables:
  AIC dev.off legend lines lm pdf points predict rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow", "x11")
  importFrom("graphics", "legend", "lines", "points", "title")
  importFrom("stats", "AIC", "lm", "predict")
to your NAMESPACE file.
prepare_Rd: GeneReg-package.Rd:12-13: Dropping empty section \usage
prepare_Rd: GeneReg-package.Rd:14-15: Dropping empty section \arguments
Package in Depends field not imported from: 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
S3 methods shown with full name in documentation object 'diseq':
  'diseq.ci'

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.
ForImp.Mahala: no visible global function definition for 'combn'
ForImp.Mahala: no visible global function definition for 'var'
ForImp.Mahala: no visible global function definition for 'quantile'
ForImp.Mahala : <anonymous>: no visible global function definition for
  'var'
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for 'var'
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for 'quantile'
ForImp.PCA: no visible global function definition for 'cov'
ForImp.PCA: no visible global function definition for 'princomp'
ForImp.PCA: no visible global function definition for 'combn'
ForImp.PCA: no visible global function definition for 'quantile'
ForImp.PCA : <anonymous> : <anonymous>: no visible global function
  definition for 'quantile'
Undefined global functions or variables:
  combn cov princomp quantile var
Consider adding
  importFrom("stats", "cov", "princomp", "quantile", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'KernSmooth'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KernSec: no visible global function definition for 'na.omit'
KernSur: no visible global function definition for 'na.fail'
KernSur: no visible global function definition for 'na.omit'
bandwidthselect: no visible global function definition for 'na.omit'
bandwidthselect: no visible global function definition for 'dpik'
correlationselect: no visible global function definition for 'cor'
nearest: no visible global function definition for 'na.fail'
nearest: no visible global function definition for 'na.omit'
per: no visible global function definition for 'na.fail'
Undefined global functions or variables:
  cor dpik na.fail na.omit
Consider adding
  importFrom("stats", "cor", "na.fail", "na.omit")
to your NAMESPACE file.
MOSS_GWAS: no visible global function definition for 'complete.cases'
MOSS_GWAS_main: no visible global function definition for 'rbinom'
MOSS_GWAS_main: no visible global function definition for 'na.omit'
MOSS_GWAS_main: no visible global function definition for 'glm'
MOSS_GWAS_main: no visible global function definition for 'poisson'
MOSS_Hierarchical: no visible global function definition for
  'as.formula'
MOSS_Hierarchical: no visible global function definition for 'rbinom'
cvFunc: no visible global function definition for 'na.omit'
findDualGenerators: no visible global function definition for 'na.omit'
findGenerators: no visible global function definition for 'na.omit'
findLogMargLik: no visible global function definition for 'na.omit'
findModel: no visible global function definition for 'as.formula'
findNeighbours: no visible global function definition for 'na.omit'
fitInteractionModels: no visible global function definition for
  'na.omit'
fitInteractionModels: no visible global function definition for 'glm'
fitInteractionModels: no visible global function definition for
  'poisson'
getSubsets: no visible global function definition for 'na.omit'
logLaplace: no visible global function definition for 'as.formula'
logLaplace: no visible global function definition for 'model.matrix'
logLaplace: no visible global function definition for 'glm'
logLaplace: no visible global function definition for 'poisson'
mWindow: no visible global function definition for 'complete.cases'
prettyFormula: no visible global function definition for 'na.omit'
randomHierModel: no visible global function definition for 'rbinom'
recode_data: no visible global function definition for 'complete.cases'
Undefined global functions or variables:
  as.formula complete.cases glm model.matrix na.omit poisson rbinom
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "glm",
             "model.matrix", "na.omit", "poisson", "rbinom")
to your NAMESPACE file.
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.
ab.create: no visible global function definition for 'new'
ab.predict: no visible binding for global variable 'predict'
gensemble: no visible global function definition for 'new'
perturb: no visible global function definition for 'rnorm'
pred_error: no visible global function definition for 'na.omit'
reg_iter_summary: no visible global function definition for 'var'
reg_iter_summary: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor na.omit new predict rnorm var
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "cor", "na.omit", "predict", "rnorm", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
splineAnalyze: no visible global function definition for 'var'
splineAnalyze: no visible global function definition for 'par'
splineAnalyze: no visible global function definition for 'plot'
splineAnalyze: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines par plot var
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "var")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.2Mb
PAEA : <anonymous>: no visible global function definition for
  'integrate'
PAEAAnalysis: no visible global function definition for
  'txtProgressBar'
PAEAAnalysis : <anonymous>: no visible global function definition for
  'setTxtProgressBar'
PAEAAnalysis: no visible global function definition for 'par'
PAEAAnalysis: no visible global function definition for 'barplot'
chdirSig: no visible global function definition for 'prcomp'
chdirSig: no visible global function definition for 'rchisq'
chdirSig: no visible global function definition for 'txtProgressBar'
chdirSig : <anonymous> : <anonymous>: no visible global function
  definition for 'setTxtProgressBar'
chdirplots : <anonymous>: no visible global function definition for
  'par'
chdirplots : <anonymous>: no visible global function definition for
  'plot'
chdirplots : <anonymous>: no visible global function definition for
  'arrows'
chdirplots : <anonymous>: no visible global function definition for
  'barplot'
multigmtPAEAAnalysis: no visible global function definition for
  'txtProgressBar'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'setTxtProgressBar'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'data'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'write.table'
Undefined global functions or variables:
  arrows barplot data integrate par plot prcomp rchisq
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("graphics", "arrows", "barplot", "par", "plot")
  importFrom("stats", "integrate", "prcomp", "rchisq")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
SimTangleData: no visible global function definition for 'runif'
SimTangleData: no visible global function definition for 'dist'
SimTangleData: no visible global function definition for 'rnorm'
SimTangleData: no visible global function definition for 'qgamma'
SimTangleData: no visible global function definition for 'pnorm'
SimTangleData: no visible global function definition for 'rmultinom'
TangleInference: no visible global function definition for 'rnorm'
TangleInferenceGauss : thetaOpt: no visible global function definition
  for 'dist'
TangleInferenceGauss : thetaOpt: no visible global function definition
  for 'optim'
TangleInferenceGauss : predError: no visible global function definition
  for 'dist'
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R         5.0Mb
    extdata   1.3Mb
Malformed Description field: should contain one or more complete sentences.
getJson: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
geoscaleBox: no visible global function definition for 'boxplot'
geoscaleBox: no visible global function definition for 'par'
geoscaleBox: no visible global function definition for 'plot'
geoscaleBox: no visible global function definition for 'text'
geoscaleBox: no visible global function definition for 'segments'
geoscaleBox: no visible global function definition for 'rect'
geoscaleBox: no visible global function definition for 'rgb'
geoscaleBox: no visible global function definition for 'polygon'
geoscaleBox: no visible global function definition for 'points'
geoscaleBox: no visible global function definition for 'axis'
geoscalePlot: no visible global function definition for 'par'
geoscalePlot: no visible global function definition for 'plot'
geoscalePlot: no visible global function definition for 'text'
geoscalePlot: no visible global function definition for 'segments'
geoscalePlot: no visible global function definition for 'rect'
geoscalePlot: no visible global function definition for 'rgb'
geoscalePlot: no visible global function definition for 'points'
geoscalePlot: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis boxplot par plot points polygon rect rgb segments text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "boxplot", "par", "plot", "points",
             "polygon", "rect", "segments", "text")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
ImagePoly: no visible global function definition for 'plot'
performSinglePlot: no visible global function definition for
  'heat.colors'
Undefined global functions or variables:
  heat.colors plot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Malformed Description field: should contain one or more complete sentences.
GESTr: no visible global function definition for 'rnorm'
GESTr: no visible global function definition for 'sd'
GESTr : <anonymous>: no visible global function definition for 'pnorm'
TranSAM : magChange: no visible global function definition for 'median'
TranSAM : dstat: no visible global function definition for 'sd'
TranSAM: no visible binding for global variable 'sd'
TranSAM: no visible global function definition for 'quantile'
findReplicateGroups: no visible global function definition for 'qnorm'
findReplicateGroups: no visible global function definition for 'sd'
fitGMM : simulateData: no visible global function definition for
  'rnorm'
fitGMM : simulateData: no visible global function definition for 'sd'
fitGMM: no visible global function definition for 'median'
fitGMM: no visible global function definition for 'ks.test'
fitRockeDurbin: no visible global function definition for 'dist'
fitRockeDurbin : findLowGenes: no visible global function definition
  for 'median'
fitRockeDurbin : findLowGenes: no visible global function definition
  for 'mad'
fitRockeDurbin: no visible binding for global variable 'sd'
getMonotonicConfidences_multiclass: no visible global function
  definition for 'pnorm'
getMonotonicConfidences_multiclass: no visible global function
  definition for 'sd'
Undefined global functions or variables:
  dist ks.test mad median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "dist", "ks.test", "mad", "median", "pnorm",
             "qnorm", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 99-112 (gitrd-vignette-introduction.Rmd) 
Error: processing vignette 'gitrd-vignette-introduction.Rmd' failed with diagnostics:
cannot open URL 'http://www.rad.cvm.gov.br/enetconsulta/frmDownloadDocumento.aspx?CodigoInstituicao=2&NumeroSequencialDocumento=2114'
Execution halted
'library' or 'require' call to 'party' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'party'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gTree: no visible global function definition for 'ctree'
gTree: no visible global function definition for 'ctree_control'
guttmanErrors: no visible global function definition for 'runif'
Undefined global functions or variables:
  ctree ctree_control runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Missing or unexported object: 'stable::dstable.quick'
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'multtest' which was already attached by Depends.
  Please remove these calls from your code.
Error in re-building vignettes:
  ...
Warning: Ignoring unknown parameters: image_colour
Quitting from lines 35-54 (ggimage.Rmd) 
Error: processing vignette 'ggimage.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10015 milliseconds with 0 out of 0 bytes received
Execution halted
Running examples in 'ggmap-Ex.R' failed
The error most likely occurred in:

> ### Name: get_map
> ### Title: Grab a map.
> ### Aliases: get_map
> 
> ### ** Examples
> 
> map <- get_map()
Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=29.763284,-95.363271&zoom=10&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Error in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") : 
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=29.763284,-95.363271&zoom=10&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
Calls: get_map -> get_googlemap -> download.file
Execution halted
Package has no Sweave vignette sources and no VignetteBuilder field.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.7Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggrasp.Rcheck/00install.out' for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'ggplot2'
A package should be listed in only one of these fields.
Package in Depends field not imported from: 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ggroc: no visible global function definition for 'ggplot'
ggroc: no visible global function definition for 'aes'
ggroc: no visible global function definition for 'geom_point'
ggroc: no visible global function definition for 'geom_line'
ggroc: no visible global function definition for 'theme'
ggroc: no visible global function definition for 'element_text'
ggroc: no visible global function definition for 'labs'
ggroc: no visible global function definition for 'ggsave'
Undefined global functions or variables:
  aes element_text geom_line geom_point ggplot ggsave labs theme
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.3Mb
Namespace with empty importFrom: 'statmod'
Malformed Title field: should not end in a period.
acovamcmc: no visible global function definition for 'rnorm'
acovamcmc: no visible global function definition for 'rgamma'
acovamcmc: no visible binding for global variable 'quantile'
acovamcmc: no visible global function definition for 'quantile'
acovamcmc: no visible global function definition for 'var'
plot.acovamcmc: no visible global function definition for 'dev.new'
plot.acovamcmc: no visible global function definition for 'par'
plot.acovamcmc: no visible global function definition for 'plot'
plot.acovamcmc: no visible global function definition for 'density'
plot.acovamcmc: no visible global function definition for 'acf'
plot.acovamcmc: no visible global function definition for 'contour'
plot.acovamcmc: no visible global function definition for 'image'
plot.acovamcmc: no visible global function definition for 'persp'
Undefined global functions or variables:
  acf contour density dev.new image par persp plot quantile rgamma
  rnorm var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "contour", "image", "par", "persp", "plot")
  importFrom("stats", "acf", "density", "quantile", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'gibbs.met/R/firstlib.R':
  .First.lib calls:
    cat("Naive Gibbs Sampling with Metropolis steps(gibbs.met) loaded\n",     "COPYRIGHT 2008 (c) Longhai Li (http://math.usask.ca/~longhai)\n",     "Type ?begin.gibbs.met for help to this package\n", sep = "")

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

met_gaussian : one_transition: no visible global function definition
  for 'rnorm'
met_gaussian : one_transition: no visible global function definition
  for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
ssa.btl: no visible global function definition for 'rbinom'
ssa.btl: no visible global function definition for 'rpois'
ssa.btl.diag: no visible global function definition for 'rbinom'
ssa.btl.diag: no visible global function definition for 'rpois'
ssa.d: no visible global function definition for 'runif'
ssa.d.diag: no visible global function definition for 'runif'
ssa.etl: no visible global function definition for 'rpois'
ssa.etl.diag: no visible global function definition for 'rpois'
ssa.otl: no visible global function definition for 'runif'
ssa.otl: no visible global function definition for 'rpois'
ssa.otl.diag: no visible global function definition for 'runif'
ssa.otl.diag: no visible global function definition for 'rpois'
ssa.plot: no visible global function definition for 'rainbow'
ssa.plot: no visible global function definition for 'matplot'
ssa.plot: no visible global function definition for 'title'
ssa.plot: no visible global function definition for 'legend'
ssa.plot: no visible global function definition for 'mtext'
ssa.run: no visible global function definition for 'flush.console'
ssa.terminate: no visible global function definition for 'sd'
Undefined global functions or variables:
  flush.console legend matplot mtext rainbow rbinom rpois runif sd
  title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "mtext", "title")
  importFrom("stats", "rbinom", "rpois", "runif", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
choro.legend: no visible global function definition for 'strwidth'
choro.legend: no visible global function definition for 'legend'
choro.legend: no visible global function definition for 'text'
jitter.points: no visible global function definition for 'rnorm'
level.plot: no visible global function definition for '.filled.contour'
map.scale: no visible global function definition for 'par'
map.scale: no visible global function definition for 'rect'
map.scale: no visible global function definition for 'lines'
map.scale: no visible global function definition for 'text'
map.scale: no visible global function definition for 'strheight'
north.arrow: no visible global function definition for 'polygon'
north.arrow: no visible global function definition for 'text'
north.arrow: no visible global function definition for 'strheight'
poly.labels: no visible global function definition for 'slot'
poly.labels : <anonymous>: no visible global function definition for
  'slot'
quantileCuts: no visible global function definition for 'quantile'
sdCuts: no visible global function definition for 'sd'
Undefined global functions or variables:
  .filled.contour legend lines par polygon quantile rect rnorm sd slot
  strheight strwidth text
Consider adding
  importFrom("graphics", ".filled.contour", "legend", "lines", "par",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("methods", "slot")
  importFrom("stats", "quantile", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice'
A package should be listed in only one of these fields.
Package in Depends field not imported from: 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'lattice:::latticeParseFormula'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'lattice:::compute.packet' 'lattice:::cond.orders'
  'lattice:::construct.scales' 'lattice:::cupdate'
  'lattice:::limits.and.aspect' 'lattice:::logLimits'
  'lattice:::needAutoKey' 'lattice:::prepanel.null'
  'lattice:::scale.limits' 'lattice:::trellis.skeleton'
  'lattice:::updateList'
  See the note in ?`:::` about the use of this operator.
panel.pyramid: no visible global function definition for
  'trellis.par.get'
panel.pyramid: no visible global function definition for
  'current.panel.limits'
panel.pyramid: no visible global function definition for 'panel.abline'
panel.pyramid: no visible global function definition for 'panel.rect'
pyramid2.formula: no visible global function definition for
  'lattice.getOption'
pyramid2.formula: no visible global function definition for
  'is.shingle'
pyramid2.formula: no visible global function definition for
  'as.factorOrShingle'
pyramidlattice: no visible global function definition for 'update'
useOuterStrips2: no visible global function definition for 'modifyList'
useOuterStrips2 : new.strip: no visible global function definition for
  'strip.default'
useOuterStrips2 : new.strip.left: no visible global function definition
  for 'strip.default'
useOuterStrips2: no visible global function definition for 'update'
Undefined global functions or variables:
  as.factorOrShingle current.panel.limits is.shingle lattice.getOption
  modifyList panel.abline panel.rect strip.default trellis.par.get
  update
Consider adding
  importFrom("stats", "update")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
fptcdf: no visible global function definition for 'dnorm'
fptcdf: no visible global function definition for 'pnorm'
fptpdf: no visible global function definition for 'pnorm'
fptpdf: no visible global function definition for 'dnorm'
lba: no visible global function definition for 'as.formula'
lba: no visible global function definition for 'model.frame'
lba : logl: no visible global function definition for 'head'
lba: no visible global function definition for 'optim'
pmod: no visible global function definition for 'model.frame'
pmod: no visible global function definition for 'model.matrix'
rlba: no visible global function definition for 'pnorm'
rlba: no visible global function definition for 'rnorm'
rlba: no visible global function definition for 'runif'
tablba: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula dnorm head model.frame model.matrix optim pnorm rnorm
  runif
Consider adding
  importFrom("stats", "as.formula", "dnorm", "model.frame",
             "model.matrix", "optim", "pnorm", "rnorm", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
anova.gllm: no visible global function definition for 'pchisq'
emgllm: no visible global function definition for 'model.matrix'
print.ld2: no visible global function definition for 'anova'
scoregllm: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  anova model.matrix pchisq
Consider adding
  importFrom("stats", "anova", "model.matrix", "pchisq")
to your NAMESPACE file.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
Authors@R field gives persons with no role:
  Mark S.
        Handcock Developer <handcock@stat.ucla.edu>
  Michael S.
        Rendall Developer <mrendall@rand.org>
Package in Depends field not imported from: 'emplik'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Calls with DUP:
   .C("gaulep", as.double(x), as.double(y), as.double(ls[i]), as.double(kappa), 
       as.double(tol), as.integer(max.ite), as.integer(n), as.integer(p), 
       as.double(beta0), DUP = FALSE)
   .C("binlep", as.double(x), as.double(y), as.double(ls[i]), as.double(kappa), 
       as.double(tol), as.integer(max.ite), as.integer(n), as.integer(p), 
       as.double(beta0), DUP = FALSE)
   .C("gaulep", as.double(train.x), as.double(train.y), as.double(ls[i]), 
       as.double(kappa), as.double(tol), as.integer(max.ite), as.integer(nj), 
       as.integer(p), as.double(beta0), DUP = FALSE)
   .C("binlep", as.double(train.x), as.double(train.y), as.double(ls[i]), 
       as.double(kappa), as.double(tol), as.integer(max.ite), as.integer(nj), 
       as.integer(p), as.double(beta0), DUP = FALSE)
   .C("gaulep", as.double(x), as.double(y), as.double(ls[i]), as.double(kappa), 
       as.double(tol), as.integer(max.ite), as.integer(n), as.integer(p), 
       as.double(beta0), DUP = FALSE)
   .C("binlep", as.double(x), as.double(y), as.double(ls[i]), as.double(kappa), 
       as.double(tol), as.integer(max.ite), as.integer(n), as.integer(p), 
       as.double(beta0), DUP = FALSE)
DUP is no longer supported and will be ignored.
SetLambda: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
GNU make is a SystemRequirements.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
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.
globalboosttest: no visible global function definition for 'predict'
globalboosttest: no visible global function definition for 'lm'
globalboosttest: no visible global function definition for 'glm'
globalboosttest: no visible binding for global variable 'binomial'
globalboosttest: no visible global function definition for 'points'
globalboosttest: no visible global function definition for 'AIC'
Undefined global functions or variables:
  AIC binomial glm lm points predict
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "AIC", "binomial", "glm", "lm", "predict")
to your NAMESPACE file.
prepare_Rd: globalboosttest.Rd:56: Dropping empty section \seealso
Malformed Description field: should contain one or more complete sentences.
.nPerms: no visible global function definition for 'terms'
expr.dev.test: no visible global function definition for 'terms'
expr.dev.test: no visible global function definition for 'model.matrix'
expr.dev.test: no visible global function definition for 'pchisq'
lancaster: no visible global function definition for 'pgamma'
liptak: no visible global function definition for 'pnorm'
summary.dev.test : ci: no visible global function definition for
  'qnorm'
varwiselogLik : <anonymous>: no visible global function definition for
  'deviance'
varwiselogLik.regression: no visible global function definition for
  'glm.fit'
Undefined global functions or variables:
  deviance glm.fit model.matrix pchisq pgamma pnorm qnorm terms
Consider adding
  importFrom("stats", "deviance", "glm.fit", "model.matrix", "pchisq",
             "pgamma", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: 'cplexAPI'
Malformed Title field: should not end in a period.
CreateFormula: no visible global function definition for 'as.formula'
GeneratePvalues: no visible binding for global variable 'binomial'
globalARTP: no visible binding for global variable 'binomial'
globalFisher: no visible binding for global variable 'binomial'
globalFisher: no visible global function definition for 'pchisq'
globalSimes: no visible binding for global variable 'binomial'
pvalFmla: no visible binding for global variable 'binomial'
pvalFmla: no visible global function definition for 'glm'
pvalFmla: no visible global function definition for 'anova'
runPermut: no visible binding for global variable 'binomial'
runPvalues: no visible binding for global variable 'binomial'
Undefined global functions or variables:
  anova as.formula binomial glm pchisq
Consider adding
  importFrom("stats", "anova", "as.formula", "binomial", "glm", "pchisq")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
ScoreTest: no visible global function definition for 'pchisq'
Var1: no visible global function definition for 'runif'
gLRT1: no visible global function definition for 'pchisq'
gLRT2: no visible global function definition for 'pchisq'
gLRT3: no visible global function definition for 'pchisq'
gLRT4: no visible global function definition for 'pf'
Undefined global functions or variables:
  pchisq pf runif
Consider adding
  importFrom("stats", "pchisq", "pf", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/GmAMisc.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
plot.bGAMM: no visible global function definition for 'par'
plot.bGAMM: no visible global function definition for 'plot'
plot.bGAMM: no visible global function definition for 'lines'
plot.bGAMM: no visible global function definition for 'rug'
Undefined global functions or variables:
  lines par plot rug
Consider adding
  importFrom("graphics", "lines", "par", "plot", "rug")
to your NAMESPACE file.
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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.
prepare_Rd: llgpcp.Rd:45-46: Dropping empty section \examples
S3 methods shown with full name in documentation object 'print.llgpcptab':
  'print.llgpcptab'

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

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

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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  'lava' 'numDeriv' 'survival'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cumres.lvmfit : myres: no visible global function definition for 'vars'
cumres.lvmfit: no visible global function definition for 'iid'
plot.cumres : sampleproc: no visible global function definition for
  'lines'
plot.cumres : predband : <anonymous>: no visible binding for global
  variable 'rgb'
plot.cumres : predband : <anonymous>: no visible global function
  definition for 'col2rgb'
plot.cumres : predband: no visible global function definition for
  'lines'
plot.cumres : predband: no visible global function definition for
  'polygon'
Undefined global functions or variables:
  col2rgb iid lines polygon rgb vars
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "lines", "polygon")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'GANPA' 'WGCNA'
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  'GANPA' 'WGCNA'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'GANPA' 'WGCNA'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GOGANPA: no visible global function definition for 'GSE.Test.Main'
selectRho: no visible global function definition for
  'scaleFreeFitIndex'
Undefined global functions or variables:
  GSE.Test.Main scaleFreeFitIndex
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'fGarch' 'fastICA'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
UprodR: no visible global function definition for 'combn'
goinit: no visible global function definition for 'as.formula'
ccor,GoGARCH : <anonymous>: no visible global function definition for
  'cov2cor'
ccor,Gopredict : <anonymous>: no visible global function definition for
  'cov2cor'
goest,Goestica: no visible global function definition for 'fastICA'
goest,Goestml: no visible global function definition for 'nlminb'
goest,Goestmm : <anonymous>: no visible global function definition for
  'combn'
goest,Goestnls: no visible global function definition for 'optim'
show,Goinit: no visible global function definition for 'head'
show,Gopredict: no visible global function definition for 'head'
update,GoGARCH: no visible global function definition for
  'update.formula'
update,Goestica: no visible global function definition for
  'update.formula'
update,Goestml: no visible global function definition for
  'update.formula'
update,Goestmm: no visible global function definition for
  'update.formula'
update,Goestnls: no visible global function definition for
  'update.formula'
Undefined global functions or variables:
  as.formula combn cov2cor fastICA head nlminb optim update.formula
Consider adding
  importFrom("stats", "as.formula", "cov2cor", "nlminb", "optim",
             "update.formula")
  importFrom("utils", "combn", "head")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
gpairs: no visible global function definition for 'hclust'
gpairs: no visible global function definition for 'dist'
gpairs : scatterplot.panel: no visible global function definition for
  'lm'
gpairs : scatterplot.panel: no visible global function definition for
  'predict'
gpairs : scatterplot.panel: no visible global function definition for
  'prcomp'
gpairs : scatterplot.panel: no visible global function definition for
  'cor'
gpairs : scatterplot.panel: no visible global function definition for
  'cor.test'
gpairs : scatterplot.panel: no visible global function definition for
  'hsv'
gpairs : scatterplot.panel: no visible global function definition for
  'na.omit'
gpairs : scatterplot.panel: no visible global function definition for
  'pf'
gpairs : scatterplot.panel: no visible global function definition for
  'grey'
Undefined global functions or variables:
  cor cor.test dist grey hclust hsv lm na.omit pf prcomp predict
Consider adding
  importFrom("grDevices", "grey", "hsv")
  importFrom("stats", "cor", "cor.test", "dist", "hclust", "lm",
             "na.omit", "pf", "prcomp", "predict")
to your NAMESPACE file.
Random.Start: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
CumulativeVarPlot: no visible global function definition for 'plot'
CumulativeVarPlot: no visible global function definition for 'axis'
PCplot: no visible global function definition for 'par'
PCplot: no visible global function definition for 'plot'
PCplot: no visible global function definition for 'rainbow'
PCplot: no visible global function definition for 'density'
gDist: no visible global function definition for 'plot'
gDist: no visible global function definition for 'density'
gDist: no visible global function definition for 'abline'
gPCA.batchdetect: no visible global function definition for 'var'
Undefined global functions or variables:
  abline axis density par plot rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "par", "plot")
  importFrom("stats", "density", "var")
to your NAMESPACE file.
The following files are already in R: 'Sweave.sty'
Please remove them from your package.
Malformed Description field: should contain one or more complete sentences.
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
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.
read.polyfile: no visible global function definition for 'as'
write.polyfile: no visible global function definition for 'is'
write.polyfile: no visible global function definition for 'as'
[,gpc.poly: no visible global function definition for 'new'
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for 'new'
coerce,data.frame-gpc.poly: no visible global function definition for
  'as'
coerce,list-gpc.poly: no visible global function definition for 'as'
coerce,matrix-gpc.poly: no visible global function definition for 'new'
coerce,numeric-gpc.poly: no visible global function definition for
  'new'
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for 'new'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'as'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'new'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'as'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'new'
tristrip,gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for
  'new'
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'bug1.R' [1s]
  Running 'reg-tests.R' [1s]
  Comparing 'reg-tests.Rout' to 'reg-tests.Rout.save' ...58c58
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
68c68
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
83c83
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
Running the tests in 'tests/bug1.R' failed.
Complete output:
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Namespaces with empty importFrom:
  'scatterplot3d' 'sqldf'
Resdata : prepdata: no visible global function definition for 'sqldf'
gpca : Build3d: no visible global function definition for 'dev.new'
gpca : Build3d: no visible global function definition for
  'scatterplot3d'
gpca : Build3d: no visible global function definition for 'text'
gpca : Build3d: no visible global function definition for 'plot'
gpca : Build3d: no visible global function definition for 'abline'
gpca : Build3d: no visible global function definition for 'rect'
gpca: no visible global function definition for 'cor'
gpca: no visible global function definition for 'dev.new'
gpca: no visible global function definition for 'plot'
gpca: no visible global function definition for 'text'
gpca: no visible global function definition for 'abline'
gpca: no visible global function definition for 'rect'
gpca: no visible global function definition for 'scatterplot3d'
gpca: no visible global function definition for 'segments'
gpca: no visible global function definition for 'points'
gpca: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline cor dev.new plot points rect scatterplot3d segments sqldf text
  write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot", "points", "rect", "segments",
             "text")
  importFrom("stats", "cor")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Missing or unexported object: 'TSA::tsdiag.Arima'
.r1: no visible global function definition for 'cor'
.r2: no visible global function definition for 'cor'
rgp: no visible global function definition for 'runif'
rgp: no visible global function definition for 'rexp'
Undefined global functions or variables:
  cor rexp runif
Consider adding
  importFrom("stats", "cor", "rexp", "runif")
to your NAMESPACE file.
gpfr: no visible global function definition for 'rnorm'
gpfr: no visible global function definition for 'runif'
gpfrpred : <anonymous>: no visible global function definition for
  'predict'
gpfrtrain: no visible global function definition for 'nlminb'
gppredict: no visible global function definition for 'predict'
gpr: no visible global function definition for 'rnorm'
gpr: no visible global function definition for 'runif'
gpr: no visible global function definition for 'lm'
gpr: no visible global function definition for 'resid'
gpr: no visible global function definition for 'nlminb'
main1: no visible global function definition for 'lm'
main1: no visible global function definition for 'resid'
main2 : <anonymous>: no visible global function definition for
  'predict'
main2: no visible global function definition for 'predict'
main3: no visible global function definition for 'lm'
main3: no visible global function definition for 'resid'
plot.gpfr: no visible global function definition for 'polygon'
plot.gpfr: no visible global function definition for 'rgb'
plot.gpfr: no visible global function definition for 'matpoints'
plot.gpfr: no visible global function definition for 'matlines'
plot.gpfr: no visible global function definition for 'lines'
plot.gpr: no visible global function definition for 'plot'
plot.gpr: no visible global function definition for 'polygon'
plot.gpr: no visible global function definition for 'rgb'
plot.gpr: no visible global function definition for 'points'
plot.gpr: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines lm matlines matpoints nlminb plot points polygon predict resid
  rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "matlines", "matpoints", "plot",
             "points", "polygon")
  importFrom("stats", "lm", "nlminb", "predict", "resid", "rnorm",
             "runif")
to your NAMESPACE file.
GP_fit: no visible global function definition for 'kmeans'
GP_fit: no visible global function definition for 'optim'
plot.GP: no visible global function definition for 'matplot'
plot.GP: no visible global function definition for 'lines'
plot.GP: no visible global function definition for 'legend'
Undefined global functions or variables:
  kmeans legend lines matplot optim
Consider adding
  importFrom("graphics", "legend", "lines", "matplot")
  importFrom("stats", "kmeans", "optim")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Checking should be performed on sources prepared by 'R CMD build'.
Packages in Depends field not imported from:
  'foreach' 'ggplot2' 'isotone' 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.0Mb
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/gpuR.Rcheck/00install.out' for details.
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    R  25.7Mb
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  'mgcv' 'rgl' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
KL: no visible global function definition for 'complete.cases'
MergeNodes: no visible global function definition for 'colors'
cross.validate: no visible global function definition for 'runif'
fit.APFA: no visible global function definition for 'complete.cases'
fit.APFA: no visible global function definition for 'aggregate'
select.beagle: no visible global function definition for 'write.table'
select.beagle: no visible global function definition for 'aggregate'
select.beagle: no visible global function definition for 'colors'
simulateAPFA: no visible global function definition for 'runif'
st: no visible global function definition for 'colors'
Undefined global functions or variables:
  aggregate colors complete.cases runif write.table
Consider adding
  importFrom("grDevices", "colors")
  importFrom("stats", "aggregate", "complete.cases", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package suggested but not available for checking: 'Sxslt'
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'Matrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GrassmannOptim: no visible global function definition for 'rnorm'
GrassmannOptim: no visible global function definition for 'runif'
GrassmannOptim : <anonymous>: no visible global function definition for
  'expm'
GrassmannOptim : <anonymous>: no visible global function definition for
  'Matrix'
Undefined global functions or variables:
  Matrix expm rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'taxstats' 'taxstats1516'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
Package suggested but not available for checking: 'doMC'
bestcut2: no visible global function definition for 'pchisq'
cov.func: no visible global function definition for 'rbinom'
cov.func: no visible global function definition for 'cov'
cov.func: no visible global function definition for 'pnorm'
cox.summary: no visible global function definition for 'predict'
em.func: no visible global function definition for 'quantile'
genSurvData: no visible global function definition for 'rweibull'
greyzone.func: no visible global function definition for 'points'
greyzone.func: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cov pchisq pnorm points predict quantile rbinom rweibull
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "cov", "pchisq", "pnorm", "predict", "quantile",
             "rbinom", "rweibull")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
grid.graph: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package in Depends field not imported from: 'spatstat'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GriegSmith: no visible global function definition for 'is.ppp'
envelopes: no visible binding for global variable 'quantile'
plot.GriegSmith: no visible global function definition for 'plot'
plot.GriegSmith: no visible global function definition for 'lines'
plot.GriegSmith: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis is.ppp lines plot quantile
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
PCgamma : <anonymous>: no visible global function definition for
  'prcomp'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'glm'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'update'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'pchisq'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'lm'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'anova'
PCgamma: no visible global function definition for 'qgamma'
PCgamma: no visible global function definition for 'pgamma'
RNAgamma : rnafunc: no visible global function definition for
  'model.matrix'
RNAgamma : rnafunc: no visible global function definition for
  'as.formula'
RNAgamma: no visible global function definition for 'qgamma'
RNAgamma: no visible global function definition for 'pgamma'
STTtoShapeParameter : f: no visible global function definition for
  'qgamma'
STTtoShapeParameter: no visible global function definition for
  'optimize'
Undefined global functions or variables:
  anova as.formula glm lm model.matrix optimize pchisq pgamma prcomp
  qgamma update
Consider adding
  importFrom("stats", "anova", "as.formula", "glm", "lm", "model.matrix",
             "optimize", "pchisq", "pgamma", "prcomp", "qgamma",
             "update")
to your NAMESPACE file.
.gsa.assignGATKTableToEnvironment: no visible global function
  definition for 'type.convert'
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'impute' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GSA: no visible global function definition for 'impute.knn'
GSA.correlate: no visible global function definition for 'quantile'
GSA.func: no visible global function definition for 'quantile'
GSA.func: no visible global function definition for 'var'
GSA.func: no visible global function definition for 'qnorm'
GSA.func: no visible global function definition for 'pt'
GSA.plot: no visible global function definition for 'plot'
GSA.plot: no visible global function definition for 'points'
GSA.plot: no visible global function definition for 'legend'
GSA.xl.correlate: no visible global function definition for 'quantile'
GSA.xl.plot: no visible global function definition for 'runif'
GSA.xl.summary.genesets: no visible global function definition for
  'quantile'
est.s0: no visible global function definition for 'quantile'
est.s0: no visible global function definition for 'mad'
est.s0: no visible global function definition for 'var'
paired.perm: no visible global function definition for 'runif'
paired.ttest.func: no visible global function definition for 'var'
tCorr.func: no visible global function definition for 'cor'
taCorr.func: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor impute.knn legend mad plot points pt qnorm quantile runif var
Consider adding
  importFrom("graphics", "legend", "plot", "points")
  importFrom("stats", "cor", "mad", "pt", "qnorm", "quantile", "runif",
             "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'GSA-internal':
  'print.GSA.func' 'print.GSA' 'summary.GSA.genesets'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package suggested but not available for checking: 'dse1'
garsim: no visible global function definition for 'rnorm'
garsim: no visible global function definition for 'rpois'
Undefined global functions or variables:
  rnorm rpois
Consider adding
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
plotgsCP: no visible global function definition for 'opts'
plotgsPower: no visible global function definition for 'opts'
qplotit: no visible global function definition for 'opts'
Undefined global functions or variables:
  opts
binding: no visible global function definition for 'rnorm'
binding: no visible binding for global variable 'var'
binding: no visible global function definition for 'uniroot'
equivonly: no visible global function definition for 'rnorm'
equivonly: no visible binding for global variable 'var'
equivonly: no visible global function definition for 'uniroot'
figureE: no visible global function definition for 'rgb'
figureEF: no visible global function definition for 'rgb'
nfix : f: no visible global function definition for 'pnorm'
nfix : f: no visible global function definition for 'qnorm'
nfix: no visible global function definition for 'uniroot'
nonbinding: no visible global function definition for 'rnorm'
nonbinding: no visible binding for global variable 'var'
nonbinding: no visible global function definition for 'uniroot'
oc: no visible global function definition for 'rnorm'
oc: no visible global function definition for 'var'
Undefined global functions or variables:
  pnorm qnorm rgb rnorm uniroot var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "pnorm", "qnorm", "rnorm", "uniroot", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/GSIF.Rcheck/00install.out' for details.
Namespaces with empty importFrom:
  'gee' 'geepack'
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
gte: no visible global function definition for 'model.extract'
gte: no visible global function definition for 'model.matrix'
gte: no visible binding for global variable 'sd'
gte: no visible global function definition for 'dnorm'
plot.gte: no visible global function definition for 'plot'
plot.gte: no visible global function definition for 'par'
plot.gte: no visible global function definition for 'polygon'
plot.gte: no visible global function definition for 'gray'
plot.gte: no visible global function definition for 'lines'
plot.gte: no visible global function definition for 'legend'
Undefined global functions or variables:
  dnorm gray legend lines model.extract model.matrix par plot polygon
  sd
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "legend", "lines", "par", "plot", "polygon")
  importFrom("stats", "dnorm", "model.extract", "model.matrix", "sd")
to your NAMESPACE file.
Found the following possibly unsafe calls:
File 'gtools/R/unByteCode.R':
  unlockBinding(name, env = env)
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.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.1/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.1/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-35\unhbox\voidb@x \penalty \@M \ {}1.
1/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
calculate.threshold: no visible global function definition for 'pchisq'
gwerAM: no visible global function definition for 'rnorm'
gwerAM: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  pchisq quantile rnorm
Consider adding
  importFrom("stats", "pchisq", "quantile", "rnorm")
to your NAMESPACE file.
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible global function definition for 'data'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible global function definition for 'data'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
browseDataAsCSV: no visible global function definition for 'write.csv'
browseDataAsCSV: no visible global function definition for 'browseURL'
tcltkDialog: no visible global function definition for 'runif'
tl_get_column_name: no visible global function definition for 'tail'
.add,gTexttcltk-guiWidgetsToolkittcltk-character: no visible global
  function definition for 'rnorm'
.font<-,gTexttcltk-guiWidgetsToolkittcltk: no visible global function
  definition for 'rnorm'
.font<-,tcltkObject-guiWidgetsToolkittcltk: no visible global function
  definition for 'rnorm'
.gdf,guiWidgetsToolkittcltk: no visible global function definition for
  'head'
.visible<-,gGraphicstcltk-guiWidgetsToolkittcltk-ANY: no visible global
  function definition for 'dev.set'
Undefined global functions or variables:
  browseURL dev.set head rnorm runif tail write.csv
Consider adding
  importFrom("grDevices", "dev.set")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "browseURL", "head", "tail", "write.csv")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'fields' 'lars'
  Please remove these calls from your code.
Package in Depends field not imported from: 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gwl.beta: no visible global function definition for 'lars'
gwl.cv.err: no visible global function definition for 'lars'
gwl.est: no visible global function definition for 'lm'
gwr.bw.est: no visible global function definition for 'lm'
gwr.est: no visible global function definition for 'lm'
gwr.rsquare: no visible global function definition for 'cor'
gwrr.est: no visible global function definition for 'lm'
Undefined global functions or variables:
  cor lars lm
Consider adding
  importFrom("stats", "cor", "lm")
to your NAMESPACE file.
GxMestimator: no visible global function definition for 'na.omit'
initialization_chol: no visible global function definition for 'cov'
initialization_corr: no visible global function definition for 'cov'
initialization_nlmain: no visible global function definition for
  'lm.fit'
print.summaryGxMclass: no visible global function definition for
  'pnorm'
print.summaryGxMclass: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  cov lm.fit na.omit pnorm printCoefmat
Consider adding
  importFrom("stats", "cov", "lm.fit", "na.omit", "pnorm",
             "printCoefmat")
to your NAMESPACE file.
installed size is 132.4Mb
  sub-directories of 1Mb or more:
    java  130.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Malformed Description field: should contain one or more complete sentences.
hf.bt: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
hsTableReader: no visible global function definition for 'object.size'
hsWriteTable: no visible global function definition for 'write.table'
Undefined global functions or variables:
  object.size write.table
Consider adding
  importFrom("utils", "object.size", "write.table")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
.hankel.critValExp: no visible global function definition for
  'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
EMvar: no visible global function definition for 'model.matrix'
RecodeHaplos: no visible global function definition for 'na.omit'
RecodeHaplos: no visible global function definition for 'tail'
anova.hapassoc: no visible global function definition for 'pchisq'
handleMissings: no visible global function definition for 'na.omit'
hapassoc: no visible global function definition for 'binomial'
hapassoc: no visible global function definition for 'formula'
hapassoc: no visible global function definition for 'glm'
hapassoc : <anonymous>: no visible global function definition for 'glm'
hapassoc: no visible global function definition for 'model.frame'
hapassoc: no visible global function definition for 'model.matrix'
hapassoc: no visible binding for global variable 'contrasts'
hapassoc: no visible global function definition for 'glm.control'
hapassoc : <anonymous>: no visible global function definition for
  'glm.control'
probY: no visible global function definition for 'dbinom'
probY: no visible global function definition for 'dpois'
probY: no visible global function definition for 'dnorm'
probY: no visible global function definition for 'dgamma'
summary.hapassoc: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  binomial contrasts dbinom dgamma dnorm dpois formula glm glm.control
  model.frame model.matrix na.omit pchisq tail
Consider adding
  importFrom("stats", "binomial", "contrasts", "dbinom", "dgamma",
             "dnorm", "dpois", "formula", "glm", "glm.control",
             "model.frame", "model.matrix", "na.omit", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
allele.marq: no visible global function definition for 'na.omit'
depart.LDL: no visible global function definition for 'aov'
freq.all: no visible global function definition for 'na.omit'
hapim.LD.add: no visible global function definition for 'optim'
hapim.LDL.add: no visible global function definition for 'optim'
obj.haplomax.HS.add: no visible global function definition for 'aov'
obj.haplomax.add: no visible global function definition for 'aov'
vrais.LD.add: no visible global function definition for 'dnorm'
vrais.LDL.add.pere: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  aov dnorm na.omit optim
Consider adding
  importFrom("stats", "aov", "dnorm", "na.omit", "optim")
to your NAMESPACE file.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
AssignQTL : <anonymous>: no visible global function definition for
  'rgamma'
AssignSingleQTL: no visible global function definition for 'rgamma'
ListQTL : <anonymous>: no visible global function definition for
  'rgamma'
SampleBaseHaplotype: no visible global function definition for 'runif'
SampleHaplotype: no visible global function definition for 'rpois'
SampleHaplotype: no visible global function definition for 'runif'
SampleHaplotype: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbinom rgamma rpois runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rpois", "runif")
to your NAMESPACE file.
clustersG: no visible global function definition for 'combn'
pairneidist: no visible global function definition for 'as.dist'
pairneidist: no visible global function definition for 'combn'
steplimit : .TempletonProb: no visible global function definition for
  'integrate'
distance,Dna: no visible global function definition for 'dist'
distance,Dna: no visible global function definition for 'combn'
distance,Dna: no visible global function definition for 'as.dist'
pairnei,matrix: no visible global function definition for 'as.dist'
show,Dna: no visible global function definition for 'head'
Undefined global functions or variables:
  as.dist combn dist head integrate
Consider adding
  importFrom("stats", "as.dist", "dist", "integrate")
  importFrom("utils", "combn", "head")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'ape' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'ape' 'hash'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  -- 1. Failure: caching in reap with long sample (@test-caching.R#76)  ----------
  all(t2[1] <= t1[1]) isn't true.
  
  == testthat results  ===========================================================
  OK: 104 SKIPPED: 5 FAILED: 1
  1. Failure: caching in reap with long sample (@test-caching.R#76) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace with empty importFrom: 'utils'
File
  LICENSE
is not mentioned in the DESCRIPTION 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.
hash: no visible global function definition for 'new'
is.hash: no visible global function definition for 'is'
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').
GNU make is a SystemRequirements.
extract_hazus_functions: no visible global function definition for
  'data'
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
detect.movement: no visible global function definition for 't.test'
generate.random.conf: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm t.test
Consider adding
  importFrom("stats", "rnorm", "t.test")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
PoincarePlot: no visible global function definition for 'plot'
PoincarePlot: no visible global function definition for 'lines'
PoincarePlot: no visible global function definition for 'lowess'
hctest: no visible global function definition for 'cor.test'
rdplot: no visible global function definition for 'plot'
rdplot: no visible global function definition for 'lines'
rdplot: no visible global function definition for 'lowess'
rdplot: no visible global function definition for 'rgb'
simer: no visible global function definition for 'runif'
simer: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  cor.test lines lowess plot rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "cor.test", "lowess", "rnorm", "runif")
to your NAMESPACE file.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data  10.0Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Promax.only: no visible global function definition for 'lm.fit'
factor.pa.ginv: no visible binding for global variable 'median'
factor.pa.ginv: no visible global function definition for 'cor'
factor.pa.ginv: no visible global function definition for 'varimax'
factor.pa.ginv: no visible global function definition for 'pchisq'
pairwise.mahalanobis: no visible global function definition for 'cor'
pairwise.mahalanobis: no visible global function definition for
  'mahalanobis'
Undefined global functions or variables:
  cor lm.fit mahalanobis median pchisq varimax
Consider adding
  importFrom("stats", "cor", "lm.fit", "mahalanobis", "median", "pchisq",
             "varimax")
to your NAMESPACE file.
coef.HDtweedie: no visible global function definition for 'rbind2'
coef.cv.HDtweedie: no visible global function definition for 'coef'
cv.tweediegrppath: no visible global function definition for 'predict'
cv.tweediegrppath: no visible binding for global variable
  'weighted.mean'
cvcompute: no visible binding for global variable 'weighted.mean'
error.bars: no visible global function definition for 'segments'
lambda.interp: no visible global function definition for 'approx'
plot.HDtweedie: no visible global function definition for 'par'
plot.HDtweedie: no visible binding for global variable 'plot.default'
plot.HDtweedie: no visible global function definition for 'gray.colors'
plot.HDtweedie: no visible global function definition for 'abline'
plot.cv.HDtweedie: no visible global function definition for 'points'
plot.cv.HDtweedie: no visible global function definition for 'axis'
plot.cv.HDtweedie: no visible global function definition for 'abline'
predict.HDtweedie: no visible global function definition for 'rbind2'
predict.HDtweedie: no visible global function definition for 'cbind2'
predict.cv.HDtweedie: no visible global function definition for
  'predict'
Undefined global functions or variables:
  abline approx axis cbind2 coef gray.colors par plot.default points
  predict rbind2 segments weighted.mean
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "abline", "axis", "par", "plot.default",
             "points", "segments")
  importFrom("methods", "cbind2", "rbind2")
  importFrom("stats", "approx", "coef", "predict", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Title field: should not end in a period.
The following directory looks like a leftover from 'knitr':
  'cache'
Please remove from your package.
Malformed Title field: should not end in a period.
heatmap.plus: no visible binding for global variable 'dist'
heatmap.plus: no visible binding for global variable 'hclust'
heatmap.plus : <anonymous>: no visible global function definition for
  'reorder'
heatmap.plus: no visible global function definition for 'as.dendrogram'
heatmap.plus: no visible global function definition for
  'order.dendrogram'
heatmap.plus: no visible binding for global variable 'sd'
heatmap.plus: no visible global function definition for 'par'
heatmap.plus: no visible global function definition for 'layout'
heatmap.plus: no visible global function definition for 'image'
heatmap.plus: no visible global function definition for 'axis'
heatmap.plus: no visible global function definition for 'mtext'
heatmap.plus: no visible global function definition for 'plot'
heatmap.plus: no visible global function definition for 'frame'
heatmap.plus: no visible global function definition for 'title'
Undefined global functions or variables:
  as.dendrogram axis dist frame hclust image layout mtext
  order.dendrogram par plot reorder sd title
Consider adding
  importFrom("graphics", "axis", "frame", "image", "layout", "mtext",
             "par", "plot", "title")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
prepare_Rd: heatmap.plus.package.Rd:69: Dropping empty section \details
prepare_Rd: heatmap.plus.package.Rd:70: Dropping empty section \value
prepare_Rd: heatmap.plus.package.Rd:73: Dropping empty section \note
prepare_Rd: heatmap.plus.package.Rd:71: Dropping empty section \references
Package suggested but not available for checking: 'glmmADMB'
Warning: no function found corresponding to methods exports from 'het.test' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  'methods' 'vars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
whites.htest: no visible global function definition for 'residuals'
whites.htest: no visible global function definition for 'lm'
whites.htest: no visible global function definition for 'pchisq'
whites.htest: no visible global function definition for 'new'
Undefined global functions or variables:
  lm new pchisq residuals
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "lm", "pchisq", "residuals")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  'grplasso' 'lattice' 'rgl' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HubNetwork: no visible global function definition for 'rbinom'
HubNetwork: no visible global function definition for 'runif'
HubNetwork: no visible global function definition for 'cov2cor'
binaryMCMC: no visible global function definition for 'rbinom'
image.hbn: no visible global function definition for 'col2rgb'
image.hbn: no visible global function definition for 'rgb'
image.hbn: no visible global function definition for 'dev.new'
image.hbn: no visible global function definition for 'par'
image.hbn: no visible global function definition for 'image'
image.hcov: no visible global function definition for 'col2rgb'
image.hcov: no visible global function definition for 'rgb'
image.hcov: no visible global function definition for 'dev.new'
image.hcov: no visible global function definition for 'par'
image.hcov: no visible global function definition for 'image'
image.hglasso: no visible global function definition for 'col2rgb'
image.hglasso: no visible global function definition for 'rgb'
image.hglasso: no visible global function definition for 'dev.new'
image.hglasso: no visible global function definition for 'par'
image.hglasso: no visible global function definition for 'image'
plot.hbn: no visible global function definition for 'rgb'
plot.hbn: no visible global function definition for 'plot'
plot.hcov: no visible global function definition for 'rgb'
plot.hcov: no visible global function definition for 'plot'
plot.hglasso: no visible global function definition for 'rgb'
plot.hglasso: no visible global function definition for 'plot'
Undefined global functions or variables:
  col2rgb cov2cor dev.new image par plot rbinom rgb runif
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rgb")
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov2cor", "rbinom", "runif")
to your NAMESPACE file.
Error in .requirePackage(package) : 
    unable to find required package 'HiTC'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
Error in .requirePackage(package) : 
    unable to find required package 'HiTC'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
Unexported objects imported by ':::' calls:
  'ggplot2:::build_guides' 'ggplot2:::guide_axis'
  'ggplot2:::scales_list'
  See the note in ?`:::` about the use of this operator.
banded: no visible global function definition for 'toeplitz'
gpband: no visible global function definition for 'toeplitz'
hierband.cv: no visible global function definition for 'cov'
hierband.cv: no visible binding for global variable 'sd'
subdiag.thresh: no visible global function definition for 'uniroot'
subdiag.thresh: no visible global function definition for 'toeplitz'
Undefined global functions or variables:
  cov sd toeplitz uniroot
Consider adding
  importFrom("stats", "cov", "sd", "toeplitz", "uniroot")
to your NAMESPACE file.
booties: no visible binding for global variable 'sd'
booties: no visible binding for global variable 'quantile'
hierDiversity: no visible global function definition for
  'txtProgressBar'
hierDiversity: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  quantile sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package suggested but not available for checking: 'XMLRPC'
calcPower: no visible global function definition for 'pchisq'
calcPower: no visible global function definition for 'qchisq'
delta2 : K1: no visible global function definition for 'qnorm'
delta2: no visible global function definition for 'qnorm'
delta2: no visible global function definition for 'pnorm'
delta2: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'gtools' which was already attached by Depends.
  Please remove these calls from your code.
all.regs: no visible global function definition for 'glm'
all.regs: no visible global function definition for 'logLik'
combos: no visible global function definition for 'menu'
current.model: no visible global function definition for 'formula'
current.model: no visible global function definition for 'glm'
current.model: no visible global function definition for 'logLik'
current.model: no visible global function definition for 'lm'
rand.hp: no visible global function definition for 'runif'
rand.hp: no visible global function definition for 'sd'
Undefined global functions or variables:
  formula glm lm logLik menu runif sd
Consider adding
  importFrom("stats", "formula", "glm", "lm", "logLik", "runif", "sd")
  importFrom("utils", "menu")
to your NAMESPACE file.
compute.contrasts: no visible binding for global variable 'sd'
compute.contrasts: no visible global function definition for 'cor'
compute.contrasts: no visible global function definition for 'sd'
plot.estfdr: no visible global function definition for 'plot'
plot.hiertest: no visible global function definition for 'plot'
plot.hiertest: no visible global function definition for 'legend'
Undefined global functions or variables:
  cor legend plot sd
Consider adding
  importFrom("graphics", "legend", "plot")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'nnet' 'stats'
  Please remove these calls from your code.
Package in Depends field not imported from: 'nnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.8Mb
CLX.sim.Covtest: no visible global function definition for 'cov'
CLX.sim.equalcov: no visible global function definition for 'cov'
CLX.sim.unequalcov: no visible global function definition for 'cov'
CLX.test.equalcov: no visible global function definition for 'cov'
CLX.test.unequalcov: no visible global function definition for 'cov'
ChenQin.sim: no visible global function definition for 'pnorm'
ChenQin.test: no visible global function definition for 'pnorm'
GCT.sim: no visible binding for global variable 'var'
GCT.sim: no visible global function definition for 'acf'
GCT.sim: no visible global function definition for 'pnorm'
GCT.test: no visible binding for global variable 'var'
GCT.test: no visible global function definition for 'acf'
GCT.test: no visible global function definition for 'pnorm'
GCT.test.missing: no visible binding for global variable 'var'
GCT.test.missing: no visible global function definition for 'acf'
GCT.test.missing: no visible global function definition for 'pnorm'
SK.sim: no visible global function definition for 'cov'
SK.sim: no visible global function definition for 'pnorm'
SK.test: no visible global function definition for 'cov'
SK.test: no visible global function definition for 'pnorm'
build2popData : <anonymous>: no visible global function definition for
  'rnorm'
build2popData: no visible global function definition for 'arima.sim'
build2popData_muYafunction : <anonymous>: no visible global function
  definition for 'rnorm'
build2popData_muYafunction: no visible global function definition for
  'arima.sim'
innovate: no visible binding for global variable 'rnorm'
rdblepareto: no visible global function definition for 'runif'
rgammashift: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  acf arima.sim cov pnorm rgamma rnorm runif var
Consider adding
  importFrom("stats", "acf", "arima.sim", "cov", "pnorm", "rgamma",
             "rnorm", "runif", "var")
to your NAMESPACE file.
Func.ABOD: no visible global function definition for 'combn'
Func.ABOD: no visible global function definition for 'var'
Func.SOD: no visible global function definition for 'var'
Func.trans : erf: no visible global function definition for 'pnorm'
Func.trans: no visible global function definition for 'sd'
Undefined global functions or variables:
  combn pnorm sd var
Consider adding
  importFrom("stats", "pnorm", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
BenjaminiHochberg: no visible global function definition for 'p.adjust'
CaoKosorok : CKfunc: no visible global function definition for 'pnorm'
CaoKosorok : <anonymous>: no visible global function definition for
  'pnorm'
StoreyTibshirani: no visible global function definition for
  'smooth.spline'
plotI_Lines: no visible global function definition for 'par'
plotI_Lines: no visible global function definition for 'lines'
plotI_Lines: no visible global function definition for 'legend'
plotI_Points: no visible global function definition for 'points'
plotI_Points: no visible global function definition for 'legend'
tStatistic : <anonymous>: no visible global function definition for
  't.test'
venn2: no visible global function definition for 'plot.new'
venn3: no visible global function definition for 'plot.new'
Undefined global functions or variables:
  legend lines p.adjust par plot.new pnorm points smooth.spline t.test
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot.new", "points")
  importFrom("stats", "p.adjust", "pnorm", "smooth.spline", "t.test")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
occupancy: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
data_simu: no visible global function definition for 'runif'
data_simu: no visible global function definition for 'rbinom'
data_simu: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rbinom rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rnorm", "runif")
to your NAMESPACE file.
overlay.sim: no visible global function definition for 'points'
plotDistr: no visible global function definition for 'dev.hold'
plotDistr: no visible global function definition for 'dev.flush'
plotDistr: no visible global function definition for 'plot'
plotDistr: no visible global function definition for 'segments'
Undefined global functions or variables:
  dev.flush dev.hold plot points segments
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold")
  importFrom("graphics", "plot", "points", "segments")
to your NAMESPACE file.
'library' or 'require' call to 'rgl' which was already attached by Depends.
  Please remove these calls from your code.
PlotOptPower: no visible global function definition for 'bmp'
PlotOptPower: no visible global function definition for
  'filled.contour'
PlotOptPower: no visible global function definition for 'title'
PlotOptPower: no visible global function definition for 'grey.colors'
PlotOptPower: no visible global function definition for 'axis'
PlotOptPower: no visible global function definition for 'polygon'
PlotOptPower: no visible global function definition for 'legend'
PlotOptPower: no visible global function definition for 'mtext'
PlotOptPower: no visible global function definition for 'dev.off'
PlotOptPower: no visible global function definition for
  'terrain.colors'
ShowOptDesign: no visible global function definition for 'head'
diffVariantError: no visible global function definition for 'pbinom'
predictPoolNCP: no visible global function definition for 'data'
probDetEqual3: no visible global function definition for 'dbinom'
probDetEqual3: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
arms: no visible global function definition for 'rnorm'
rballunif: no visible global function definition for 'rnorm'
rballunif: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
HMeasure: no visible global function definition for 'complete.cases'
HMeasure : HMeasure.single: no visible global function definition for
  'chull'
HMeasure : HMeasure.single: no visible global function definition for
  'pbeta'
plotROC: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'lines'
plotROC: no visible global function definition for 'legend'
plotROC: no visible global function definition for 'dbeta'
plotROC: no visible global function definition for 'density'
Undefined global functions or variables:
  chull complete.cases dbeta density legend lines pbeta plot
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "dbeta", "density", "pbeta")
to your NAMESPACE file.
The following files look like leftovers/mistakes:
  'hmeasure.dvi'
Please remove them from your package.
baumwelchcont: no visible global function definition for 'dnorm'
hmmcontSimul: no visible global function definition for 'rnorm'
hmmcontSimul: no visible global function definition for 'rbinom'
plot.ContObservHMM: no visible global function definition for 'plot'
plot.ContObservHMM: no visible global function definition for 'lines'
statesDistributionsPlot: no visible global function definition for
  'dnorm'
statesDistributionsPlot: no visible global function definition for 'sd'
statesDistributionsPlot: no visible global function definition for
  'plot'
statesDistributionsPlot: no visible global function definition for
  'lines'
statesDistributionsPlot: no visible global function definition for
  'legend'
summary.ContObservHMM: no visible global function definition for 'sd'
Undefined global functions or variables:
  dnorm legend lines plot rbinom rnorm sd
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "dnorm", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
dishonestCasino: no visible global function definition for 'plot'
dishonestCasino: no visible global function definition for 'axis'
dishonestCasino: no visible global function definition for 'text'
dishonestCasino: no visible global function definition for 'rect'
dishonestCasino: no visible global function definition for 'rgb'
dishonestCasino: no visible global function definition for 'points'
Undefined global functions or variables:
  axis plot points rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "plot", "points", "rect", "text")
to your NAMESPACE file.
Package suggested but not available for checking: 'glmmADMB'
PlotBasic: no visible global function definition for 'dev.new'
PlotBasic: no visible global function definition for 'par'
PlotBasic: no visible global function definition for 'plot'
PlotBasic: no visible global function definition for 'grid'
PlotBasic: no visible global function definition for 'lines'
PlotChoice : plotgraph: no visible global function definition for 'par'
PlotChoice : plotgraph: no visible global function definition for
  'plot'
PlotChoice : plotgraph: no visible global function definition for
  'grid'
PlotChoice : plotgraph: no visible global function definition for
  'points'
PlotChoice : plotgraph: no visible global function definition for
  'lines'
PlotChoice : plotgraph: no visible global function definition for
  'axis'
PlotChoice : plotgraph: no visible global function definition for
  'mtext'
Undefined global functions or variables:
  axis dev.new grid lines mtext par plot points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "grid", "lines", "mtext", "par", "plot",
             "points")
to your NAMESPACE file.
hornpa: no visible global function definition for 'rnorm'
hornpa: no visible global function definition for 'cor'
hornpa: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cor quantile rnorm
Consider adding
  importFrom("stats", "cor", "quantile", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
hpbayes.plot: no visible global function definition for 'par'
hpbayes.plot: no visible global function definition for 'plot'
hpbayes.plot: no visible global function definition for 'points'
postpri.plot: no visible global function definition for 'par'
postpri.plot: no visible global function definition for 'plot'
postpri.plot: no visible global function definition for 'points'
postpri.plot: no visible global function definition for 'segments'
postpri.plot: no visible global function definition for 'boxplot'
Undefined global functions or variables:
  boxplot par plot points segments
Consider adding
  importFrom("graphics", "boxplot", "par", "plot", "points", "segments")
to your NAMESPACE file.
ApproxC: no visible global function definition for 'convolve'
DMC: no visible global function definition for 'median'
DMC: no visible global function definition for 'ecdf'
ToSWF: no visible global function definition for 'write.table'
Undefined global functions or variables:
  convolve ecdf median write.table
Consider adding
  importFrom("stats", "convolve", "ecdf", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
bracket: no visible global function definition for 'segments'
Undefined global functions or variables:
  segments
Consider adding
  importFrom("graphics", "segments")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    2.5Mb
    libs   1.5Mb
File 'hSDM/libs/i386/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.o'
File 'hSDM/libs/x64/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
hsicCCA: no visible global function definition for 'median'
hsicCCA: no visible global function definition for 'dist'
hsicCCAfunc: no visible global function definition for 'rnorm'
hsicCCAfunc: no visible global function definition for 'runif'
hsicCCAfunc: no visible global function definition for 'optim'
ktaCCA: no visible global function definition for 'median'
ktaCCA: no visible global function definition for 'dist'
ktaCCAfunc: no visible global function definition for 'rnorm'
ktaCCAfunc: no visible global function definition for 'runif'
ktaCCAfunc: no visible global function definition for 'optim'
Undefined global functions or variables:
  dist median optim rnorm runif
Consider adding
  importFrom("stats", "dist", "median", "optim", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.d: no visible global function definition for 'dgeom'
get.d: no visible global function definition for 'dnbinom'
get.d: no visible global function definition for 'dpois'
get.pdf: no visible global function definition for 'dnorm'
get.pdf: no visible global function definition for 'dpois'
get.pdf: no visible global function definition for 'dmvnorm'
hsmm: no visible global function definition for 'uniroot'
hsmm.sim: no visible global function definition for 'rbinom'
hsmm.sim: no visible global function definition for 'rnorm'
hsmm.sim: no visible global function definition for 'rpois'
hsmm.sim: no visible global function definition for 'rmvnorm'
loggeom.update: no visible global function definition for 'plogis'
rmt: no visible global function definition for 'rt'
rmt: no visible global function definition for 'rnorm'
rmt: no visible global function definition for 'rchisq'
rvm: no visible global function definition for 'runif'
Undefined global functions or variables:
  dgeom dmvnorm dnbinom dnorm dpois plogis rbinom rchisq rmvnorm rnorm
  rpois rt runif uniroot
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dnorm", "dpois", "plogis",
             "rbinom", "rchisq", "rnorm", "rpois", "rt", "runif",
             "uniroot")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Huber: no visible global function definition for 'quantile'
SSVD.iter.thresh: no visible global function definition for 'mad'
error.est.full: no visible global function definition for 'mad'
error.est.full : <anonymous>: no visible global function definition for
  'median'
low_rank: no visible global function definition for 'median'
low_rank: no visible global function definition for 'mad'
low_rank: no visible global function definition for 'sd'
select.indices: no visible global function definition for 'mad'
select.indices: no visible global function definition for 'median'
select.indices: no visible global function definition for 'pnorm'
select.indices: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  mad median p.adjust pnorm quantile sd
Consider adding
  importFrom("stats", "mad", "median", "p.adjust", "pnorm", "quantile",
             "sd")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
BasicHTML: no visible global function definition for 'png'
BasicHTML: no visible global function definition for 'dev.list'
BasicHTML: no visible global function definition for 'dev.off'
FramedHTML: no visible global function definition for 'graphics.off'
Undefined global functions or variables:
  dev.list dev.off graphics.off png
Consider adding
  importFrom("grDevices", "dev.list", "dev.off", "graphics.off", "png")
to your NAMESPACE file.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    data  12.8Mb
    doc    1.3Mb
getToHost: no visible global function definition for 'make.socket'
getToHost: no visible global function definition for 'write.socket'
getToHost: no visible global function definition for 'read.socket'
getToHost: no visible global function definition for 'close.socket'
postToHost: no visible global function definition for 'runif'
simplePostToHost: no visible global function definition for
  'make.socket'
simplePostToHost: no visible global function definition for
  'write.socket'
simplePostToHost: no visible global function definition for
  'read.socket'
simplePostToHost: no visible global function definition for
  'close.socket'
Undefined global functions or variables:
  close.socket make.socket read.socket runif write.socket
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "close.socket", "make.socket", "read.socket",
             "write.socket")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Package in Depends field not imported from: 'testthat'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Calculate3D: no visible global function definition for 'persp'
CalculateHUM_Ex: no visible global function definition for 'combn'
CalculateHUM_Plot: no visible global function definition for 'plot'
CalculateHUM_Plot: no visible global function definition for 'polygon'
CalculateHUM_Plot: no visible global function definition for 'text'
CalculateHUM_Plot: no visible global function definition for 'points'
CalculateHUM_Plot: no visible global function definition for 'lines'
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: 'hurricaneexposuredata'
Malformed Title field: should not end in a period.
HWEImportSamp: no visible global function definition for 'dnorm'
HWEImportSamp: no visible global function definition for 'rnorm'
HWEmodelsMLE: no visible global function definition for 'optim'
HWEsimdat: no visible global function definition for 'rmultinom'
LambdaOptim: no visible global function definition for 'rnorm'
LambdaOptim : LambdaPriorChoice: no visible global function definition
  for 'quantile'
LambdaOptim: no visible global function definition for 'optim'
SinglefPrior: no visible global function definition for 'rnorm'
SinglefReject: no visible global function definition for 'runif'
TriangNormHWE: no visible global function definition for 'pbeta'
Undefined global functions or variables:
  dnorm optim pbeta quantile rmultinom rnorm runif
Consider adding
  importFrom("stats", "dnorm", "optim", "pbeta", "quantile", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
HW.plain: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
getHwriterVersion: no visible global function definition for
  'sessionInfo'
hmapRowCol: no visible global function definition for 'na.omit'
hwriteImage: no visible global function definition for 'dev.print'
hwriteImage: no visible binding for global variable 'png'
showExample: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL dev.print na.omit png sessionInfo
Consider adding
  importFrom("grDevices", "dev.print", "png")
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "sessionInfo")
to your NAMESPACE file.
Checking should be performed on sources prepared by 'R CMD build'.
Package in Depends field not imported from: 'coda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
hybridMC: no visible global function definition for 'txtProgressBar'
hybridMC : pbFun: no visible global function definition for
  'setTxtProgressBar'
hybridMC: no visible global function definition for 'mcmc'
Undefined global functions or variables:
  mcmc setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
ARPIEM2012.Lmom.sample: no visible global function definition for 'var'
ARPIEM2012.freq: no visible binding for global variable 'quantile'
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.Qind_camp: no visible global
  function definition for 'rnorm'
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.Qind_reg_moltiplicativo: no
  visible global function definition for 'rnorm'
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.LCV_camp.LCA_camp: no visible
  global function definition for 'rnorm'
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.LCV_camp.LCA_reg_additivo: no
  visible global function definition for 'rnorm'
ARPIEM2012.sim.Lmoments :
  ARPIEM2012.sim.LCV_reg_moltiplicativo.LCA_reg_additivo: no visible
  global function definition for 'rnorm'
Undefined global functions or variables:
  quantile rnorm var
Consider adding
  importFrom("stats", "quantile", "rnorm", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'minpack.lm' 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Dstart: no visible global function definition for 'coef'
Dstart: no visible global function definition for 'lm'
SSkosugi: no visible global function definition for 'pnorm'
SSkosugi: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  coef dnorm lm pnorm
Consider adding
  importFrom("stats", "coef", "dnorm", "lm", "pnorm")
to your NAMESPACE file.
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'lo' to 'locut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'hi' to 'hicut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hyphenatr)
  > 
  > test_check("hyphenatr")
  -- 1. Failure: we can do something (@test-hyphenatr.R#16)  ---------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "tÃ¤=gelÃ®ch"
  y[1]: "tä=gelîch"
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: we can do something (@test-hyphenatr.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hyphenatr)
  > 
  > test_check("hyphenatr")
  -- 1. Failure: we can do something (@test-hyphenatr.R#16)  ---------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "tÃ¤=gelÃ®ch"
  y[1]: "tä=gelîch"
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: we can do something (@test-hyphenatr.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Packages in Depends field not imported from:
  'R.utils' 'ape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
requiprobable: no visible global function definition for 'extract'
requiprobable : make.tree: no visible global function definition for
  'extract'
requiprobable : make.tree: no visible global function definition for
  'runif'
rgenetree: no visible global function definition for 'dbinom'
rgenetree: no visible global function definition for 'dnbinom'
rgenetree: no visible global function definition for 'runif'
rgenetree: no visible global function definition for 'rbinom'
rgenetree: no visible global function definition for 'rnbinom'
Undefined global functions or variables:
  dbinom dnbinom extract rbinom rnbinom runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "rbinom", "rnbinom", "runif")
to your NAMESPACE file.
conint: no visible global function definition for 'sd'
findroot: no visible global function definition for 'integrate'
hypothesis: no visible global function definition for 'sd'
hypothesis: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate sd
Consider adding
  importFrom("stats", "integrate", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MCMCpack' 'coda' 'foreach'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
ibdhap.barplot: no visible global function definition for 'plot'
ibdhap.barplot: no visible global function definition for 'rect'
ibdhap.compare.loci: no visible global function definition for 'hist'
ibdhap.compare.segs: no visible global function definition for 'tail'
ibdhap.make.calls: no visible global function definition for
  'count.fields'
ibdhap.make.calls: no visible global function definition for
  'read.table'
ibdhap.make.true: no visible global function definition for
  'read.table'
ibdhap.names: no visible global function definition for 'count.fields'
ibdhap.names: no visible global function definition for 'read.table'
ibdhap.reduce.states: no visible global function definition for
  'read.table'
ibdhap.reduce.states: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  count.fields hist plot read.table rect tail write.table
Consider adding
  importFrom("graphics", "hist", "plot", "rect")
  importFrom("utils", "count.fields", "read.table", "tail",
             "write.table")
to your NAMESPACE file.
create.ibd.dat: no visible global function definition for 'read.table'
create.pairs.frame: no visible global function definition for 'terms'
ibd.moments: no visible global function definition for 'var'
ibdreg: no visible global function definition for 'terms'
ibdreg: no visible global function definition for 'as.formula'
linkage.tests: no visible global function definition for 'pchisq'
pchibar: no visible global function definition for 'pchisq'
plot.linkage.all: no visible global function definition for 'plot'
plot.linkage.all: no visible global function definition for 'title'
plotpval: no visible global function definition for 'plot'
plotpval: no visible global function definition for 'lines'
sim.ibd.var: no visible global function definition for 'read.table'
sim.mark.prop: no visible global function definition for 'runif'
Undefined global functions or variables:
  as.formula lines pchisq plot read.table runif terms title var
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("stats", "as.formula", "pchisq", "runif", "terms", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
CreateVoronoi: no visible global function definition for 'slot'
CreateVoronoi : <anonymous>: no visible global function definition for
  'slot'
CreateVoronoi: no visible global function definition for 'chull'
ExtractIMFi2D: no visible global function definition for 'par'
LocatedAtBoundary: no visible global function definition for
  'txtProgressBar'
LocatedAtBoundary: no visible global function definition for
  'setTxtProgressBar'
PlotFit: no visible global function definition for 'par'
iBEEMD: no visible global function definition for 'is'
iBEEMD: no visible global function definition for 'sd'
iBEEMD: no visible global function definition for 'txtProgressBar'
iBEEMD: no visible global function definition for 'rnorm'
iBEEMD: no visible global function definition for 'setTxtProgressBar'
iBEEMD: no visible global function definition for 'terrain.colors'
rbfcreate: no visible global function definition for 'is'
rbfcreate : rbfAssemble: no visible global function definition for
  'dist'
rbfinterp: no visible global function definition for 'is'
rbfinterp: no visible global function definition for 'dist'
Undefined global functions or variables:
  chull dist is par rnorm sd setTxtProgressBar slot terrain.colors
  txtProgressBar
Consider adding
  importFrom("grDevices", "chull", "terrain.colors")
  importFrom("graphics", "par")
  importFrom("methods", "is", "slot")
  importFrom("stats", "dist", "rnorm", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Title field: should not end in a period.
Iboot: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
..placeOrder: no visible global function definition for 'str'
.reqMktData.vignette: no visible global function definition for
  'flush.console'
e_portfolio_value: no visible global function definition for 'str'
print.eventPortfolioValue: no visible global function definition for
  'str'
print.twsContract: no visible global function definition for 'str'
print.twsContractDetails: no visible global function definition for
  'str'
print.twsOrder: no visible global function definition for 'str'
print.twsOrderState: no visible global function definition for 'str'
print.twsScannerSubscription: no visible global function definition for
  'str'
reqAccountUpdates: no visible binding for global variable 'timestamp'
reqContractDetails: no visible binding for global variable 'timestamp'
reqHistoricalData: no visible global function definition for
  'flush.console'
reqHistoricalData: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  flush.console str timestamp write.table
Consider adding
  importFrom("utils", "flush.console", "str", "timestamp", "write.table")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ICA: no visible global function definition for 'runif'
plot.ICA: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
ICCbare: no visible global function definition for 'na.omit'
ICCbare: no visible global function definition for 'formula'
ICCbare: no visible global function definition for 'replications'
ICCbare: no visible global function definition for 'aggregate'
ICCbare: no visible global function definition for 'anova'
ICCbare: no visible global function definition for 'aov'
ICCbareF: no visible global function definition for 'aggregate'
ICCest: no visible global function definition for 'na.omit'
ICCest: no visible global function definition for 'anova'
ICCest: no visible global function definition for 'aov'
ICCest: no visible global function definition for 'aggregate'
ICCest: no visible global function definition for 'qf'
ICCest: no visible global function definition for 'qnorm'
Nest: no visible global function definition for 'qnorm'
effort : CIW: no visible global function definition for 'qf'
effort: no visible global function definition for 'plot'
effort: no visible global function definition for 'axis'
effort: no visible global function definition for 'lines'
effort: no visible global function definition for 'legend'
Undefined global functions or variables:
  aggregate anova aov axis formula legend lines na.omit plot qf qnorm
  replications
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "aggregate", "anova", "aov", "formula", "na.omit",
             "qf", "qnorm", "replications")
to your NAMESPACE file.
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    R     14.5Mb
    doc    4.8Mb
    libs   2.9Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'efficiency.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'KernSmooth' which was already attached by Depends.
  Please remove these calls from your code.
bickde: no visible global function definition for 'optimize'
iclocpoly: no visible global function definition for 'approx'
iclocpoly: no visible global function definition for 'sd'
iclocpoly: no visible global function definition for 'dnorm'
iclocpoly: no visible global function definition for 'pnorm'
iclocpoly: no visible global function definition for 'var'
inmost: no visible global function definition for 'stack'
Undefined global functions or variables:
  approx dnorm optimize pnorm sd stack var
Consider adding
  importFrom("stats", "approx", "dnorm", "optimize", "pnorm", "sd",
             "var")
  importFrom("utils", "stack")
to your NAMESPACE file.
INCAncinner : dian: no visible global function definition for 'cutree'
INCAncinner : bestela: no visible global function definition for
  'cutree'
center: no visible global function definition for 'var'
dbhatta: no visible global function definition for 'as.dist'
dcor: no visible global function definition for 'cor'
dcor: no visible global function definition for 'as.dist'
dgower: no visible global function definition for 'as.dist'
dmahal: no visible global function definition for 'as.dist'
dproc2: no visible global function definition for 'as.dist'
plot.incaix: no visible global function definition for 'barplot'
plot.incanc: no visible global function definition for 'plot'
plot.incanc: no visible global function definition for 'lines'
plot.incanc: no visible global function definition for 'legend'
selectioncluster : dian: no visible global function definition for
  'cutree'
selectioncluster : bestela: no visible global function definition for
  'cutree'
Undefined global functions or variables:
  as.dist barplot cor cutree legend lines plot var
Consider adding
  importFrom("graphics", "barplot", "legend", "lines", "plot")
  importFrom("stats", "as.dist", "cor", "cutree", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'lattice' 'caTools' 'gdata' 'gtools' 'gplots' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'caTools' 'gdata' 'gplots' 'gtools' 'lattice' 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.8Mb
PH.ICsurv.EM: no visible global function definition for 'quantile'
PH.ICsurv.EM: no visible global function definition for 'optim'
fast.PH.ICsurv.EM: no visible global function definition for 'quantile'
fast.PH.ICsurv.EM: no visible global function definition for 'optim'
Undefined global functions or variables:
  optim quantile
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

idbg.interact: no visible global function definition for
  'capture.output'
idbg.interact: no visible global function definition for 'timestamp'
idbg.print_breakpoints: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output timestamp
Consider adding
  importFrom("utils", "capture.output", "timestamp")
to your NAMESPACE file.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
comp.uri: no visible global function definition for 'quantile'
est.IDR: no visible global function definition for 'ecdf'
get.pseudo.mix: no visible global function definition for 'pnorm'
get.uri.2d: no visible global function definition for 'smooth.spline'
get.uri.2d: no visible global function definition for 'predict'
Undefined global functions or variables:
  ecdf pnorm predict quantile smooth.spline
Consider adding
  importFrom("stats", "ecdf", "pnorm", "predict", "quantile",
             "smooth.spline")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'XML' 'vegan'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'ie2miscdata'
Package suggested but not available for checking: 'ie2miscdata'
ROC_plot: no visible global function definition for 'pdf'
ROC_plot: no visible global function definition for 'par'
ROC_plot: no visible global function definition for 'dev.off'
Ymean_compare: no visible binding for global variable 'sd'
Ymean_compare: no visible global function definition for 'pdf'
Ymean_compare: no visible global function definition for 'par'
Ymean_compare: no visible global function definition for 'dev.off'
data_simulation: no visible global function definition for 'rnorm'
gibbs_sampling: no visible global function definition for 'rnorm'
mcmc_trace_plot: no visible global function definition for 'pdf'
mcmc_trace_plot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off par pdf rnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "rnorm", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

ifa.em: no visible global function definition for 'runif'
ifa.init.pca: no visible global function definition for 'var'
ifa.init.pca: no visible global function definition for 'cor'
ifa.init.pca: no visible global function definition for 'runif'
ifa.init.random: no visible global function definition for 'runif'
ifa.init.random: no visible global function definition for 'var'
Undefined global functions or variables:
  cor runif var
Consider adding
  importFrom("stats", "cor", "runif", "var")
to your NAMESPACE file.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.8Mb
Malformed Description field: should contain one or more complete sentences.
ihs.mle: no visible global function definition for 'as.formula'
pihs: no visible global function definition for 'pnorm'
qihs: no visible global function definition for 'qnorm'
rihs: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  as.formula pnorm qnorm rnorm
Consider adding
  importFrom("stats", "as.formula", "pnorm", "qnorm", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ilc.Rcheck/00install.out' for details.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    include   2.8Mb
    libs     12.9Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
IMIS: no visible global function definition for 'sample.prior'
IMIS: no visible global function definition for 'var'
IMIS: no visible global function definition for 'cov'
IMIS: no visible global function definition for 'prior'
IMIS: no visible global function definition for 'likelihood'
IMIS : posterior: no visible global function definition for 'prior'
IMIS : posterior: no visible global function definition for
  'likelihood'
IMIS: no visible global function definition for 'optim'
IMIS: no visible global function definition for 'rnorm'
IMIS: no visible global function definition for 'mahalanobis'
IMIS: no visible global function definition for 'cov.wt'
IMIS: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  cov cov.wt dnorm likelihood mahalanobis optim prior rnorm
  sample.prior var
Consider adding
  importFrom("stats", "cov", "cov.wt", "dnorm", "mahalanobis", "optim",
             "rnorm", "var")
to your NAMESPACE file.
prepare_Rd: IMIS.Rd:26: Dropping empty section \keyword
heter_IV2: no visible global function definition for 'poly'
heter_IV2: no visible global function definition for 'lm'
heter_IV2: no visible global function definition for 'step'
heter_IV2: no visible global function definition for 'pnorm'
heter_IV2: no visible global function definition for 'qnorm'
homo_IV1: no visible global function definition for 'coef'
homo_IV1: no visible global function definition for 'pnorm'
homo_IV1: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  coef lm pnorm poly qnorm step
Consider adding
  importFrom("stats", "coef", "lm", "pnorm", "poly", "qnorm", "step")
to your NAMESPACE file.
prepare_Rd: heter_IV2.Rd:82-84: Dropping empty section \note
prepare_Rd: heter_IV2.Rd:88-90: Dropping empty section \seealso
prepare_Rd: homo_IV1.Rd:65-67: Dropping empty section \note
prepare_Rd: homo_IV1.Rd:71-73: Dropping empty section \seealso
prepare_Rd: impact.Rd:31-33: Dropping empty section \source
'library' or 'require' calls to packages already attached by Depends:
  'inline' 'lpSolve'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'inline' 'lpSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
FctReducedNodevalues: no visible global function definition for
  'signature'
FctReducedNodevalues: no visible global function definition for
  'cfunction'
TotalVar: no visible global function definition for 'lp'
Undefined global functions or variables:
  cfunction lp signature
Consider adding
  importFrom("methods", "signature")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
generate.ExpressionData: no visible global function definition for
  'rnorm'
impute.MinDet: no visible binding for global variable 'quantile'
impute.MinProb: no visible binding for global variable 'quantile'
impute.MinProb: no visible binding for global variable 'sd'
impute.MinProb: no visible global function definition for 'median'
impute.MinProb: no visible global function definition for 'rnorm'
impute.QRILC: no visible global function definition for 'qnorm'
impute.QRILC: no visible global function definition for 'quantile'
impute.QRILC: no visible global function definition for 'lm'
insertMVs: no visible global function definition for 'rnorm'
model.Selector: no visible global function definition for 'qnorm'
model.Selector: no visible global function definition for 'quantile'
model.Selector: no visible global function definition for 'lm'
model.Selector: no visible global function definition for 'ecdf'
model.Selector: no visible global function definition for 'pnorm'
pep2prot: no visible binding for global variable 'median'
Undefined global functions or variables:
  ecdf lm median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "ecdf", "lm", "median", "pnorm", "qnorm",
             "quantile", "rnorm", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
impute.mdr: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'count_compare'
heal_data: no visible global function definition for 'optimum_k'
heal_data: no visible global function definition for 'optimum_w'
heal_data: no visible global function definition for 'pred_for_w'
Undefined global functions or variables:
  optimum_k optimum_w pred_for_w
Warning: no function found corresponding to methods exports from 'IM' for: 'initialize'

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

Probably some imports need to be declared in the NAMESPACE file.
Warning: no function found corresponding to methods exports from 'IM' for: 'initialize'

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

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  'bmp' 'jpeg' 'methods' 'png'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Title field: should not end in a period.
GenerateMixData: no visible global function definition for 'rnbinom'
GenerateMixData: no visible global function definition for 'rbeta'
GenerateMixData: no visible global function definition for 'rbinom'
GenerateMixData: no visible global function definition for 'rpois'
InitializePars: no visible global function definition for 'aggregate'
InitializePars: no visible global function definition for 'rnorm'
MultiStart: no visible global function definition for 'rnorm'
MultiStart: no visible global function definition for 'runif'
inarmix: no visible global function definition for 'terms'
inarmix: no visible global function definition for 'model.frame'
inarmix: no visible global function definition for 'model.response'
inarmix: no visible global function definition for 'model.matrix'
print.diagnose.inarmix: no visible global function definition for
  'plot'
print.diagnose.inarmix: no visible global function definition for
  'lines'
print.summary.inarmix: no visible global function definition for
  'printCoefmat'
summary.inarmix: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  aggregate lines model.frame model.matrix model.response plot pnorm
  printCoefmat rbeta rbinom rnbinom rnorm rpois runif terms
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "aggregate", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "rbeta",
             "rbinom", "rnbinom", "rnorm", "rpois", "runif", "terms")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rsprng'
Malformed Title field: should not end in a period.
'library' or 'require' call to 'xtable' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Rmpi' 'rsprng' 'snow'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
A.dep.tests: no visible global function definition for 'combn'
A.dep.tests: no visible global function definition for 'pchisq'
dependogram: no visible global function definition for 'makeCluster'
dependogram: no visible global function definition for
  'clusterSetupSPRNG'
dependogram: no visible global function definition for 'clusterCall'
dependogram: no visible global function definition for 'stopCluster'
dependogram: no visible global function definition for 'combn'
dependogram: no visible global function definition for 'plot'
dependogram: no visible global function definition for 'points'
dependogram: no visible global function definition for 'segments'
Undefined global functions or variables:
  clusterCall clusterSetupSPRNG combn makeCluster pchisq plot points
  segments stopCluster
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "pchisq")
  importFrom("utils", "combn")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
IDM.bootCI: no visible global function definition for 'cov'
IDM.bootCI: no visible global function definition for 'cor'
IDM.bootCI: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cor cov quantile
Consider adding
  importFrom("stats", "cor", "cov", "quantile")
to your NAMESPACE file.
Package in Depends field not imported from: 'sandwich'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
infer,coxph: no visible global function definition for 'coef'
infer,coxph: no visible global function definition for 'vcov'
infer,coxph: no visible global function definition for 'sandwich'
infer,coxph: no visible global function definition for 'pnorm'
infer,coxph: no visible global function definition for 'qnorm'
infer,gee: no visible global function definition for 'coef'
infer,gee: no visible global function definition for 'pnorm'
infer,gee: no visible global function definition for 'qnorm'
infer,glm: no visible global function definition for 'coef'
infer,glm: no visible global function definition for 'sandwich'
infer,glm: no visible global function definition for 'vcov'
infer,glm: no visible global function definition for 'pnorm'
infer,glm: no visible global function definition for 'qnorm'
infer,lm: no visible global function definition for 'coef'
infer,lm: no visible global function definition for 'sandwich'
infer,lm: no visible global function definition for 'vcov'
infer,lm: no visible global function definition for 'pnorm'
infer,lm: no visible global function definition for 'qnorm'
infer,lme: no visible global function definition for 'coef'
infer,lme: no visible global function definition for 'fixed.effects'
infer,lme: no visible global function definition for 'vcov'
infer,lme: no visible global function definition for 'pnorm'
infer,lme: no visible global function definition for 'qnorm'
infer,mer: no visible global function definition for 'coef'
infer,mer: no visible global function definition for 'vcov'
infer,mer: no visible global function definition for 'pnorm'
infer,mer: no visible global function definition for 'qnorm'
infer,mer: no visible binding for global variable 'fm1'
Undefined global functions or variables:
  coef fixed.effects fm1 pnorm qnorm sandwich vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "vcov")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
contrib: no visible global function definition for 'aggregate'
est.expDeath : surv_p: no visible global function definition for
  'survfit'
est.expDeath : surv_p: no visible global function definition for
  'approx'
function1: no visible global function definition for 'coxph.detail'
inference.SMR: no visible global function definition for 'qnorm'
var.expDeath : surv_p: no visible global function definition for
  'survfit'
var.expDeath : surv_p: no visible global function definition for
  'approx'
Undefined global functions or variables:
  aggregate approx coxph.detail qnorm survfit
Consider adding
  importFrom("stats", "aggregate", "approx", "qnorm")
to your NAMESPACE file.
BugReports field should be the URL of a single webpage
gen.intercepts: no visible global function definition for 'contr.SAS'
Undefined global functions or variables:
  contr.SAS
Consider adding
  importFrom("stats", "contr.SAS")
to your NAMESPACE file.
entropy: no visible global function definition for 'na.omit'
interinformation: no visible global function definition for 'na.omit'
multiinformation: no visible global function definition for 'na.omit'
mutinformation: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
getInfra: no visible global function definition for 'txtProgressBar'
getInfra: no visible global function definition for 'download.file'
getInfra: no visible global function definition for 'setTxtProgressBar'
getInfra : <anonymous>: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "download.file", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Unexported object imported by a ':::' call: 'ltm:::crf.GPCM'
  See the note in ?`:::` about the use of this operator.
Jeffreys: no visible global function definition for 'integrate'
Jeffreys: no visible global function definition for 'splinefun'
count.rows: no visible global function definition for 'tail'
count.rows: no visible global function definition for 'head'
cprobs : <anonymous>: no visible global function definition for
  'plogis'
inf.func.ltm : f: no visible global function definition for 'plogis'
iota: no visible global function definition for 'integrate'
iota: no visible global function definition for 'optimize'
iota: no visible global function definition for 'pchisq'
iota.c : rirm: no visible global function definition for 'coef'
iota.c: no visible global function definition for 'integrate'
iota.c: no visible global function definition for 'sd'
iota.u: no visible global function definition for 'integrate'
iprobs : <anonymous>: no visible global function definition for
  'plogis'
logL.ltm : logL: no visible global function definition for 'dbinom'
logL.ltm : logL: no visible global function definition for 'plogis'
logL.ltm : logL : <anonymous>: no visible global function definition
  for 'plogis'
rJeffreys : Jpinv.min: no visible global function definition for
  'integrate'
rJeffreys : Jpinv: no visible global function definition for 'nlminb'
rJeffreys : Jpinv: no visible global function definition for 'qnorm'
rJeffreys: no visible global function definition for 'runif'
Undefined global functions or variables:
  coef dbinom head integrate nlminb optimize pchisq plogis qnorm runif
  sd splinefun tail
Consider adding
  importFrom("stats", "coef", "dbinom", "integrate", "nlminb",
             "optimize", "pchisq", "plogis", "qnorm", "runif", "sd",
             "splinefun")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ExPosition' 'prettyGraphs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Title field: should not end in a period.
'library' or 'require' calls to packages already attached by Depends:
  'compiler' 'deSolve' 'lattice' 'nlme'
  Please remove these calls from your code.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'insideRODE/R/zzz.r':
  .First.lib calls:
    require(nlme)
    require(lattice)
    require(deSolve)
    require(compiler)

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

cfLSODE: no visible global function definition for 'deriv'
cfODE: no visible global function definition for 'deriv'
cfVODE: no visible global function definition for 'deriv'
cpLSODE: no visible global function definition for 'deriv'
cpODE: no visible global function definition for 'deriv'
cpVODE: no visible global function definition for 'deriv'
nlmLSODE: no visible global function definition for 'deriv'
nlmLSODEcp: no visible global function definition for 'deriv'
nlmODE: no visible global function definition for 'deriv'
nlmODEcp: no visible global function definition for 'deriv'
nlmVODE: no visible global function definition for 'deriv'
nlmVODEcp: no visible global function definition for 'deriv'
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
cgrad: no visible global function definition for 'res'
doshade: no visible global function definition for 'projection'
doshade: no visible global function definition for 'extent'
doshade: no visible global function definition for 'res'
doshade: no visible global function definition for 'raster'
doshade: no visible global function definition for 'extent<-'
Undefined global functions or variables:
  extent extent<- projection raster res
Running examples in 'insol-Ex.R' failed
The error most likely occurred in:

> ### Name: aspect
> ### Title: Aspect or orientation of the slope
> ### Aliases: aspect
> 
> ### ** Examples
> 
> # Create a west-east facing ramp
> slpwe=rep(1,10)  %o% c(1:5,4:1)
> # calculate the aspect at every node or grid cell (it should be 270 or 90 degrees):
> cgr=cgrad(slpwe,1)
> aspect(cgr,degrees=TRUE)
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
 [1,]  270  270  270  270   90   90   90   90   90
 [2,]  270  270  270  270   90   90   90   90   90
 [3,]  270  270  270  270   90   90   90   90   90
 [4,]  270  270  270  270   90   90   90   90   90
 [5,]  270  270  270  270   90   90   90   90   90
 [6,]  270  270  270  270   90   90   90   90   90
 [7,]  270  270  270  270   90   90   90   90   90
 [8,]  270  270  270  270   90   90   90   90   90
 [9,]  270  270  270  270   90   90   90   90   90
[10,]  270  270  270  270   90   90   90   90   90
> 
> # Calculate the aspect of a rough mountain area in the pyrinees
> zipfile=tempfile()
> download.file("http://www.meteoexploration.com/R/insol/data/dempyrenees.asc.zip",zipfile)
trying URL 'http://www.meteoexploration.com/R/insol/data/dempyrenees.asc.zip'
Warning in download.file("http://www.meteoexploration.com/R/insol/data/dempyrenees.asc.zip",  :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file("http://www.meteoexploration.com/R/insol/data/dempyrenees.asc.zip",  : 
  cannot open URL 'http://www.meteoexploration.com/R/insol/data/dempyrenees.asc.zip'
Execution halted
Running examples in 'insol-Ex.R' failed
The error most likely occurred in:

> ### Name: aspect
> ### Title: Aspect or orientation of the slope
> ### Aliases: aspect
> 
> ### ** Examples
> 
> # Create a west-east facing ramp
> slpwe=rep(1,10)  %o% c(1:5,4:1)
> # calculate the aspect at every node or grid cell (it should be 270 or 90 degrees):
> cgr=cgrad(slpwe,1)
> aspect(cgr,degrees=TRUE)
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
 [1,]  270  270  270  270   90   90   90   90   90
 [2,]  270  270  270  270   90   90   90   90   90
 [3,]  270  270  270  270   90   90   90   90   90
 [4,]  270  270  270  270   90   90   90   90   90
 [5,]  270  270  270  270   90   90   90   90   90
 [6,]  270  270  270  270   90   90   90   90   90
 [7,]  270  270  270  270   90   90   90   90   90
 [8,]  270  270  270  270   90   90   90   90   90
 [9,]  270  270  270  270   90   90   90   90   90
[10,]  270  270  270  270   90   90   90   90   90
> 
> # Calculate the aspect of a rough mountain area in the pyrinees
> zipfile=tempfile()
> download.file("http://www.meteoexploration.com/R/insol/data/dempyrenees.asc.zip",zipfile)
trying URL 'http://www.meteoexploration.com/R/insol/data/dempyrenees.asc.zip'
Warning in download.file("http://www.meteoexploration.com/R/insol/data/dempyrenees.asc.zip",  :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file("http://www.meteoexploration.com/R/insol/data/dempyrenees.asc.zip",  : 
  cannot open URL 'http://www.meteoexploration.com/R/insol/data/dempyrenees.asc.zip'
Execution halted
Missing or unexported object: 'devtools::find_rtools'
Malformed Title field: should not end in a period.
Malformed Title field: should not end in a period.
ClearBottomMenuPlot: no visible global function definition for 'rect'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertX'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertX'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'polygon'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertX'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertY'
InteractiveIGraph : keybd: no visible global function definition for
  'readClipboard'
InteractiveIGraph : keybd: no visible global function definition for
  'par'
PlotRegionGeneral: no visible global function definition for 'polygon'
plot.InteractiveIGraph: no visible global function definition for
  'plot'
plot.InteractiveIGraph: no visible global function definition for 'par'
plot.Menu: no visible global function definition for 'par'
plot.Menu: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'strwidth'
plot.MenuItem: no visible binding for global variable 'strheight'
plot.MenuItem: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'text'
plot.MenuLine: no visible binding for global variable 'rect'
Undefined global functions or variables:
  grconvertX grconvertY par plot polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
interact: no visible global function definition for 'cor'
plot.interact: no visible global function definition for 'plot'
standardize.matrix: no visible binding for global variable 'var'
standardize.matrix: no visible binding for global variable 'sd'
Undefined global functions or variables:
  cor plot sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "sd", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
HH: no visible global function definition for 'var'
HH: no visible global function definition for 'qnorm'
exactCI: no visible global function definition for 'quantile'
sample.n: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  qnorm quantile rbinom var
Consider adding
  importFrom("stats", "qnorm", "quantile", "rbinom", "var")
to your NAMESPACE file.
Interpol: no visible global function definition for 'splinefun'
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
prepare_Rd: AAdescriptor.Rd:25-27: Dropping empty section \details
prepare_Rd: AAdescriptor.Rd:39-41: Dropping empty section \note
prepare_Rd: AAdescriptor.Rd:45-47: Dropping empty section \seealso
prepare_Rd: AAindex.Rd:11-12: Dropping empty section \format
prepare_Rd: AAindex.Rd:1080-1081: Dropping empty section \source
prepare_Rd: AAindex.Rd:1085-1086: Dropping empty section \examples
prepare_Rd: Interpol.Rd:35-37: Dropping empty section \details
prepare_Rd: Interpol.Rd:47-49: Dropping empty section \note
prepare_Rd: Interpol.Rd:53-55: Dropping empty section \seealso
prepare_Rd: V3.Rd:11-12: Dropping empty section \format
prepare_Rd: V3.Rd:13-14: Dropping empty section \details
prepare_Rd: V3.Rd:15-16: Dropping empty section \source
prepare_Rd: V3.Rd:20-21: Dropping empty section \examples
Packages in Depends field not imported from:
  'chron' 'date'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Mo.Th.Ra.: no visible global function definition for 'aggregate'
daily_mean: no visible global function definition for 'aggregate'
date.time: no visible global function definition for 'chron'
date.time: no visible global function definition for 'years'
date.time: no visible global function definition for 'days'
date.time: no visible global function definition for 'hours'
par_calibration: no visible global function definition for 'date.mdy'
par_calibration: no visible global function definition for 'as.date'
par_calibration: no visible global function definition for 'aggregate'
plot_meas_sim: no visible global function definition for 'as.date'
plot_meas_sim: no visible global function definition for 'date.mdy'
plot_meas_sim: no visible global function definition for 'plot'
plot_meas_sim: no visible global function definition for 'par'
plot_meas_sim: no visible global function definition for 'legend'
shape_calibration: no visible global function definition for 'date.mdy'
shape_calibration: no visible global function definition for 'as.date'
shape_calibration: no visible global function definition for
  'aggregate'
Undefined global functions or variables:
  aggregate as.date chron date.mdy days hours legend par plot years
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "aggregate")
to your NAMESPACE file.
icScoreTest: no visible global function definition for 'pnorm'
icScoreTest: no visible global function definition for 'pchisq'
icfit.formula: no visible global function definition for 'terms'
icfit.formula: no visible global function definition for
  'model.extract'
icfitBootCI: no visible global function definition for 'binom.test'
ictest.formula: no visible global function definition for
  'model.extract'
plot.icfit: no visible global function definition for 'gray'
plot.icfit: no visible global function definition for 'plot'
plot.icfit: no visible global function definition for 'axis'
plot.icfit : polygon.icfit: no visible global function definition for
  'polygon'
scoresFromFit: no visible global function definition for 'dnorm'
scoresFromFit: no visible global function definition for 'qnorm'
wsrHLYpclt: no visible global function definition for 'model.matrix'
wsrHLYpclt: no visible global function definition for 'pchisq'
wsrHLYpclt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  axis binom.test dnorm gray model.extract model.matrix pchisq plot
  pnorm polygon qnorm terms
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis", "plot", "polygon")
  importFrom("stats", "binom.test", "dnorm", "model.extract",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
interventionEffects: no visible binding for global variable 'sd'
interventionEffects: no visible global function definition for 'pt'
interventionEffects: no visible global function definition for 'sd'
interventionalInference: no visible global function definition for 'sd'
interventionalInferenceAdvanced: no visible global function definition
  for 'sd'
linesROC: no visible global function definition for 'segments'
plotMaxML: no visible global function definition for 'plot'
plotMaxML: no visible global function definition for 'segments'
Undefined global functions or variables:
  plot pt sd segments
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "pt", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'maxLik' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'maxLik'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ILik : rbern: no visible global function definition for 'runif'
ILik : q: no visible global function definition for 'dnorm'
ILik : SlambdaG: no visible global function definition for 'rnorm'
ILik : Pi_hat: no visible global function definition for 'rnorm'
ILik : q: no visible global function definition for 'dgamma'
ILik : SlambdaG: no visible global function definition for 'rgamma'
ILik : Pi_hat: no visible global function definition for 'rgamma'
ILik: no visible global function definition for 'maxLik'
ILik: no visible global function definition for 'coef'
ILik: no visible global function definition for 'hessian'
ILik: no visible global function definition for 'plot'
Undefined global functions or variables:
  coef dgamma dnorm hessian maxLik plot rgamma rnorm runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dgamma", "dnorm", "rgamma", "rnorm",
             "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/IntNMF.Rcheck/00install.out' for details.
intReg: no visible binding for global variable 'plogis'
intReg: no visible binding for global variable 'pnorm'
intReg: no visible binding for global variable 'pcauchy'
intReg: no visible binding for global variable 'dlogis'
intReg: no visible binding for global variable 'dnorm'
intReg: no visible binding for global variable 'dcauchy'
intReg: no visible global function definition for 'model.matrix'
intReg: no visible global function definition for 'model.weights'
intReg: no visible global function definition for 'model.offset'
intReg: no visible global function definition for 'model.response'
intReg: no visible global function definition for 'glm.fit'
intReg: no visible global function definition for 'binomial'
intReg: no visible binding for global variable 'coef'
intReg: no visible global function definition for 'lm'
intReg: no visible global function definition for 'coef'
intReg: no visible global function definition for 'var'
model.matrix.intReg: no visible global function definition for
  'model.frame'
print.intReg: no visible global function definition for 'coef'
print.summary.intReg: no visible global function definition for
  'logLik'
print.summary.intReg: no visible global function definition for
  'printCoefmat'
summary.intReg: no visible global function definition for 'coef'
Undefined global functions or variables:
  binomial coef dcauchy dlogis dnorm glm.fit lm logLik model.frame
  model.matrix model.offset model.response model.weights pcauchy plogis
  pnorm printCoefmat var
Consider adding
  importFrom("stats", "binomial", "coef", "dcauchy", "dlogis", "dnorm",
             "glm.fit", "lm", "logLik", "model.frame", "model.matrix",
             "model.offset", "model.response", "model.weights",
             "pcauchy", "plogis", "pnorm", "printCoefmat", "var")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
f.B: no visible global function definition for 'pnorm'
f.B.neglog.deriv: no visible global function definition for 'pnorm'
f.B.neglog.deriv: no visible global function definition for 'dnorm'
f.grovest3 : f.est: no visible global function definition for 'survfit'
f.grovest3 : f.est: no visible global function definition for 'plot'
f.grovest3 : f.est: no visible global function definition for 'lines'
f.grovest3: no visible global function definition for 'model.frame'
f.grovest3: no visible global function definition for 'model.extract'
invGauss: no visible global function definition for 'model.frame'
invGauss: no visible global function definition for 'model.extract'
invGauss: no visible global function definition for 'model.matrix'
predict.invGauss: no visible global function definition for
  'model.frame'
predict.invGauss: no visible global function definition for
  'model.extract'
predict.invGauss: no visible global function definition for
  'model.matrix'
predict.invGauss: no visible binding for global variable 'formula'
predict.invGauss: no visible binding for global variable 'data'
summary.invGauss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  data dnorm formula lines model.extract model.frame model.matrix plot
  pnorm survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "dnorm", "formula", "model.extract", "model.frame",
             "model.matrix", "pnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
flowsRandom: no visible global function definition for 'dmultinom'
readBed: no visible global function definition for 'read.table'
Undefined global functions or variables:
  dmultinom read.table
Consider adding
  importFrom("stats", "dmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
File 'iotools/libs/i386/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   7.5Mb
Warning: no function found corresponding to methods exports from 'ipdmeta' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
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.
ipd.meta.power.base.function : power: no visible global function
  definition for 'qnorm'
ipd.meta.power.base.function : power: no visible global function
  definition for 'pnorm'
ipd.meta.power.base.function: no visible global function definition for
  'qnorm'
ipdlme.hetero: no visible global function definition for 'new'
ipdlme.homo: no visible global function definition for 'new'
plot_ipdlme: no visible global function definition for 'par'
plot_ipdlme: no visible global function definition for 'abline'
plot_ipdlme: no visible global function definition for 'axis'
plot_ipdlme: no visible global function definition for 'segments'
confint,ipdlme: no visible global function definition for 'qt'
plot,ipdlme: no visible global function definition for 'par'
plot,ipdlme: no visible global function definition for 'abline'
plot,ipdlme: no visible global function definition for 'axis'
plot,ipdlme: no visible global function definition for 'segments'
summary,ipdlme: no visible global function definition for 'pt'
Undefined global functions or variables:
  abline axis new par pnorm pt qnorm qt segments
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "pt", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'testthat.R' [69s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ipeaData)
  > 
  > test_check("ipeaData")
  [1] "NA. 05/1999 a 03/2009. Acesso em: 19/11/2018"
  -- 1. Error: ipeaData (@test_functions_ipea_data.R#19)  ------------------------
  Recv failure: Connection was reset
  1: suppressWarnings(result <- ipeadata("SERIE SEM RETORNO")) at testthat/test_functions_ipea_data.R:19
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: ipeadata("SERIE SEM RETORNO")
  4: get_metadata(serie)
  5: basic_call(api_call, type)
  6: GET(api)
  7: request_perform(req, hu$handle$handle)
  8: request_fetch(req$output, req$url, handle)
  9: request_fetch.write_memory(req$output, req$url, handle)
  10: curl::curl_fetch_memory(url, handle = handle)
  
  -- 2. Error: search_serie (@test_functions_ipea_data.R#24)  --------------------
  Timeout was reached: Connection timed out after 10015 milliseconds
  1: search_serie("pib", fields_search = ("SERNOME")) at testthat/test_functions_ipea_data.R:24
  2: basic_call(api_call, type)
  3: GET(api)
  4: request_perform(req, hu$handle$handle)
  5: request_fetch(req$output, req$url, handle)
  6: request_fetch.write_memory(req$output, req$url, handle)
  7: curl::curl_fetch_memory(url, handle = handle)
  
  == testthat results  ===========================================================
  OK: 5 SKIPPED: 0 FAILED: 2
  1. Error: ipeaData (@test_functions_ipea_data.R#19) 
  2. Error: search_serie (@test_functions_ipea_data.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  'MCMCpack' 'mvtnorm' 'truncnorm'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
code.simple.gaps: no visible global function definition for 'tail'
multistateMCMC: no visible global function definition for 'write.table'
multistateMCMC: no visible global function definition for 'read.table'
multistateMCMC: no visible global function definition for 'tail'
multistateML: no visible global function definition for 'tail'
multistateML: no visible global function definition for 'write.table'
multistateML: no visible global function definition for 'read.table'
phylo2mafft: no visible global function definition for 'write.table'
read.beast : foo: no visible global function definition for 'head'
read.beast: no visible global function definition for 'tail'
read.starbeast: no visible global function definition for 'head'
trimEnds : replaceWithN : getIndex: no visible global function
  definition for 'head'
unresolve.clade: no visible global function definition for 'tail'
unresolve.clade: no visible global function definition for 'head'
write.fas: no visible global function definition for 'tail'
Undefined global functions or variables:
  head read.table tail write.table
Consider adding
  importFrom("utils", "head", "read.table", "tail", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RBGL' 'graph' 'igraph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
convert_MITAB_to_edgeList: no visible global function definition for
  'combn'
convert_edgeList_to_graph: no visible global function definition for
  'ftM2graphNEL'
convert_edgeList_to_graph: no visible global function definition for
  'graph.data.frame'
convert_graph_to_edgeList: no visible global function definition for
  'edgeWeights'
convert_graph_to_edgeList: no visible global function definition for
  'get.edgelist'
convert_graph_to_edgeList: no visible global function definition for
  'E'
create_id_conversion_table: no visible global function definition for
  'write.table'
get_irefindex: no visible global function definition for 'read.table'
get_irefindex: no visible global function definition for
  'download.file'
get_irefindex: no visible global function definition for 'unzip'
summary_graph: no visible global function definition for
  'connectedComp'
summary_graph: no visible global function definition for 'subGraph'
summary_graph: no visible global function definition for 'clusters'
summary_graph: no visible global function definition for 'subgraph'
summary_graph: no visible global function definition for 'plot'
summary_graph: no visible binding for global variable
  'layout.fruchterman.reingold'
Undefined global functions or variables:
  E clusters combn connectedComp download.file edgeWeights ftM2graphNEL
  get.edgelist graph.data.frame layout.fruchterman.reingold plot
  read.table subGraph subgraph unzip write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "combn", "download.file", "read.table", "unzip",
             "write.table")
to your NAMESPACE file.
'library' or 'require' call to 'lpSolve' which was already attached by Depends.
  Please remove these calls from your code.
NeedsCompilation field should likely be 'yes'
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  inst/irtppcpp/include/SPGO/makefile
  inst/irtppcpp/makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Malformed Description field: should contain one or more complete sentences.
dendrify: no visible binding for global variable 'item'
dendrify: no visible binding for global variable 'node'
dendrify: no visible binding for global variable 'value'
exogenize: no visible binding for global variable 'item'
Undefined global functions or variables:
  item node value
isbf: no visible global function definition for 'var'
isbf: no visible global function definition for 'qnorm'
isbfReg: no visible global function definition for 'var'
isbfReg: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
residualplot: no visible global function definition for 'predict'
residualplot: no visible global function definition for 'rstandard'
residualplot: no visible global function definition for
  'complete.cases'
residualplot: no visible global function definition for 'plot'
residualplot: no visible global function definition for 'points'
residualplot: no visible global function definition for 'lines'
residualplot: no visible global function definition for 'smooth.spline'
residualplot: no visible global function definition for 'sd'
residualplot: no visible global function definition for 'rgb'
residualplot: no visible global function definition for 'polygon'
Undefined global functions or variables:
  complete.cases lines plot points polygon predict rgb rstandard sd
  smooth.spline
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "complete.cases", "predict", "rstandard", "sd",
             "smooth.spline")
to your NAMESPACE file.
'library' or 'require' call to 'scatterplot3d' which was already attached by Depends.
  Please remove these calls from your code.
histInterval : buildHist: no visible global function definition for
  'hist'
intervalGraph3D: no visible global function definition for 'par'
regInterval: no visible global function definition for 'lm'
Undefined global functions or variables:
  hist lm par
Consider adding
  importFrom("graphics", "hist", "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
EstimateIsingLL: no visible global function definition for 'combn'
EstimateIsingLL: no visible global function definition for 'loglin'
EstimateIsingPL: no visible global function definition for 'nlm'
EstimateIsingUni : <anonymous>: no visible global function definition
  for 'glm'
EstimateIsingUni : <anonymous>: no visible binding for global variable
  'binomial'
EstimateIsingUni: no visible binding for global variable 'coef'
Undefined global functions or variables:
  binomial coef combn glm loglin nlm
Consider adding
  importFrom("stats", "binomial", "coef", "glm", "loglin", "nlm")
  importFrom("utils", "combn")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
C.cal: no visible global function definition for 'as.stepfun'
bandwidth.choose.cv: no visible global function definition for 'isoreg'
g.density: no visible global function definition for 'as.stepfun'
g.density: no visible global function definition for 'dnorm'
h.density: no visible global function definition for 'dnorm'
iso.bt.unit: no visible global function definition for 'quantile'
iso.bt.unit.sub: no visible global function definition for 'isoreg'
iso.bt.unit.sub: no visible global function definition for 'as.stepfun'
iso.bt.wald.unit: no visible global function definition for 'var'
iso.ci: no visible global function definition for 'isoreg'
iso.ci.transform.unit: no visible global function definition for
  'as.stepfun'
Undefined global functions or variables:
  as.stepfun dnorm isoreg quantile var
Consider adding
  importFrom("stats", "as.stepfun", "dnorm", "isoreg", "quantile", "var")
to your NAMESPACE file.
ACO : bordacircular: no visible global function definition for
  'medianCircular'
Undefined global functions or variables:
  medianCircular
'library' or 'require' call to 'proxy' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
isopam : core: no visible global function definition for 'dist'
isopam : core: no visible global function definition for 'write.table'
isopam : core: no visible global function definition for 'as.dist'
isopam : core: no visible global function definition for
  'txtProgressBar'
isopam : core: no visible global function definition for
  'setTxtProgressBar'
isopam : core: no visible global function definition for 'aggregate'
isopam: no visible binding for global variable 'var'
isopam: no visible global function definition for 'na.omit'
isopam: no visible global function definition for 'write.table'
isopam: no visible global function definition for 'bmp'
isopam: no visible global function definition for 'dev.off'
isotab: no visible global function definition for 'aggregate'
isotab : fshtest: no visible global function definition for 'dhyper'
isotab : fshtest : pnhyper: no visible global function definition for
  'phyper'
Undefined global functions or variables:
  aggregate as.dist bmp dev.off dhyper dist na.omit phyper
  setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.off")
  importFrom("stats", "aggregate", "as.dist", "dhyper", "dist",
             "na.omit", "phyper", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
ufit: no visible global function definition for 'stepfun'
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/itemanalysis.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'partitions' 'VGAM' 'MASS' 'ape' 'apTreeshape' 'geiger' 'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'MASS' 'VGAM' 'apTreeshape' 'ape' 'geiger' 'gtools' 'partitions'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'Matching' 'R2jags' 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bpsm: no visible global function definition for 'glm'
bpsm: no visible global function definition for 'binomial'
bpsm: no visible global function definition for 'Match'
bpsm: no visible global function definition for 'cov'
bpsm: no visible global function definition for 'vcov'
bpsm : inits: no visible global function definition for 'runif'
bpsm: no visible global function definition for 'jags'
bpsr: no visible global function definition for 'glm'
bpsr: no visible global function definition for 'binomial'
bpsr: no visible global function definition for 'lm'
bpsr : inits: no visible global function definition for 'runif'
bpsr: no visible global function definition for 'jags'
modelpsm: no visible binding for global variable 'D'
modelpsr: no visible binding for global variable 'D'
Undefined global functions or variables:
  D Match binomial cov glm jags lm runif vcov
Consider adding
  importFrom("stats", "D", "binomial", "cov", "glm", "lm", "runif",
             "vcov")
to your NAMESPACE file.
ivbma.cv.study: no visible global function definition for 'predict'
ivbma.diagnostics: no visible global function definition for 'pchisq'
ivbma.init: no visible global function definition for 'rbinom'
ivbma.init: no visible global function definition for 'cov'
ivbma.score: no visible global function definition for 'median'
ivbma.score: no visible global function definition for 'var'
predict.ivbma: no visible global function definition for 'rnorm'
rinvwish: no visible global function definition for 'rchisq'
rinvwish: no visible global function definition for 'rnorm'
rinvwish.old: no visible global function definition for 'rchisq'
rinvwish.old: no visible global function definition for 'rnorm'
rmvnorm: no visible global function definition for 'rnorm'
rmvnorm.precision: no visible global function definition for 'rnorm'
summary.ivbma: no visible global function definition for 'quantile'
update.L: no visible global function definition for 'runif'
update.M: no visible global function definition for 'runif'
update.M.SUR: no visible global function definition for 'runif'
Undefined global functions or variables:
  cov median pchisq predict quantile rbinom rchisq rnorm runif var
Consider adding
  importFrom("stats", "cov", "median", "pchisq", "predict", "quantile",
             "rbinom", "rchisq", "rnorm", "runif", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
ivFixed.formula: no visible global function definition for
  'model.matrix'
ivFixed.formula: no visible global function definition for
  'model.response'
summary.ivFixed: no visible global function definition for 'coef'
summary.ivFixed: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
clusterVCV: no visible global function definition for 'estfun'
covc: no visible global function definition for 'sandwich'
ftest: no visible global function definition for 'vcovHC'
Undefined global functions or variables:
  estfun sandwich vcovHC
Malformed Title field: should not end in a period.
ARsensitivity.ci: no visible global function definition for 'residuals'
ARsensitivity.ci: no visible global function definition for 'lm'
ARsensitivity.ci: no visible global function definition for 'qf'
ARsensitivity.ci: no visible global function definition for 'fitted'
ARsensitivity.power: no visible global function definition for 'qf'
ARsensitivity.power: no visible global function definition for 'pf'
ARsensitivity.size: no visible global function definition for 'qf'
ARsensitivity.size: no visible global function definition for 'pf'
anderson.rubin.ci: no visible global function definition for 'qf'
anderson.rubin.ci: no visible global function definition for 'fitted'
anderson.rubin.ci: no visible global function definition for 'lm'
power.iv: no visible global function definition for 'qf'
power.iv: no visible global function definition for 'pf'
Undefined global functions or variables:
  fitted lm pf qf residuals
Consider adding
  importFrom("stats", "fitted", "lm", "pf", "qf", "residuals")
to your NAMESPACE file.
hausman: no visible global function definition for 'pchisq'
ivbe: no visible global function definition for 'cor'
ivbe: no visible global function definition for 'pt'
ivfixed: no visible global function definition for 'cor'
ivfixed: no visible global function definition for 'pt'
ivpan.formula: no visible global function definition for 'model.matrix'
ivpan.formula: no visible global function definition for
  'model.response'
ivrandom: no visible global function definition for 'cor'
ivrandom: no visible global function definition for 'pt'
summary.ivpan: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  cor model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response", "pchisq",
             "printCoefmat", "pt")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
histw: no visible global function definition for 'plot.new'
histw: no visible global function definition for 'plot.window'
histw: no visible global function definition for 'axis'
histw: no visible global function definition for 'rect'
histw: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis lines plot.new plot.window rect
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
to your NAMESPACE file.
boxplot.james: no visible global function definition for 'mtext'
getBestSolutionValues.james : <anonymous>: no visible global function
  definition for 'tail'
isMinimizing: no visible global function definition for 'head'
isMinimizing: no visible global function definition for 'tail'
mergeJAMES.james: no visible global function definition for 'glob2rx'
plotConvergence.james : <anonymous> : <anonymous>: no visible global
  function definition for 'tail'
plotConvergence.james: no visible global function definition for 'tail'
plotConvergence.james: no visible global function definition for 'head'
plotConvergence.james : <anonymous>: no visible global function
  definition for 'tail'
plotConvergence.james: no visible global function definition for
  'matplot'
plotConvergence.james: no visible global function definition for
  'mtext'
summary.james: no visible global function definition for 'sd'
summary.james: no visible global function definition for 'median'
summary.james: no visible global function definition for 'IQR'
Undefined global functions or variables:
  IQR glob2rx head matplot median mtext sd tail
Consider adding
  importFrom("graphics", "matplot", "mtext")
  importFrom("stats", "IQR", "median", "sd")
  importFrom("utils", "glob2rx", "head", "tail")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'gtools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

make_template: no visible global function definition for 'invalid'
Undefined global functions or variables:
  invalid
.getJavaGDObject: no visible global function definition for '.jmkref'
.javaGD.copy.device: no visible global function definition for
  'dev.cur'
.javaGD.copy.device: no visible binding for global variable 'pdf'
.javaGD.copy.device: no visible global function definition for
  'dev.set'
.javaGD.copy.device: no visible global function definition for
  'dev.copy'
.javaGD.copy.device: no visible global function definition for 'par'
.javaGD.copy.device: no visible global function definition for
  'dev.off'
.javaGD.get.size: no visible global function definition for 'dev.cur'
.javaGD.resize: no visible global function definition for 'dev.cur'
JavaGD: no visible global function definition for '.jinit'
Undefined global functions or variables:
  .jinit .jmkref dev.copy dev.cur dev.off dev.set par pdf
Consider adding
  importFrom("grDevices", "dev.copy", "dev.cur", "dev.off", "dev.set",
             "pdf")
  importFrom("graphics", "par")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Package suggested but not available for checking: 'doMC'
getSysinfo: no visible global function definition for 'sessionInfo'
getVecInfo: no visible global function definition for 'sd'
isSeriesConstant: no visible global function definition for 'median'
labelMargins: no visible global function definition for 'mtext'
plotBG: no visible global function definition for 'plot'
plotBG: no visible global function definition for 'polygon'
plotBG: no visible global function definition for 'par'
plotColorScale: no visible global function definition for 'par'
plotColorScale: no visible global function definition for 'text'
plotImageRotated: no visible global function definition for
  'heat.colors'
plotImageRotated: no visible global function definition for 'par'
plotImageRotated: no visible global function definition for 'plot'
plotImageRotated: no visible global function definition for 'image'
plotImageRotated: no visible global function definition for 'axis'
plotNLines: no visible global function definition for 'par'
plotNLines: no visible global function definition for 'plot'
plotNLines: no visible global function definition for 'mtext'
plotNLines: no visible global function definition for 'axis'
plotNLines: no visible global function definition for 'points'
plotNLines: no visible global function definition for 'sd'
userCoords: no visible global function definition for 'par'
Undefined global functions or variables:
  axis heat.colors image median mtext par plot points polygon sd
  sessionInfo text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "image", "mtext", "par", "plot",
             "points", "polygon", "text")
  importFrom("stats", "median", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'doMC'
'library' or 'require' call to 'igraph' which was already attached by Depends.
  Please remove these calls from your code.
JGL: no visible global function definition for 'cov'
admm.iters: no visible global function definition for 'cov'
admm.iters.unconnected: no visible global function definition for 'var'
plot.jgl: no visible global function definition for 'plot'
Undefined global functions or variables:
  cov plot var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "var")
to your NAMESPACE file.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    dict  19.2Mb
powerLongSurv: no visible global function definition for 'qnorm'
powerLongSurv: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
JBTest: no visible global function definition for 'pchisq'
generateSignificance: no visible global function definition for 'pnorm'
packages: no visible global function definition for 'install.packages'
shift: no visible global function definition for 'tail'
shift: no visible global function definition for 'head'
splitBy: no visible global function definition for 'head'
Undefined global functions or variables:
  head install.packages pchisq pnorm tail
Consider adding
  importFrom("stats", "pchisq", "pnorm")
  importFrom("utils", "head", "install.packages", "tail")
to your NAMESPACE file.
RE.ADT: no visible global function definition for 'sd'
RE.ADT: no visible global function definition for 'pnorm'
RE.Johnson: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm sd
Consider adding
  importFrom("stats", "pnorm", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
binteg: no visible global function definition for 'contourLines'
binteg: no visible global function definition for 'approx'
binteg: no visible global function definition for 'par'
plot1: no visible global function definition for 'plot'
plot1: no visible global function definition for 'par'
plot1: no visible global function definition for 'rect'
plot1: no visible global function definition for 'axis'
plot1: no visible global function definition for 'contour'
plot1: no visible global function definition for 'contourLines'
plot1: no visible binding for global variable 'approx'
plot1: no visible global function definition for 'lines'
plot1: no visible global function definition for 'text'
plot2: no visible global function definition for 'plot'
plot2: no visible global function definition for 'abline'
plot2: no visible global function definition for 'lines'
plot2: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline approx axis contour contourLines legend lines par plot rect
  text
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "abline", "axis", "contour", "legend", "lines",
             "par", "plot", "rect", "text")
  importFrom("stats", "approx")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Rsolnp' 'dglm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sonarCSV: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
File 'jsonlite/libs/i386/jsonlite.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection'
File 'jsonlite/libs/x64/jsonlite.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
qtls: no visible global function definition for 'quantile'
qtls: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm quantile
Consider adding
  importFrom("stats", "pnorm", "quantile")
to your NAMESPACE file.
expression_up : <anonymous>: no visible global function definition for
  'quantile'
expression_up : <anonymous>: no visible global function definition for
  'IQR'
expression_up : <anonymous>: no visible global function definition for
  'median'
expression_up : <anonymous>: no visible global function definition for
  'sd'
plot_up: no visible global function definition for 'plot'
plot_up: no visible global function definition for 'text'
Undefined global functions or variables:
  IQR median plot quantile sd text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "IQR", "median", "quantile", "sd")
to your NAMESPACE file.
.hichi: no visible global function definition for 'pchisq'
.powchi: no visible global function definition for 'qchisq'
CI3Cats: no visible global function definition for 'qchisq'
CI4Cats: no visible global function definition for 'qchisq'
CI5Cats: no visible global function definition for 'qchisq'
CIBinary: no visible global function definition for 'qchisq'
FixedN3Cats: no visible global function definition for 'qchisq'
FixedN4Cats: no visible global function definition for 'qchisq'
FixedN5Cats: no visible global function definition for 'qchisq'
FixedNBinary: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  pchisq qchisq
Consider adding
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
KappaV: no visible global function definition for 'over'
KappaV: no visible global function definition for 'layout'
KappaV: no visible global function definition for 'terrain.colors'
KappaV: no visible global function definition for 'as'
Undefined global functions or variables:
  as layout over terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "layout")
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
ikcirt.fun.mss.eta: no visible global function definition for 'var'
ikcirt.fun.mss.eta: no visible global function definition for 'pnorm'
ikcirt.fun.mss.lambda: no visible global function definition for 'var'
ikcirt.fun.mss.lambda: no visible global function definition for
  'pnorm'
ikcirt.fun.mss.mu: no visible global function definition for 'pnorm'
kcirt.fitEE: no visible binding for global variable 'sd'
kcirt.fitEE: no visible global function definition for 'var'
kcirt.fitEE: no visible global function definition for 'cor'
kcirt.fitMSS: no visible global function definition for 'var'
kcirt.fitMSS: no visible global function definition for 'pnorm'
kcirt.fitMSS: no visible global function definition for 'sfInit'
kcirt.fitMSS: no visible global function definition for 'sfExport'
kcirt.fitMSS: no visible global function definition for 'rnorm'
kcirt.fitMSS: no visible global function definition for
  'txtProgressBar'
kcirt.fitMSS: no visible global function definition for 'sfIsRunning'
kcirt.fitMSS: no visible global function definition for 'sfStop'
kcirt.fitMSS: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor pnorm rnorm sd sfExport sfInit sfIsRunning sfStop txtProgressBar
  var
Consider adding
  importFrom("stats", "cor", "pnorm", "rnorm", "sd", "var")
  importFrom("utils", "txtProgressBar")
to your NAMESPACE file.
as.matrix.multiPhylo : tip2tip: no visible global function definition
  for 'cophenetic'
bw.nn : <anonymous>: no visible global function definition for
  'quantile'
dist.diss: no visible binding for global variable 'median'
dist.diss: no visible global function definition for 'dist'
hist.kdetrees: no visible binding for global variable 'density'
kdetrees : cutoff: no visible global function definition for 'quantile'
kdetrees.complete: no visible global function definition for 'plot'
kdetrees.complete: no visible global function definition for 'hist'
kdetrees.complete: no visible global function definition for
  'write.csv'
plot.kdetrees: no visible binding for global variable 'density'
Undefined global functions or variables:
  cophenetic density dist hist median plot quantile write.csv
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "cophenetic", "density", "dist", "median",
             "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
SeasonalMannKendall: no visible global function definition for 'is.ts'
SeasonalMannKendall: no visible global function definition for
  'frequency'
SeasonalMannKendall: no visible global function definition for 'cycle'
SeasonalMannKendall: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  cycle frequency is.ts pnorm
Consider adding
  importFrom("stats", "cycle", "frequency", "is.ts", "pnorm")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Malformed Title field: should not end in a period.
Checking should be performed on sources prepared by 'R CMD build'.
Packages in Depends field not imported from:
  'chron' 'date' 'evir'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ALbw: no visible global function definition for 'sd'
ALbw: no visible global function definition for 'quantile'
CVbw: no visible global function definition for 'quantile'
PBbw: no visible global function definition for 'sd'
PBbw: no visible global function definition for 'IQR'
kernel_function: no visible global function definition for 'dnorm'
kernel_function_distribution: no visible global function definition for
  'pnorm'
simp_int: no visible global function definition for 'approx'
Undefined global functions or variables:
  IQR approx dnorm pnorm quantile sd
Consider adding
  importFrom("stats", "IQR", "approx", "dnorm", "pnorm", "quantile",
             "sd")
to your NAMESPACE file.
kissmigDummyS: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'rkward'
distrct.analysis : <anonymous> : <anonymous>: no visible global
  function definition for 'cor'
grand.table: no visible global function definition for 'write.csv2'
grand.table: no visible global function definition for 'write.csv'
klausur: no visible global function definition for 'sd'
klausur: no visible global function definition for 'na.omit'
klausur.gen.marks : suggestion : <anonymous>: no visible global
  function definition for 'qnorm'
klausur.mufo: no visible global function definition for 'sd'
klausur.report: no visible global function definition for 'dev.off'
klausur.report : tabellenbau: no visible global function definition for
  'capture.output'
plot,klausuR-missing: no visible global function definition for
  'na.omit'
plot,klausuR-missing: no visible global function definition for 'sd'
plot,klausuR-missing : <anonymous>: no visible global function
  definition for 'dnorm'
Undefined global functions or variables:
  capture.output cor dev.off dnorm na.omit qnorm sd write.csv
  write.csv2
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "cor", "dnorm", "na.omit", "qnorm", "sd")
  importFrom("utils", "capture.output", "write.csv", "write.csv2")
to your NAMESPACE file.
klin.solve : <anonymous>: no visible global function definition for
  'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
comp.npci: no visible global function definition for 'qnorm'
epband.fun: no visible global function definition for 'data'
epband.fun: no visible binding for global variable
  'critical.value.nair.90'
epband.fun: no visible binding for global variable
  'critical.value.nair.95'
epband.fun: no visible binding for global variable
  'critical.value.nair.99'
hall.wellner.fun: no visible global function definition for 'data'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.90'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.95'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.99'
lrt.confints: no visible global function definition for 'qchisq'
rothman.fun: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
noe.compute.pv: no visible global function definition for 'punif'
Undefined global functions or variables:
  punif
Consider adding
  importFrom("stats", "punif")
to your NAMESPACE file.
dscore: no visible global function definition for 'glm'
dscore: no visible binding for global variable 'binomial'
dscore: no visible global function definition for 'pnorm'
pearson.group: no visible global function definition for 'cor'
spearman.group: no visible global function definition for 'cor'
sscore: no visible global function definition for 'glm'
sscore: no visible binding for global variable 'binomial'
sscore: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  binomial cor glm pnorm
Consider adding
  importFrom("stats", "binomial", "cor", "glm", "pnorm")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'kmlcov' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
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.
C_zero : <anonymous>: no visible global function definition for 'runif'
get_extra_centroid_index: no visible global function definition for
  'head'
get_within_cluster_ss: no visible global function definition for
  'aggregate'
kmod: no visible global function definition for 'head'
kmod: no visible global function definition for 'tail'
Undefined global functions or variables:
  aggregate head runif tail
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
knncat: no visible global function definition for 'quantile'
plot.knncat: no visible global function definition for 'plot'
plot.knncat: no visible global function definition for 'box'
plot.knncat: no visible global function definition for 'axis'
plot.knncat: no visible global function definition for 'text'
Undefined global functions or variables:
  axis box plot quantile text
Consider adding
  importFrom("graphics", "axis", "box", "plot", "text")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'cluster'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dataFiller : central.value: no visible global function definition for
  'median'
dataFiller: no visible global function definition for 'daisy'
dataFiller: no visible global function definition for 'complete.cases'
knnMCN: no visible global function definition for 'cov'
knnVCN: no visible global function definition for 'dist'
Undefined global functions or variables:
  complete.cases cov daisy dist median
Consider adding
  importFrom("stats", "complete.cases", "cov", "dist", "median")
to your NAMESPACE file.
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for 'rbeta'
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for 'runif'
calculate.power : <anonymous>: no visible binding for global variable
  'quantile'
generate.benchmark.data: no visible global function definition for
  'runif'
generate.benchmark.data: no visible global function definition for
  'rnorm'
generate.benchmark.data: no visible global function definition for
  'rbinom'
generate.patchwork.copula: no visible global function definition for
  'rbeta'
generate.patchwork.copula: no visible global function definition for
  'runif'
novelTest.chisq: no visible global function definition for 'pchisq'
novelTest.chisq4nn: no visible global function definition for 'pchisq'
optimise.copula.mi : <anonymous>: no visible global function definition
  for 'optimize'
power.plot: no visible global function definition for 'plot'
power.plot: no visible global function definition for 'axis'
power.plot : <anonymous>: no visible global function definition for
  'points'
power.plot: no visible global function definition for 'legend'
roc.plot: no visible global function definition for 'colorRampPalette'
roc.plot : <anonymous>: no visible global function definition for
  'plot'
roc.plot : <anonymous> : <anonymous>: no visible global function
  definition for 'points'
run.tests : <anonymous> : <anonymous>: no visible global function
  definition for 'runif'
Undefined global functions or variables:
  axis colorRampPalette legend optimize pchisq plot points quantile
  rbeta rbinom rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "legend", "plot", "points")
  importFrom("stats", "optimize", "pchisq", "quantile", "rbeta",
             "rbinom", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
Packages suggested but not available for checking:
  'koRpus.lang.de' 'koRpus.lang.es' 'koRpus.lang.fr' 'koRpus.lang.it'
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
assign_clustpp: no visible global function definition for 'kmeans'
kpod: no visible global function definition for 'kmeans'
makeData: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
image.kriging: no visible global function definition for 'heat.colors'
image.kriging: no visible global function definition for 'image'
kriging: no visible global function definition for 'lm'
plot.kriging: no visible global function definition for 'plot'
plot.kriging: no visible global function definition for 'curve'
Undefined global functions or variables:
  curve heat.colors image lm plot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "curve", "image", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
kselection: no visible global function definition for 'txtProgressBar'
kselection: no visible global function definition for
  'setTxtProgressBar'
plot.Kselection: no visible global function definition for 'plot'
plot.Kselection: no visible global function definition for 'lines'
plot.Kselection: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines plot setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'BB' 'nleqslv'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ktsolve: 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 hidden files and directories:
  .Rbuildindex.10034
  .Rbuildindex.31551
  .Rbuildindex.31678
  .Rbuildindex.9995
  inst/doc/.fr-hy2VZf
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Biobase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
S3 methods shown with full name in documentation object 'predict.ktsp':
  'predict.ktsp'

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

S3 methods shown with full name in documentation object 'summary.ktsp':
  'summary.ktsp'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'XML' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
auc: no visible global function definition for 'approx'
kulife.colors: no visible global function definition for 'palette'
rootonorm: no visible global function definition for 'sd'
rootonorm: no visible global function definition for 'hist'
rootonorm: no visible global function definition for 'pnorm'
rootonorm: no visible global function definition for 'dnorm'
rootonorm: no visible global function definition for 'plot'
rootonorm: no visible global function definition for 'rect'
rootonorm: no visible global function definition for 'lines'
rootonorm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approx dnorm hist lines palette plot pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "plot", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE file.
compareModelResults: no visible global function definition for
  'reshape'
erf: no visible global function definition for 'pnorm'
getModelComparisonTable: no visible global function definition for
  'read.csv'
hantushSstar: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate pnorm read.csv reshape
Consider adding
  importFrom("stats", "integrate", "pnorm", "reshape")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  'dim' to 'dims'
Found the following hidden files and directories:
  .Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
extended.figures: no visible global function definition for 'par'
extended.figures: no visible global function definition for 'runif'
extended.figures : figure2: no visible global function definition for
  'hist'
extended.figures : figure2: no visible global function definition for
  'axis'
extended.figures : figure3 : <anonymous>: no visible global function
  definition for 'median'
extended.figures : figure3: no visible global function definition for
  'barplot'
Undefined global functions or variables:
  axis barplot hist median par runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "median", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
LDuncan.aov : prob: no visible global function definition for 'qtukey'
LDuncan.aov: no visible global function definition for 'qtukey'
LScottKnott.aov : sk: no visible global function definition for
  'pchisq'
LScottKnott.aov: no visible global function definition for 'read.table'
LTukey.aov: no visible global function definition for 'qtukey'
Undefined global functions or variables:
  pchisq qtukey read.table
Consider adding
  importFrom("stats", "pchisq", "qtukey")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  'GPArotation' 'mice'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
angoff: no visible global function definition for 'cov2cor'
angoff: no visible global function definition for 'runif'
cov.lambda4: no visible global function definition for 'cov2cor'
cov.lambda4: no visible global function definition for 'median'
guttman: no visible global function definition for 'cov2cor'
impute.cov: no visible global function definition for 'cov'
impute.cov: no visible global function definition for 'complete'
impute.cov: no visible global function definition for 'mice'
kristof: no visible global function definition for 'cov2cor'
kristof: no visible global function definition for 'runif'
lambda1: no visible global function definition for 'cov2cor'
lambda2: no visible global function definition for 'cov2cor'
lambda3: no visible global function definition for 'cov2cor'
lambda3: no visible binding for global variable 'sd'
lambda5: no visible global function definition for 'cov2cor'
lambda6: no visible global function definition for 'cov2cor'
omega.tot: no visible global function definition for 'cov2cor'
omega.tot: no visible global function definition for 'factanal'
quant.lambda4: no visible global function definition for 'cov2cor'
quant.lambda4: no visible global function definition for 'runif'
quant.lambda4: no visible global function definition for 'quantile'
raju: no visible global function definition for 'cov2cor'
raju: no visible global function definition for 'runif'
user.lambda4: no visible global function definition for 'runif'
user.lambda4: no visible binding for global variable 'sd'
Undefined global functions or variables:
  complete cov cov2cor factanal median mice quantile runif sd
Consider adding
  importFrom("stats", "cov", "cov2cor", "factanal", "median", "quantile",
             "runif", "sd")
to your NAMESPACE file.
GNU make is a SystemRequirements.
getGO: no visible global function definition for 'new'
getGO: no visible global function definition for 'getGeneric'
graph.kd: no visible global function definition for 'as'
Undefined global functions or variables:
  as getGeneric new
Consider adding
  importFrom("methods", "as", "getGeneric", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Kern.FUN: no visible global function definition for 'dnorm'
Prob.Covariate.ShortEvent: no visible global function definition for
  'bw.nrd'
optimize.mse.BW: no visible global function definition for 'optimize'
Undefined global functions or variables:
  bw.nrd dnorm optimize
Consider adding
  importFrom("stats", "bw.nrd", "dnorm", "optimize")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'rgdal' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BSL: no visible global function definition for 'read.asciigrid'
BSL: no visible global function definition for 'quantile'
PIF: no visible global function definition for 'read.asciigrid'
PIF: no visible global function definition for 'quantile'
RCS: no visible global function definition for 'quantile'
clouds: no visible global function definition for 'read.asciigrid'
geoshift: no visible global function definition for 'bbox'
histmatch: no visible global function definition for 'hist'
minnaert: no visible global function definition for 'coefficients'
minnaert: no visible global function definition for 'lm'
minnaert: no visible global function definition for 'predict'
topocorr: no visible global function definition for 'lm'
topocorr: no visible global function definition for 'coefficients'
Undefined global functions or variables:
  bbox coefficients hist lm predict quantile read.asciigrid
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coefficients", "lm", "predict", "quantile")
to your NAMESPACE file.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  'MASS' 'lattice' 'lme4' 'rms' 'zipfR'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.4Mb
    help   1.1Mb
betabreaker: no visible global function definition for 'predict'
coef.lars: no visible global function definition for 'predict'
cv.lars: no visible global function definition for 'predict'
cv.lars: no visible binding for global variable 'var'
error.bars: no visible global function definition for 'segments'
plot.lars: no visible global function definition for 'plot'
plot.lars: no visible global function definition for 'matplot'
plot.lars: no visible global function definition for 'title'
plot.lars: no visible global function definition for 'abline'
plot.lars: no visible global function definition for 'axis'
plotCVLars: no visible global function definition for 'plot'
predict.lars: no visible global function definition for 'approx'
Undefined global functions or variables:
  abline approx axis matplot plot predict segments title var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "plot", "segments",
             "title")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
gl1ce: no visible binding for global variable 'gaussian'
gl1ce: no visible global function definition for 'glm.control'
gl1ce: no visible global function definition for 'model.extract'
gl1ce: no visible global function definition for 'terms'
gl1ce: no visible global function definition for 'model.matrix'
gl1ce: no visible binding for global variable 'sd'
l1ce: no visible global function definition for 'model.extract'
l1ce: no visible global function definition for 'terms'
l1ce: no visible global function definition for 'model.matrix'
l1ce: no visible binding for global variable 'sd'
merge.formula: no visible global function definition for 'as.formula'
plot.l1celist: no visible global function definition for 'matplot'
plot.l1celist: no visible global function definition for 'rug'
predict.l1ce: no visible global function definition for 'model.matrix'
print.summary.gl1ce: no visible binding for global variable 'quantile'
print.summary.gl1ce: no visible global function definition for
  'quantile'
print.summary.l1ce: no visible binding for global variable 'quantile'
print.summary.l1ce: no visible global function definition for
  'quantile'
residuals.l1ce: no visible global function definition for
  'residuals.glm'
summary.l1ce: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula gaussian glm.control matplot model.extract model.matrix
  pnorm quantile residuals.glm rug sd terms
Consider adding
  importFrom("graphics", "matplot", "rug")
  importFrom("stats", "as.formula", "gaussian", "glm.control",
             "model.extract", "model.matrix", "pnorm", "quantile",
             "residuals.glm", "sd", "terms")
to your NAMESPACE file.
glassoscore: no visible global function definition for 'var'
glassoscore: no visible global function definition for 'pchisq'
lassoscore: no visible global function definition for 'txtProgressBar'
lassoscore: no visible global function definition for
  'setTxtProgressBar'
lassoscore: no visible global function definition for 'pchisq'
plot.glassoscore: no visible global function definition for 'legend'
plot.lassoscore: no visible global function definition for 'legend'
plot.mbscore: no visible global function definition for 'legend'
qqpval: no visible global function definition for 'ppoints'
qqpval: no visible global function definition for 'qbeta'
qqpval: no visible global function definition for 'points'
qqpval: no visible global function definition for 'plot'
qqpval: no visible global function definition for 'abline'
qqpval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline legend pchisq plot points polygon ppoints qbeta
  setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points", "polygon")
  importFrom("stats", "pchisq", "ppoints", "qbeta", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/lavaan.shiny.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'mets::concordance' by 'survival::concordance' when loading 'lava.tobit'
See 'd:/Rcompile/CRANpkg/local/3.5/lava.tobit.Rcheck/00install.out' for details.
lbfgs: no visible global function definition for 'hasArg'
Undefined global functions or variables:
  hasArg
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Title field: should not end in a period.
LCA: no visible global function definition for 'dist'
LCA: no visible global function definition for 'combn'
LCA: no visible global function definition for 'p.adjust'
LCA: no visible global function definition for 'pchisq'
LCA : <anonymous>: no visible global function definition for 'pchisq'
LCD: no visible global function definition for 'ecdf'
estimateB: no visible global function definition for 'median'
evaluateDiffSignificance: no visible global function definition for
  'ecdf'
fitPTLmodel: no visible global function definition for 'lm'
getPTLparams: no visible global function definition for 'nls'
getPTLparams: no visible global function definition for 'coef'
predictPTLparams: no visible global function definition for
  'predict.lm'
Undefined global functions or variables:
  coef combn dist ecdf lm median nls p.adjust pchisq predict.lm
Consider adding
  importFrom("stats", "coef", "dist", "ecdf", "lm", "median", "nls",
             "p.adjust", "pchisq", "predict.lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
cclcda.default: no visible global function definition for 'as.formula'
cclcda.default: no visible global function definition for 'chisq.test'
cclcda.formula: no visible global function definition for 'model.frame'
cclcda2.default: no visible global function definition for 'runif'
cclcda2.default: no visible global function definition for 'chisq.test'
cclcda2.formula: no visible global function definition for
  'model.frame'
lcda.default: no visible global function definition for 'as.formula'
lcda.formula: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  as.formula chisq.test model.frame runif
Consider adding
  importFrom("stats", "as.formula", "chisq.test", "model.frame", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'doMC'
Malformed Title field: should not end in a period.
multistart : <anonymous>: no visible global function definition for
  'runif'
plot.FreD.x: no visible global function definition for 'modifyList'
plot.FreD.x: no visible global function definition for 'abline'
plot.FreD.x: no visible global function definition for 'points'
Undefined global functions or variables:
  abline modifyList points runif
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "runif")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
ARConfIntEst: no visible global function definition for 'sd'
PTLinkFunc: no visible global function definition for 'pnorm'
PTLinkFunc: no visible global function definition for 'qnorm'
PTMultiPeriodPD: no visible global function definition for 'uniroot'
PTOnePeriodPD : f: no visible global function definition for 'pbinom'
PTOnePeriodPD: no visible global function definition for 'uniroot'
QMMGetRLogitPD: no visible global function definition for 'ecdf'
QMMPDlinkFunc: no visible global function definition for 'qnorm'
QMMPlot: no visible global function definition for 'plot'
QMMPlot: no visible global function definition for 'lines'
QMMPlot: no visible global function definition for 'legend'
VDBCalibratePD: no visible global function definition for 'ecdf'
VDBGetK: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  ecdf legend lines pbinom plot pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "ecdf", "pbinom", "pnorm", "qnorm", "sd",
             "uniroot")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
prepare_Rd: HWE2sided.Rd:15-16: Dropping empty section \details
prepare_Rd: HWE2sided.table.Rd:17-18: Dropping empty section \details
prepare_Rd: LD2sided.pvals.Rd:13-14: Dropping empty section \details
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Package suggested but not available for checking: 'doMC'
BEAPFrOG: no visible global function definition for 'jags.model'
BEAPFrOG: no visible global function definition for 'coda.samples'
LEAPFrOG_EM: no visible global function definition for 'write.table'
LEAPFrOG_EM: no visible global function definition for 'constrOptim'
LEAPFrOG_plot: no visible global function definition for 'par'
LEAPFrOG_plot: no visible global function definition for 'barplot'
LEAPFrOG_plot: no visible global function definition for 'legend'
constrOptim2: no visible global function definition for 'optim'
Undefined global functions or variables:
  barplot coda.samples constrOptim jags.model legend optim par
  write.table
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "constrOptim", "optim")
  importFrom("utils", "write.table")
to your NAMESPACE file.
AlternateSVD: no visible binding for global variable 'sd'
IPOD: no visible global function definition for 'mad'
IPOD: no visible global function definition for 'pnorm'
Pvalue: no visible global function definition for 'pf'
ROCplot: no visible global function definition for 'png'
ROCplot: no visible global function definition for 'matplot'
ROCplot: no visible global function definition for 'legend'
ROCplot: no visible global function definition for 'dev.off'
leapp: no visible global function definition for 'png'
leapp: no visible global function definition for 'plot'
leapp: no visible global function definition for 'dev.off'
ridge: no visible global function definition for 'sd'
ridge: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dev.off legend mad matplot pf plot png pnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "matplot", "plot")
  importFrom("stats", "mad", "pf", "pnorm", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Fmntd.a : Fmntd.a.sub: no visible global function definition for
  'weighted.mean'
Fmpd : Fmpd.sub: no visible global function definition for 'as.dist'
Fmpd.a : Fmpd.a.sub: no visible global function definition for
  'weighted.mean'
Fsntd : Fsntd.sub: no visible global function definition for 'sd'
com.trait.moments : skewness: no visible global function definition for
  'var'
com.trait.moments : kurtosis: no visible global function definition for
  'var'
com.trait.moments : sd.funk: no visible global function definition for
  'sd'
com.trait.weighted : weight.mean.funk: no visible global function
  definition for 'weighted.mean'
Undefined global functions or variables:
  as.dist sd var weighted.mean
Consider adding
  importFrom("stats", "as.dist", "sd", "var", "weighted.mean")
to your NAMESPACE file.
'library' or 'require' call to 'snow' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.5Mb
Depends: includes the non-default packages:
  'sn' 'moments' 'BB' 'Bolstad2' 'optimx' 'Rmpfr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'BB' 'Bolstad2' 'Rmpfr' 'moments' 'optimx' 'sn'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotBox: no visible global function definition for 'sd'
plotBox: no visible global function definition for 'rect'
plotBox: no visible global function definition for 'qnorm'
plotBox: no visible global function definition for 'segments'
plotInit: no visible global function definition for 'plot'
plotInit: no visible global function definition for 'runif'
plotInit: no visible global function definition for 'mtext'
plotInit: no visible global function definition for 'segments'
plotStack: no visible global function definition for 'points'
Undefined global functions or variables:
  mtext plot points qnorm rect runif sd segments
Consider adding
  importFrom("graphics", "mtext", "plot", "points", "rect", "segments")
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Plotranges.double: no visible global function definition for 'strwidth'
Plotranges.double: no visible global function definition for
  'strheight'
Plotranges.double: no visible global function definition for 'plot.new'
Plotranges.double: no visible global function definition for 'par'
Plotranges.double: no visible global function definition for
  'plot.window'
Plotranges.double: no visible global function definition for 'mtext'
Plotranges.double: no visible global function definition for 'abline'
Plotranges.double: no visible global function definition for 'points'
Plotranges.double: no visible global function definition for 'segments'
Plotranges.double: no visible global function definition for 'text'
Plotranges.double: no visible global function definition for 'axis'
Plotranges.double: no visible global function definition for 'box'
Plotranges.double: no visible global function definition for 'title'
Undefined global functions or variables:
  abline axis box mtext par plot.new plot.window points segments
  strheight strwidth text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "mtext", "par",
             "plot.new", "plot.window", "points", "segments",
             "strheight", "strwidth", "text", "title")
to your NAMESPACE file.
class.calib: no visible global function definition for 'lm'
class.calib: no visible global function definition for 'coef'
class.calib: no visible global function definition for 'qt'
hoad.calib: no visible global function definition for 'lm'
hoad.calib: no visible global function definition for 'anova'
hoad.calib: no visible global function definition for 'qt'
hoad.calib: no visible global function definition for 'rnorm'
huntlam.calib: no visible global function definition for 'lm'
huntlam.calib: no visible global function definition for 'anova'
huntlam.calib: no visible global function definition for 'rnorm'
huntlam.calib: no visible global function definition for 'qnorm'
inver.calib: no visible global function definition for 'lm'
inver.calib: no visible global function definition for 'coef'
inver.calib: no visible global function definition for 'anova'
inver.calib: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  anova coef lm qnorm qt rnorm
Consider adding
  importFrom("stats", "anova", "coef", "lm", "qnorm", "qt", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'doMC'
Malformed Description field: should contain one or more complete sentences.
gcomb: no visible global function definition for 'complete.cases'
linkim: no visible global function definition for 'runif'
missing.dist: no visible global function definition for
  'complete.cases'
pgdata1: no visible global function definition for 'barplot'
pgdata1: no visible global function definition for 'layout'
pgdata1: no visible global function definition for 'par'
pgdata1: no visible global function definition for 'rainbow'
singim: no visible global function definition for 'complete.cases'
singim: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot complete.cases layout par rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "barplot", "layout", "par")
  importFrom("stats", "complete.cases", "runif")
to your NAMESPACE file.
gen.lms: no visible global function definition for 'na.omit'
plot.idf: no visible global function definition for 'plot'
plot.idf: no visible global function definition for 'mtext'
plot.idf: no visible global function definition for 'points'
plot.idf: no visible global function definition for 'segments'
plot.idf: no visible global function definition for 'ftable'
plot.idf: no visible global function definition for 'image'
plot.idf: no visible global function definition for 'gray'
plot.idf: no visible global function definition for 'abline'
plot.s.linlir: no visible global function definition for 'plot'
plot.s.linlir: no visible global function definition for 'mtext'
plot.s.linlir: no visible global function definition for 'polygon'
plot.s.linlir: no visible global function definition for 'points'
plot.s.linlir: no visible global function definition for 'curve'
s.linlir: no visible global function definition for 'na.omit'
s.linlir: no visible global function definition for 'dbinom'
s.linlir: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq plot
  points polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "plot",
             "points", "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
'library' or 'require' call to 'lpSolve' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'lpSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
solveLP: no visible global function definition for 'lp'
Undefined global functions or variables:
  lp
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
last: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
getMatrix : <anonymous>: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to 'scatterplot3d' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
lm.beta: no visible global function definition for 'coef'
lm.beta: no visible global function definition for 'model.matrix'
lm.beta: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  coef model.frame model.matrix
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix")
to your NAMESPACE file.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for 'lm'
lmec: no visible global function definition for 'pnorm'
lmec: no visible global function definition for 'dnorm'
lmec : vtrnorm2: no visible global function definition for 'runif'
lmec : vtrnorm2: no visible global function definition for 'qnorm'
lmec : vtrnorm2: no visible global function definition for 'pnorm'
lmec: no visible global function definition for 'rnorm'
lmec: no visible global function definition for 'ar'
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
mq.diagnostics : mq_missinggenotype_plot: no visible global function
  definition for 'plot.missing'
Undefined global functions or variables:
  plot.missing
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
approx.Z : <anonymous>: no visible global function definition for
  'approx'
smspline: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  approx model.frame
Consider adding
  importFrom("stats", "approx", "model.frame")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'emulator' 'methods' 'miscTools' 'penalized'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AnalyticalOptim: no visible global function definition for 'optim'
LLConstructor : LL: no visible global function definition for 'dpois'
MixtureDensity: no visible global function definition for 'glm'
MixtureDensity : f_hat: no visible global function definition for
  'predict'
NullDensity : f0: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dpois glm optim predict
Consider adding
  importFrom("stats", "dpois", "glm", "optim", "predict")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to 'akima' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported objects:
  'lattice::render.3d.trellis' 'lattice::render.contour.trellis'
Malformed Title field: should not end in a period.
available.loglevels: no visible global function definition for
  'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some 'make' programs ignore lines not ending in LF.
Malformed Title field: should not end in a period.
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.
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.
Logger: 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').
Malformed Title field: should not end in a period.
EstimateProbability: no visible global function definition for
  'predict'
LOGICOIL: no visible binding for global variable 'pssm'
LOGICOIL: no visible binding for global variable 'LOGICOILfit'
LOGICOIL: no visible binding for global variable 'Model_Parameters'
plot_LOGICOIL: no visible global function definition for 'png'
plot_LOGICOIL: no visible global function definition for 'par'
plot_LOGICOIL: no visible global function definition for 'plot'
plot_LOGICOIL: no visible global function definition for 'lines'
plot_LOGICOIL: no visible global function definition for 'axis'
plot_LOGICOIL: no visible global function definition for 'mtext'
plot_LOGICOIL: no visible global function definition for 'legend'
plot_LOGICOIL: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par plot
  png predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
test_compute_gradient: no visible global function definition for
  'rnorm'
test_compute_probabilities: no visible global function definition for
  'rnorm'
test_logitchoice: no visible global function definition for 'rnorm'
test_solver: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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.
Malformed Description field: should contain one or more complete sentences.
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.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
lsp: no visible global function definition for 'var'
plot.lsp: no visible global function definition for 'plot'
plot.lsp: no visible global function definition for 'lines'
plot.lsp: no visible global function definition for 'abline'
randlsp: no visible global function definition for 'is.ts'
randlsp: no visible global function definition for 'par'
randlsp: no visible global function definition for 'hist'
randlsp: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline hist is.ts lines par plot var
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "plot")
  importFrom("stats", "is.ts", "var")
to your NAMESPACE file.
fplot: no visible global function definition for 'rnorm'
fplot: no visible global function definition for 'plot'
fplot: no visible global function definition for 'segments'
fplot: no visible global function definition for 'points'
fplot: no visible global function definition for 'text'
fplot.foodweb: no visible global function definition for 'plot'
fplot.foodweb: no visible global function definition for 'segments'
fplot.foodweb: no visible global function definition for 'points'
fplot.foodweb: no visible global function definition for 'text'
gplot: no visible global function definition for 'runif'
groupplot: no visible global function definition for 'rnorm'
groupplot: no visible global function definition for 'plot'
groupplot: no visible global function definition for 'segments'
groupplot: no visible global function definition for 'points'
groupplot: no visible global function definition for 'text'
groupplot.foodweb: no visible global function definition for 'rnorm'
groupplot.foodweb: no visible global function definition for 'plot'
groupplot.foodweb: no visible global function definition for 'segments'
groupplot.foodweb: no visible global function definition for 'points'
groupplot.foodweb: no visible global function definition for 'text'
Undefined global functions or variables:
  plot points rnorm runif segments text
Consider adding
  importFrom("graphics", "plot", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
amendColumns: no visible global function definition for 'setNames'
fillColumns: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.5Mb
Package suggested but not available for checking: 'doMC'
Checking should be performed on sources prepared by 'R CMD build'.
EstimateTFDR: no visible global function definition for 'quantile'
GetSoftThresh: no visible global function definition for 'lm'
LPC: no visible global function definition for 'lm'
PlotFDRs: no visible global function definition for 'quantile'
PlotFDRs: no visible global function definition for 'plot'
PlotFDRs: no visible global function definition for 'points'
PlotFDRs: no visible global function definition for 'legend'
PredictiveAdvantage: no visible global function definition for 'par'
PredictiveAdvantage: no visible global function definition for 'plot'
PredictiveAdvantage: no visible global function definition for 'points'
PredictiveAdvantage: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lm par plot points quantile
Consider adding
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "lm", "quantile")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
lpint : <anonymous>: no visible global function definition for
  'integrate'
lpint: no visible global function definition for 'integrate'
lpint : lpint : <anonymous>: no visible global function definition for
  'integrate'
lplikint : lplikint.fun : <anonymous>: no visible global function
  definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
'library' or 'require' call to 'Rsymphony' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
mipSolve.Rsymphony: no visible global function definition for
  'Rsymphony_solve_LP'
Undefined global functions or variables:
  Rsymphony_solve_LP
learnPattern.default: no visible global function definition for 'runif'
plot.learnPattern: no visible global function definition for 'matplot'
plotMDS: no visible global function definition for 'par'
plotMDS: no visible global function definition for 'rainbow'
plotMDS: no visible global function definition for 'plot'
plotMDS: no visible global function definition for 'pairs'
visualizePattern: no visible global function definition for 'par'
visualizePattern: no visible global function definition for 'plot'
visualizePattern: no visible global function definition for 'points'
visualizePattern: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend matplot pairs par plot points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "plot",
             "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
LP.comoment: no visible global function definition for 'cor'
LP.comoment: no visible global function definition for 'cov'
LP.moment: no visible global function definition for 'cor'
LPTrans: no visible global function definition for 'ecdf'
VAR: no visible global function definition for 'embed'
VAR: no visible global function definition for 'lm'
Undefined global functions or variables:
  cor cov ecdf embed lm
Consider adding
  importFrom("stats", "cor", "cov", "ecdf", "embed", "lm")
to your NAMESPACE file.
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.
Malformed Description field: should contain one or more complete sentences.
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.
lss: no visible binding for global variable 'na.exclude'
lss: no visible global function definition for 'model.extract'
lss: no visible binding for global variable 'response'
lss: no visible global function definition for 'model.matrix'
lss: no visible global function definition for 'rexp'
lss: no visible global function definition for 'pnorm'
lss.betag: no visible global function definition for 'l1fit'
Undefined global functions or variables:
  l1fit model.extract model.matrix na.exclude pnorm response rexp
Consider adding
  importFrom("stats", "model.extract", "model.matrix", "na.exclude",
             "pnorm", "rexp")
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.
Malformed Description field: should contain one or more complete sentences.
fit.LTR: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'robustbase'
  Please remove these calls from your code.
ltsbase: no visible global function definition for 'lm'
ltsbase: no visible global function definition for 'lines'
ltsbase: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines lm
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "lm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  'genetics' 'survival'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'genetics' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.Z.HWP: no visible global function definition for 'is.genotype'
get.Z.HWP: no visible global function definition for 'allele.count'
get.Z.dep: no visible global function definition for 'model.matrix'
get.Z.dep: no visible global function definition for 'formula'
get.Z.saturated: no visible global function definition for 'formula'
get.Z.saturated: no visible global function definition for
  'model.matrix'
get.lambda: no visible global function definition for 'is.genotype'
get.lambda: no visible global function definition for 'model.matrix'
get.lambda: no visible global function definition for 'heterozygote'
luca: no visible global function definition for 'is.genotype'
luca: no visible global function definition for 'genotype'
luca: no visible global function definition for 'Surv'
luca: no visible global function definition for 'coxph.fit'
luca: no visible global function definition for 'coxph.control'
summary.luca: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  Surv allele.count coxph.control coxph.fit formula genotype
  heterozygote is.genotype model.matrix pchisq
Consider adding
  importFrom("stats", "formula", "model.matrix", "pchisq")
to your NAMESPACE file.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lucr)
  > 
  > test_check("lucr")
  -- 1. Failure: Simple amounts can be converted (@test_conversion.R#4)  ---------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12.00"
  y[1]: "£12.00"
  
  -- 2. Failure: Complex amounts can be converted (@test_conversion.R#8)  --------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12,000.00"
  y[1]: "£12,000.00"
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: Simple amounts can be converted (@test_conversion.R#4) 
  2. Failure: Complex amounts can be converted (@test_conversion.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lucr)
  > 
  > test_check("lucr")
  -- 1. Failure: Simple amounts can be converted (@test_conversion.R#4)  ---------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12.00"
  y[1]: "£12.00"
  
  -- 2. Failure: Complex amounts can be converted (@test_conversion.R#8)  --------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12,000.00"
  y[1]: "£12,000.00"
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: Simple amounts can be converted (@test_conversion.R#4) 
  2. Failure: Complex amounts can be converted (@test_conversion.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   1.6Mb
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').
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
    proj   5.0Mb
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
Malformed Description field: should contain one or more complete sentences.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/MachineShop.Rcheck/00install.out' for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    TS_files     5.8Mb
    base_files   6.3Mb
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.
'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.
GNU make is a SystemRequirements.
'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.
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs  34.2Mb
Malformed Description field: should contain one or more complete sentences.
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.
mp_corpus: no visible binding for global variable 'annotations'
print.ManifestoAvailability: no visible binding for global variable
  'annotations'
Undefined global functions or variables:
  annotations
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/MAPA.Rcheck/00install.out' for details.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
cf1.sample: no visible global function definition for 'rexp'
cf1.sample: no visible global function definition for 'rmultinom'
dherlang : <anonymous> : <anonymous>: no visible global function
  definition for 'dgamma'
erhmm.param.kmeans: no visible global function definition for 'kmeans'
erhmm.param.kmeans: no visible global function definition for 'var'
erhmm.param.kmeans: no visible global function definition for 'runif'
gmmpp.param.kmeans: no visible global function definition for 'kmeans'
gmmpp.param.kmeans: no visible global function definition for 'runif'
herlang.param.kmeans: no visible global function definition for
  'kmeans'
herlang.param.kmeans: no visible global function definition for 'var'
map.param.kmeans: no visible global function definition for 'kmeans'
map.param.kmeans: no visible global function definition for 'runif'
ph.param.random: no visible global function definition for 'runif'
ph.sample: no visible global function definition for 'rmultinom'
ph.sample: no visible global function definition for 'rexp'
pherlang : <anonymous> : <anonymous>: no visible global function
  definition for 'pgamma'
rherlang: no visible global function definition for 'rmultinom'
rherlang : <anonymous>: no visible global function definition for
  'rgamma'
Undefined global functions or variables:
  dgamma kmeans pgamma rexp rgamma rmultinom runif var
Consider adding
  importFrom("stats", "dgamma", "kmeans", "pgamma", "rexp", "rgamma",
             "rmultinom", "runif", "var")
to your NAMESPACE file.
'library' or 'require' call to 'mgcv' which was already attached by Depends.
  Please remove these calls from your code.
ageprofile: no visible global function definition for 'model.frame'
ageprofile: no visible binding for global variable 'poisson'
ageprofile: no visible global function definition for 'predict.gam'
ageprofile: no visible global function definition for 'as.formula'
ageprofile: no visible global function definition for 'summary.gam'
ageprofile: no visible global function definition for 'contrasts<-'
ageprofile: no visible global function definition for 'anova.gam'
plotap: no visible global function definition for 'dev.new'
plotap: no visible global function definition for 'plot'
plotap: no visible global function definition for 'lines'
plotap: no visible global function definition for 'points'
plotap: no visible global function definition for 'legend'
splitter: no visible global function definition for 'reshape'
tabm: no visible global function definition for 'coef'
tabm: no visible global function definition for 'AIC'
Undefined global functions or variables:
  AIC anova.gam as.formula coef contrasts<- dev.new legend lines
  model.frame plot points poisson predict.gam reshape summary.gam
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "AIC", "as.formula", "coef", "contrasts<-",
             "model.frame", "poisson", "reshape")
to your NAMESPACE file.
calcStats: no visible global function definition for 'as.formula'
calcStats: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  as.formula na.omit
Consider adding
  importFrom("stats", "as.formula", "na.omit")
to your NAMESPACE file.
plot.topics: no visible global function definition for 'hist'
plot.topics: no visible global function definition for 'grey'
plot.topics: no visible global function definition for 'plot'
plot.topics: no visible global function definition for 'par'
plot.topics: no visible global function definition for 'image'
plot.topics: no visible global function definition for 'axis'
plot.topics: no visible global function definition for 'points'
plot.topics: no visible global function definition for 'text'
rdir: no visible global function definition for 'rgamma'
summary.topics: no visible global function definition for 'pchisq'
tpxResids: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  axis grey hist image par pchisq plot points rgamma text
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "axis", "hist", "image", "par", "plot",
             "points", "text")
  importFrom("stats", "pchisq", "rgamma")
to your NAMESPACE file.
'library' or 'require' call to 'MARSS' 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: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'MARSS:::is.diagonal'
  See the note in ?`:::` about the use of this operator.
'library' or 'require' calls in package code:
  'gsl' 'taRifx'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
marqLevAlg: no visible global function definition for 'flush.console'
print.marqLevAlg: no visible global function definition for 'qnorm'
print.marqLevAlg: no visible global function definition for 'pchisq'
summary.marqLevAlg: no visible global function definition for 'qnorm'
summary.marqLevAlg: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  flush.console pchisq qnorm
Consider adding
  importFrom("stats", "pchisq", "qnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
mAr.pca: no visible binding for global variable 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
mata.wald: no visible global function definition for 'uniroot'
tailarea.t: no visible global function definition for 'pt'
tailarea.z: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm pt uniroot
Consider adding
  importFrom("stats", "pnorm", "pt", "uniroot")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.4Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/matie.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
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.
Package suggested but not available for checking: 'gputools'
'library' or 'require' call to 'bigmemory' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
MAT: no visible global function definition for 'dev.new'
MAT: no visible global function definition for 'plot'
MAT: no visible global function definition for 'points'
MAT: no visible global function definition for 'abline'
MAT: no visible global function definition for 'text'
MAT: no visible global function definition for 'legend'
MAT: no visible global function definition for 'lines'
MAT: no visible global function definition for 'par'
MAT: no visible global function definition for 'barplot'
MAT: no visible global function definition for 'cor'
print.MAT: no visible global function definition for 'sd'
print.MAT: no visible global function definition for 'cor'
simM3PL: no visible global function definition for 'rnorm'
simM3PL: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par plot points rnorm runif
  sd text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "plot", "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Malformed Title field: should not end in a period.
GSTplot : <anonymous>: no visible global function definition for
  't.test'
GSTplot: no visible global function definition for 'rt'
GSTplot: no visible global function definition for 'layout'
GSTplot: no visible global function definition for 'par'
GSTplot: no visible global function definition for 'plot'
GSTplot: no visible global function definition for 'text'
GSTplot: no visible global function definition for 'lines'
GSTplot: no visible global function definition for 'polygon'
GSTplot: no visible global function definition for 'abline'
GSTplot: no visible global function definition for 'ecdf'
GSTplot: no visible global function definition for 'knots'
GSTplot : <anonymous>: no visible global function definition for 'aov'
GSTplot: no visible global function definition for 'qf'
MAVTn : <anonymous>: no visible global function definition for 'aov'
MAVTn: no visible global function definition for 'p.adjust'
MAVTn: no visible global function definition for 'plot'
MAVTn: no visible global function definition for 'par'
MAVTn: no visible global function definition for 'abline'
MAVTn: no visible global function definition for 'legend'
MAVTn: no visible global function definition for 'locator'
Tols : olsf: no visible global function definition for 't.test'
Tols: no visible global function definition for 'cor'
Undefined global functions or variables:
  abline aov cor ecdf knots layout legend lines locator p.adjust par
  plot polygon qf rt t.test text
Consider adding
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "locator", "par", "plot", "polygon", "text")
  importFrom("stats", "aov", "cor", "ecdf", "knots", "p.adjust", "qf",
             "rt", "t.test")
to your NAMESPACE file.
Package in Depends field not imported from: 'mnormt'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catt.test: no visible global function definition for 'pnorm'
fnorm2: no visible global function definition for 'sadmvn'
fnorm3: no visible global function definition for 'sadmvn'
Undefined global functions or variables:
  pnorm sadmvn
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
tune.maxent: 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 Makefile(s) without a final LF:
  src/Makevars
Some 'make' programs ignore lines not ending in LF.
File 'maxent/libs/i386/maxent.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sgd.o'
File 'maxent/libs/x64/maxent.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sgd.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'doMC'
Malformed Description field: should contain one or more complete sentences.
MI.2: no visible global function definition for 'xtabs'
RNASeq.Data: no visible binding for global variable 'quantile'
loc.node: no visible global function definition for 'head'
loc.node: no visible global function definition for 'tail'
plotHybrid.Tree: no visible global function definition for 'par'
plotHybrid.Tree: no visible global function definition for 'plot'
plotHybrid.Tree: no visible global function definition for 'text'
plotHybrid.Tree: no visible global function definition for 'image'
plotHybrid.Tree: no visible global function definition for 'grey'
plotHybrid.Tree: no visible global function definition for
  'heat.colors'
plotHybrid.Tree: no visible global function definition for 'head'
plotHybrid.Tree: no visible global function definition for 'segments'
plotbr: no visible global function definition for 'segments'
Undefined global functions or variables:
  grey head heat.colors image par plot quantile segments tail text
  xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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.
confint.mblm: no visible global function definition for 'wilcox.test'
mblm: no visible global function definition for 'terms'
mblm: no visible global function definition for 'median'
mblm: no visible global function definition for 'lm'
summary.mblm: no visible global function definition for 'mad'
summary.mblm: no visible global function definition for 'wilcox.test'
summary.mblm: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef lm mad median terms wilcox.test
Consider adding
  importFrom("stats", "coef", "lm", "mad", "median", "terms",
             "wilcox.test")
to your NAMESPACE file.
Package in Depends field not imported from: 'logistf'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mbmdr : NextModel: no visible global function definition for
  'read.table'
mbmdr : OffsetFit: no visible global function definition for 'glm'
mbmdr : Regresion: no visible global function definition for 'logistf'
mbmdr : Regresion: no visible global function definition for 'glm'
mbmdr: no visible global function definition for 'write.table'
mbmdr.PermTest: no visible global function definition for 'read.table'
mbmdr.PermTest: no visible global function definition for 'qnorm'
print.mbmdr: no visible global function definition for 'read.table'
summary.mbmdr: no visible global function definition for 'read.table'
Undefined global functions or variables:
  glm logistf qnorm read.table write.table
Consider adding
  importFrom("stats", "glm", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
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.
Package suggested but not available for checking: 'cplexAPI'
Package in Depends field not imported from: 'coda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mcgibbsit: no visible global function definition for 'is.mcmc.list'
mcgibbsit: no visible global function definition for 'start'
mcgibbsit: no visible global function definition for 'end'
mcgibbsit: no visible global function definition for 'thin'
mcgibbsit: no visible global function definition for 'nvar'
mcgibbsit: no visible global function definition for 'mcmc'
mcgibbsit: no visible global function definition for 'mcmc.list'
mcgibbsit: no visible global function definition for 'varnames'
mcgibbsit: no visible global function definition for 'qnorm'
mcgibbsit: no visible global function definition for 'niter'
mcgibbsit: no visible global function definition for 'quantile'
mcgibbsit : to.table: no visible global function definition for
  'window'
mcgibbsit: no visible global function definition for 'var'
read.mcmc: no visible global function definition for 'mcmc.list'
read.mcmc: no visible global function definition for 'mcmc'
Undefined global functions or variables:
  end is.mcmc.list mcmc mcmc.list niter nvar qnorm quantile start thin
  var varnames window
Consider adding
  importFrom("stats", "end", "qnorm", "quantile", "start", "var",
             "window")
to your NAMESPACE file.
call_localoptim: no visible global function definition for 'optim'
call_localoptim: no visible global function definition for 'nlminb'
call_localoptim: no visible global function definition for
  'txtProgressBar'
call_localoptim: no visible global function definition for
  'setTxtProgressBar'
call_localoptim : <anonymous>: no visible global function definition
  for 'optim'
call_localoptim : <anonymous>: no visible global function definition
  for 'nlminb'
multiStartoptim: no visible global function definition for 'median'
Undefined global functions or variables:
  median nlminb optim setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "median", "nlminb", "optim")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
mcheatmaps : coscolorFun: no visible global function definition for
  'rgb'
mcheatmaps : halfcmat: no visible global function definition for
  'order.dendrogram'
mcheatmaps : fullcmat: no visible global function definition for
  'order.dendrogram'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'hclust'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'as.dist'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'sd'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'cophenetic'
mcheatmaps : printDiag: no visible global function definition for
  'order.dendrogram'
mcheatmaps: no visible global function definition for 'strwidth'
mcheatmaps: no visible global function definition for 'pdf'
mcheatmaps: no visible global function definition for 'plot.new'
mcheatmaps: no visible global function definition for 'as.dendrogram'
mcheatmaps: no visible global function definition for 'reorder'
mcheatmaps: no visible global function definition for 'par'
mcheatmaps: no visible global function definition for 'plot'
mcheatmaps: no visible global function definition for
  'order.dendrogram'
mcheatmaps: no visible global function definition for 'heat.colors'
mcheatmaps: no visible global function definition for 'terrain.colors'
mcheatmaps: no visible global function definition for 'as.dist'
mcheatmaps: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  as.dendrogram as.dist cophenetic dev.off hclust heat.colors
  order.dendrogram par pdf plot plot.new reorder rgb sd strwidth
  terrain.colors
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
             "terrain.colors")
  importFrom("graphics", "par", "plot", "plot.new", "strwidth")
  importFrom("stats", "as.dendrogram", "as.dist", "cophenetic", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.6Mb
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'scatterplot3d' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.nsga2: no visible global function definition for 'plot'
plot.nsga2: no visible global function definition for 'lines'
plot.nsga2: no visible global function definition for 'pairs'
plot.nsga2.collection: no visible global function definition for
  'devAskNewPage'
plot.nsga2.collection: no visible binding for global variable 'plot'
Undefined global functions or variables:
  devAskNewPage lines pairs plot
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "lines", "pairs", "plot")
to your NAMESPACE file.
Package in Depends field not imported from: 'metafor'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'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.
Depends: includes the non-default packages:
  'lattice' 'locfit' 'maptools' 'quantreg' 'RANN' 'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Malformed Description field: should contain one or more complete sentences.
'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.
Checking should be performed on sources prepared by 'R CMD build'.
anova.mdm : <anonymous>: no visible global function definition for
  'formula'
anova.mdm : <anonymous>: no visible global function definition for
  'deviance'
anova.mdm: no visible global function definition for 'pchisq'
entropy.plot: no visible global function definition for 'plot'
entropy.plot: no visible global function definition for 'axis'
entropy.plot: no visible global function definition for 'box'
entropy.plot: no visible global function definition for 'segments'
entropy.plot: no visible global function definition for 'points'
mdm: no visible global function definition for 'model.matrix'
mdm: no visible global function definition for 'model.response'
mdm: no visible global function definition for 'model.weights'
mdm: no visible global function definition for 'model.offset'
mdm: no visible binding for global variable 'weighted.mean'
mdm: no visible global function definition for '.getXlevels'
simdata: no visible global function definition for 'rainbow'
simdata: no visible global function definition for 'runif'
simdata: no visible global function definition for 'rpois'
simdata: no visible global function definition for 'rnorm'
simdata: no visible global function definition for 'matplot'
simdata: no visible global function definition for 'rug'
Undefined global functions or variables:
  .getXlevels axis box deviance formula matplot model.matrix
  model.offset model.response model.weights pchisq plot points rainbow
  rnorm rpois rug runif segments weighted.mean
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "box", "matplot", "plot", "points",
             "rug", "segments")
  importFrom("stats", ".getXlevels", "deviance", "formula",
             "model.matrix", "model.offset", "model.response",
             "model.weights", "pchisq", "rnorm", "rpois", "runif",
             "weighted.mean")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
Depends: includes the non-default packages:
  'MASS' 'boot' 'RColorBrewer' 'scatterplot3d' 'tcltk' 'tcltk2'
  'tkrplot' 'rpanel' 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
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: lattice
Error: package or namespace load failed for 'mdsr':
 .onAttach failed in attachNamespace() for 'mdsr', details:
  call: value[[3L]](cond)
  error: Package 'lattice' version 0.20.38 cannot be unloaded:
 Error in unloadNamespace(package) : namespace 'lattice' is imported by 'Matrix', 'nlme', 'mosaic' so cannot be unloaded
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
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.
Depends: includes the non-default packages:
  'seqinr' 'pcaMethods' 'Matrix' 'ROCR' 'Hmisc' 'KernSmooth' 'seqLogo'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'Hmisc' 'KernSmooth' 'Matrix' 'ROCR' 'methods' 'pcaMethods' 'seqLogo'
  'seqinr'
  Please remove these calls from your code.
.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.
'library' or 'require' calls in package code:
  'adegenet' 'geosphere'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.5Mb
workspace_management : tellme: no visible global function definition
  for 'file.edit'
workspace_management: no visible global function definition for
  'object.size'
Undefined global functions or variables:
  file.edit object.size
Consider adding
  importFrom("utils", "file.edit", "object.size")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.0Mb
Malformed Description field: should contain one or more complete sentences.
dometa: no visible global function definition for 'qchisq'
dometa: no visible global function definition for 'median'
dometa: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'qnorm'
forestplot: no visible global function definition for 'plot'
forestplot: no visible global function definition for 'points'
forestplot: no visible global function definition for 'text'
metagwa.files: no visible global function definition for 'read.csv'
metagwa.files: no visible global function definition for 'write.csv'
metagwa.tables: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  median pchisq plot points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "plot", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
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.
INFORMATION: Es konnten keine Dateien mit dem angegebenen
Muster gefunden werden.
Quitting from lines 63-72 (metaBMA.Rmd) 
Error: processing vignette 'metaBMA.Rmd' failed with diagnostics:
Unable to call JAGS
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'gsl' 'rmeta'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
metacor.DSL: no visible global function definition for 'qnorm'
metacor.DSL: no visible global function definition for 'pnorm'
metacor.DSL: no visible global function definition for 'metaplot'
metacor.OP: no visible global function definition for 'hyperg_2F1'
metacor.OP: no visible global function definition for 'qnorm'
metacor.OP: no visible global function definition for 'pnorm'
metacor.OP: no visible global function definition for 'metaplot'
Undefined global functions or variables:
  hyperg_2F1 metaplot pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
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.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Malformed Description field: should contain one or more complete sentences.
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.
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').
Packages suggested but not available for checking: 'doMC' '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.
prepare_Rd: DropDupGenes.Rd:29-31: Dropping empty section \details
prepare_Rd: DropDupGenes.Rd:41-43: Dropping empty section \note
prepare_Rd: DropDupGenes.Rd:47-49: Dropping empty section \seealso
prepare_Rd: MetaPCA-package.Rd:29-30: Dropping empty section \seealso
prepare_Rd: MetaPCA.Rd:76-78: Dropping empty section \details
prepare_Rd: MetaPCA.Rd:88-90: Dropping empty section \note
prepare_Rd: MetaPCA.Rd:94-96: Dropping empty section \seealso
prepare_Rd: PlotPC2D.Rd:80-82: Dropping empty section \details
prepare_Rd: PlotPC2D.Rd:92-94: Dropping empty section \note
prepare_Rd: PlotPC2D.Rd:98-100: Dropping empty section \seealso
prepare_Rd: PreprocessMetaAnalysis.Rd:39-41: Dropping empty section \details
prepare_Rd: PreprocessMetaAnalysis.Rd:51-53: Dropping empty section \note
prepare_Rd: PreprocessMetaAnalysis.Rd:57-59: Dropping empty section \seealso
prepare_Rd: requireAll.Rd:19-21: Dropping empty section \details
prepare_Rd: requireAll.Rd:31-33: Dropping empty section \note
prepare_Rd: requireAll.Rd:25-27: Dropping empty section \references
prepare_Rd: requireAll.Rd:37-39: Dropping empty section \seealso
Package suggested but not available for checking: 'doMC'
'library' or 'require' call to 'survival' 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:
  'foreach' 'iterators' 'proto'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fishercomb: no visible global function definition for 'pchisq'
fishercomb: no visible global function definition for 'p.adjust'
invnorm : <anonymous>: no visible global function definition for
  'qnorm'
invnorm: no visible global function definition for 'pnorm'
invnorm: no visible global function definition for 'p.adjust'
sim.function : <anonymous>: no visible global function definition for
  'rnorm'
sim.function : <anonymous>: no visible global function definition for
  'rnbinom'
Undefined global functions or variables:
  p.adjust pchisq pnorm qnorm rnbinom rnorm
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
             "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/MetaStan.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
GNU make is a SystemRequirements.
estim: no visible global function definition for 'var'
metareg: no visible global function definition for 'pchisq'
metareg: no visible global function definition for 'pnorm'
metareg: no visible global function definition for 'pt'
metatest: no visible global function definition for 'model.matrix'
metatest: no visible global function definition for 'model.response'
permute: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  model.matrix model.response pchisq pnorm pt rbinom var
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pchisq",
             "pnorm", "pt", "rbinom", "var")
to your NAMESPACE file.
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.
'library' or 'require' call to 'nlme' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'BRugs' 'R2WinBUGS' 'coda' 'rjags'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'nlme:::VarCorr'
  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:
  'VC.est.fixed' 'VC.est.random'
Package has no Sweave vignette sources and no VignetteBuilder field.
Malformed Description field: should contain one or more complete sentences.
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.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.1Mb
    libs   4.1Mb
    misc   1.1Mb
Packages in Depends field not imported from:
  'MASS' 'abind' 'pls'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
show,mewTyp: no visible global function definition for 'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ExPosition' 'prettyGraphs'
  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: 'doMC'
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.
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.
Malformed Description field: should contain one or more complete sentences.
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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'RJSONIO' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for 'packageVersion'
.onAttach: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible global function definition for 'fromJSON'
call.MGRAST: no visible binding for global variable '.MGRAST'
call.MGRAST: no visible global function definition for 'download.file'
call.MGRAST: no visible global function definition for 'isValidJSON'
call.MGRAST: no visible global function definition for 'fromJSON'
doc.MGRAST: no visible binding for global variable '.MGRAST'
doc.MGRAST: no visible global function definition for 'str'
load.MGRAST: no visible binding for global variable '.MGRAST'
parse.MGRAST: no visible binding for global variable '.MGRAST'
this.package: no visible binding for global variable '.MGRAST'
Undefined global functions or variables:
  .MGRAST download.file fromJSON isValidJSON packageVersion str
Consider adding
  importFrom("utils", "download.file", "packageVersion", "str")
to your NAMESPACE file.
calc_z_var: no visible binding for global variable 'median'
diffScore: no visible global function definition for 'new'
diffScore: no visible global function definition for 'model.matrix'
logNORMcdf: no visible global function definition for 'pnorm'
mGSZ.adj.mean.std: no visible binding for global variable 'sd'
pick.data.cols: no visible binding for global variable 'var'
plotProfile: no visible binding for global variable 'quantile'
plotProfile: no visible global function definition for 'plot'
plotProfile: no visible global function definition for 'lines'
plotProfile: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines median model.matrix new plot pnorm quantile sd var
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("methods", "new")
  importFrom("stats", "median", "model.matrix", "pnorm", "quantile",
             "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File
  LICENSE
is not mentioned in the DESCRIPTION file.
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 'plot'
plotMH: no visible global function definition for 'frame'
plotMH: no visible global function definition for 'text'
Undefined global functions or variables:
  frame hist optim plot quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "plot", "text")
  importFrom("stats", "optim", "quantile", "runif", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
.snqProfitImposeConvexityStEr: no visible global function definition
  for 'runif'
predict.snqProfitEst: no visible global function definition for
  'model.matrix'
predict.snqProfitEst: no visible global function definition for 'qt'
predict.snqProfitEst: no visible global function definition for
  'df.residual'
predict.snqProfitEst: no visible global function definition for
  'residuals'
snqProfitCoef: no visible global function definition for 'pt'
snqProfitEla: no visible global function definition for 'pt'
snqProfitEst: no visible global function definition for 'as.formula'
snqProfitEst: no visible global function definition for 'coef'
snqProfitEst: no visible global function definition for 'vcov'
snqProfitEst: no visible global function definition for 'fitted'
snqProfitEst: no visible global function definition for 'df.residual'
snqProfitImposeConvexity: no visible global function definition for
  'optim'
snqProfitSystem: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  as.formula coef df.residual fitted model.matrix optim pt qt residuals
  runif vcov
Consider adding
  importFrom("stats", "as.formula", "coef", "df.residual", "fitted",
             "model.matrix", "optim", "pt", "qt", "residuals", "runif",
             "vcov")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'microcontax.data'
Unknown package 'microcontax.data' in Rd xrefs
runMicrosamplingDesignApp: warning in dev_package_deps(pkg =
  system.file(package = "microsamplingDesign"), dependencies =
  "Suggests"): partial argument match of 'pkg' to 'pkgdir'
Malformed Description field: should contain one or more complete sentences.
'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.
Packages in Depends field not imported from:
  'SDMTools' 'raster'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MigClim.genClust: no visible global function definition for 'raster'
MigClim.migrate: no visible global function definition for 'raster'
MigClim.migrate: no visible global function definition for
  'dataframe2asc'
MigClim.migrate: no visible global function definition for
  'writeRaster'
MigClim.migrate: no visible global function definition for 'cellStats'
MigClim.migrate: no visible global function definition for 'read.table'
MigClim.migrate: no visible global function definition for
  'write.table'
MigClim.plot: no visible global function definition for 'raster'
MigClim.plot: no visible global function definition for 'rainbow'
MigClim.plot: no visible global function definition for 'jpeg'
MigClim.plot: no visible global function definition for 'ymax'
MigClim.plot: no visible global function definition for 'ymin'
MigClim.plot: no visible global function definition for 'xmax'
MigClim.plot: no visible global function definition for 'xmin'
MigClim.plot: no visible global function definition for 'image'
MigClim.plot: no visible global function definition for 'dev.off'
MigClim.plot: no visible global function definition for 'png'
MigClim.plot: no visible global function definition for 'dev.new'
MigClim.plot: no visible global function definition for 'plot'
Undefined global functions or variables:
  cellStats dataframe2asc dev.new dev.off image jpeg plot png rainbow
  raster read.table write.table writeRaster xmax xmin ymax ymin
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "jpeg", "png", "rainbow")
  importFrom("graphics", "image", "plot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File 'MigClim/libs/i386/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.o'
File 'MigClim/libs/x64/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.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.
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
  'plot'
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 plot points polygon predict resid
  rug sd text
Consider adding
  importFrom("graphics", "lines", "mtext", "plot", "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.
Malformed Description field: should contain one or more complete sentences.
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.
miney : plot.initial.matrix: no visible global function definition for
  'plot'
miney : plot.initial.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'plot'
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 plot rect text title
Consider adding
  importFrom("graphics", "locator", "plot", "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.
'library' or 'require' calls in package code:
  'parallel' 'snowfall'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
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.
.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 'plot'
.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 plot qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot", "plot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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'
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.
MIcombine.default: no visible binding for global variable 'vcov'
MIcombine.default: no visible binding for global variable 'coef'
MIcombine.default: no visible global function definition for 'var'
MIcombine.imputationResultList: no visible binding for global variable
  'vcov'
MIcombine.imputationResultList: no visible binding for global variable
  'coef'
close.DBimputationList: no visible global function definition for 'is'
getvars: no visible global function definition for 'is'
print.MIresult: no visible global function definition for 'coef'
print.MIresult: no visible global function definition for 'vcov'
summary.MIresult: no visible global function definition for 'coef'
summary.MIresult: no visible global function definition for 'vcov'
summary.MIresult: no visible global function definition for 'qt'
Undefined global functions or variables:
  coef is qt var vcov
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "coef", "qt", "var", "vcov")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   4.0Mb
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.
Packages suggested but not available for checking: 'Rmosek' 'REBayes'
Packages unavailable to check Rd xrefs: 'REBayes', 'Rmosek'
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.
Malformed Title field: should not end in a period.
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.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
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.
'library' or 'require' calls in package code:
  'cairoDevice' 'gplots'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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'
confusionDendrogram: no visible global function definition for 'plot'
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 'plot'
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'
plot.mlearning: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline axis barplot image legend lines mtext par plot rect stars text
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "mtext", "par", "plot", "rect", "stars", "text")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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').
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
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
File which contains pragma(s) suppressing diagnostics:
  'src/lemon/core.h'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/MmgraphR.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
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.
Namespace with empty importFrom: 'gee'
Malformed Description field: should contain one or more complete sentences.
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').
Checking should be performed on sources prepared by 'R CMD build'.
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.
bin.by.date: no visible binding for global variable 'quantile'
bin.by.date: no visible global function definition for 'na.omit'
biplot: no visible global function definition for 'na.omit'
biplot.character: no visible global function definition for 'runif'
biplot.character: no visible global function definition for 'opts'
biplot.character: no visible global function definition for
  'theme_blank'
distributionplot: no visible global function definition for 'na.omit'
distributionplot.character: no visible global function definition for
  'head'
distributionplot.factor: no visible global function definition for
  'opts'
distributionplot.factor: no visible global function definition for
  'theme_text'
mapmobility: no visible global function definition for 'lines'
responseplot: no visible global function definition for 'na.omit'
scatterplot: no visible global function definition for 'na.omit'
scatterplot: no visible global function definition for 'opts'
scatterplot: no visible global function definition for 'theme_text'
sharedtimeplot: no visible global function definition for 'na.omit'
timeplot: no visible global function definition for 'na.omit'
timeplot: no visible global function definition for 'opts'
timeplot.character: no visible global function definition for 'runif'
timeplot.character: no visible global function definition for 'rnorm'
timeplot.character: no visible binding for global variable 'text'
userplot: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  head lines na.omit opts quantile rnorm runif text theme_blank
  theme_text
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("stats", "na.omit", "quantile", "rnorm", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'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.
'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.
Error in re-building vignettes:
  ...
Quitting from lines 55-68 (modistools-vignette.Rmd) 
Error: processing vignette 'modistools-vignette.Rmd' failed with diagnostics:
second argument must be a list
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Keyboard character used is undefined
(inputenc)                in inputencoding `utf8'.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
.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.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/molaR.Rcheck/00install.out' for details.
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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   1.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
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.
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.
.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').
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
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'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
plot.apos: no visible global function definition for 'plot'
plot.apos: no visible global function definition for 'abline'
plot.apos: no visible global function definition for 'text'
plot.rst: no visible global function definition for 'matplot'
plot.rst: no visible global function definition for 'abline'
plot.rst: no visible global function definition for 'text'
track : background: no visible global function definition for 'par'
track : background: no visible global function definition for 'plot'
track : background: no visible global function definition for 'axTicks'
track : background: no visible global function definition for 'abline'
track : background: no visible global function definition for 'box'
track : tracks: no visible global function definition for 'lines'
track : magselect: no visible global function definition for 'na.omit'
track : add.stars: no visible global function definition for 'points'
track : addlab.eqc: no visible global function definition for 'points'
track : addlab.eqc: no visible global function definition for 'text'
track : add.planet: no visible global function definition for 'text'
track : add.planet: no visible global function definition for 'points'
track : add.ecliptic: no visible global function definition for 'lines'
track : add.brightlab: no visible global function definition for 'text'
track: no visible global function definition for 'par'
track: no visible binding for global variable 'axis'
track: no visible global function definition for 'title'
Undefined global functions or variables:
  abline axTicks axis box lines matplot na.omit par plot points text
  title
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "lines",
             "matplot", "par", "plot", "points", "text", "title")
  importFrom("stats", "na.omit")
to your NAMESPACE file.
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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Malformed Title field: should not end in a period.
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.
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.HMDdata: no visible global function definition for 'plot'
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 plot poisson quantile time
Consider adding
  importFrom("graphics", "matplot", "plot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
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'
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File '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 'plot'
diagram.mpa: no visible global function definition for 'abline'
diagram.mpa: no visible global function definition for 'text'
plotmpa: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "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 'plot'
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 plot points rect
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "rect")
  importFrom("stats", "cov", "dist", "median")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Title field: should not end in a period.
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.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
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 significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/mrMLM.GUI.Rcheck/00install.out' for details.
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
Malformed Title field: should not end in a period.
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.
Malformed Title field: should not end in a period.
MRwarp: no visible global function definition for 'dev.new'
MRwarp: no visible global function definition for 'plot'
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 plot points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "lines", "plot", "points")
to your NAMESPACE file.
File 'MRwarping/libs/i386/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'
File 'MRwarping/libs/x64/MRwarping.dll':
  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 'plot'
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 plot png points
  rainbow read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "plot", "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').
'library' or 'require' call to 'XML' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
csv2list: no visible global function definition for 'read.csv'
kgml_i: no visible global function definition for 'xmlTreeParse'
kgml_i: no visible global function definition for 'xmlRoot'
kgml_i: no visible global function definition for 'xmlAttrs'
list2xml: no visible global function definition for 'xmlNode'
list2xml: no visible global function definition for 'append.xmlNode'
msea_ora: no visible global function definition for 'fisher.test'
msea_ora: no visible global function definition for 'p.adjust'
msea_sub: no visible global function definition for 'sd'
msea_sub: no visible global function definition for 'cor.test'
pathway_class: no visible global function definition for 'untar'
pca_scaled: no visible binding for global variable 'sd'
pca_scaled: no visible global function definition for 'cor.test'
pca_scaled: no visible global function definition for 'p.adjust'
pca_scaled: no visible binding for global variable 'var'
read_pathway: no visible global function definition for 'xmlTreeParse'
read_pathway: no visible global function definition for 'xmlRoot'
read_pathway: no visible global function definition for 'xmlToList'
read_pathway: no visible global function definition for 'xmlAttrs'
Undefined global functions or variables:
  append.xmlNode cor.test fisher.test p.adjust read.csv sd untar var
  xmlAttrs xmlNode xmlRoot xmlToList xmlTreeParse
Consider adding
  importFrom("stats", "cor.test", "fisher.test", "p.adjust", "sd", "var")
  importFrom("utils", "read.csv", "untar")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'amap' 'clValid' 'cluster' 'fpc' 'mzR' 'xcms'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/MSeasy.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  'MSeasy' 'tcltk'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'grDevices' 'xcms'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
bic.dfgps: no visible global function definition for 'var'
coef.dfgps: no visible binding for global variable 'var'
coef.step.dfgps: no visible binding for global variable 'var'
coefmat.dfgps: no visible binding for global variable 'var'
cp.dfgps: no visible global function definition for 'var'
dfgps: no visible global function definition for 'complete.cases'
msgps: no visible global function definition for 'complete.cases'
msgps: no visible global function definition for 'var'
plot.df: no visible global function definition for 'plot'
plot.df: no visible global function definition for 'par'
plot.msgps: no visible global function definition for 'plot'
plot.msgps: no visible global function definition for 'par'
plot.msgps: no visible global function definition for 'abline'
predict.msgps: no visible global function definition for
  'complete.cases'
Undefined global functions or variables:
  abline complete.cases par plot var
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "complete.cases", "var")
to your NAMESPACE file.
MSIseq.classify: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
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.
'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.
'library' or 'require' call to 'XML' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'NightDay' 'RSQLite' 'XML' 'geosphere' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
drawMap: no visible global function definition for 'plot'
drawMap: no visible global function definition for 'box'
drawMap: no visible global function definition for 'points'
getFlights: no visible binding for global variable 'htmlTreeParse'
getFlights: no visible binding for global variable 'xpathSApply'
getFlights: no visible binding for global variable 'xmlAttrs'
getFlights: no visible binding for global variable 'free'
movie.routes: no visible global function definition for
  'txtProgressBar'
movie.routes: no visible global function definition for 'jpeg'
movie.routes: no visible global function definition for 'plot'
movie.routes: no visible global function definition for
  'setTxtProgressBar'
movie.routes: no visible global function definition for 'dev.off'
plot.routes: no visible global function definition for 'plot'
plot.routes: no visible global function definition for 'points'
plot.routes: no visible global function definition for 'mtext'
plot.routes : a: no visible global function definition for 'points'
plot.routes : a: no visible global function definition for 'text'
plot.routes : a: no visible global function definition for
  'gcIntermediate'
plot.routes : a: no visible global function definition for 'lines'
routes: no visible global function definition for 'data'
routes: no visible global function definition for 'distHaversine'
routes: no visible global function definition for 'gcIntermediate'
Undefined global functions or variables:
  box data dev.off distHaversine free gcIntermediate htmlTreeParse jpeg
  lines mtext plot points setTxtProgressBar text txtProgressBar
  xmlAttrs xpathSApply
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "box", "lines", "mtext", "plot", "points",
             "text")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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'
kmCok: no visible global function definition for 'plot'
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 plot qnorm qt validObject
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "new", "validObject")
  importFrom("stats", "lm", "model.matrix", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
kphaz.plot: no visible global function definition for 'stepfun'
muhaz: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx stepfun
Consider adding
  importFrom("stats", "approx", "stepfun")
to your NAMESPACE file.
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 'plot'
plotOptionValues: no visible global function definition for 'persp'
Undefined global functions or variables:
  persp plot
Consider adding
  importFrom("graphics", "persp", "plot")
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.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/multilevelPSA.Rcheck/00install.out' for details.
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 'plot'
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 'plot'
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 plot
  points ppoints qchisq read.table write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Malformed Description field: should contain one or more complete sentences.
.moments: no visible global function definition for 'ppois'
.truncpoi: no visible global function definition for 'ppois'
Undefined global functions or variables:
  ppois
Consider adding
  importFrom("stats", "ppois")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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 'plot'
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 plot pt rbinom rgamma runif terms title var
Consider adding
  importFrom("graphics", "par", "plot", "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.
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.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
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.
File 'multxpert/R/zzz.R':
  .onLoad calls:
    cat("multxpert: Implementation of commonly used p-value based and parametric\n",     "multiple testing procedures and parallel gatekeeping procedures.\n",     "For more information visit http://multxpert.com/wiki/MultXpert_package\n",     sep = "")

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

paradjp: no visible global function definition for 'pt'
parci: no visible global function definition for 'qt'
pdunnett: no visible global function definition for 'GenzBretz'
pvalci: no visible global function definition for 'qnorm'
qdunnett: no visible global function definition for 'GenzBretz'
Undefined global functions or variables:
  GenzBretz pt qnorm qt
Consider adding
  importFrom("stats", "pt", "qnorm", "qt")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'car' 'pdist' 'pls' 'gplots' 'mvtnorm' 'robustbase' 'gtools' 'bitops'
  'caTools' 'pcaPP' 'rrcov'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  '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.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
plotFID: no visible global function definition for 'plot'
plotFID: no visible global function definition for 'points'
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
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').
Malformed Description field: should contain one or more complete sentences.
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.
Malformed Title field: should not end in a period.
':::' calls which should be '::':
  'base:::call' 'base:::importIntoEnv' 'base:::lockEnvironment'
  'base:::match.call' 'base:::print.default' 'base:::print.function'
  'tools:::Rd2txt' 'utils:::?'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'tools:::.Rd_get_metadata' 'tools:::.get_package_metadata'
  'tools:::.install_package_Rd_indices'
  'tools:::.install_package_Rd_objects'
  'tools:::.install_package_description'
  'tools:::.install_package_namespace_info' 'tools:::.read_description'
  'tools:::.writePkgIndices' 'tools:::.writeVignetteHtmlIndex'
  'tools:::RdTags' 'tools:::fetchRdDB' 'tools:::makeLazyLoadDB'
  'tools:::prepare_Rd'
  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:
  'Save' 'body.print.function' 'cd' 'rbind.data.frame'
  'search.task.trees' 'untetherBalloon'
Checking should be performed on sources prepared by 'R CMD build'.
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.
contour.mvcwt: no visible global function definition for 'par'
get.min.scale: no visible global function definition for 'median'
image.mvcwt: no visible global function definition for 'par'
plot.mvcwt: no visible global function definition for 'par'
print.mvcwt: no visible global function definition for 'str'
Undefined global functions or variables:
  median par str
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "median")
  importFrom("utils", "str")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/mvdalab.Rcheck/00install.out' for details.
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.
prepare_Rd: mvsf.Rd:16-17: Dropping empty section \details
Package in Depends field not imported from: 'gtools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mvtmeta_fe: no visible global function definition for 'combinations'
Undefined global functions or variables:
  combinations
Malformed Description field: should contain one or more complete sentences.
'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.
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.
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.
Malformed Description field: should contain one or more complete sentences.
update_episode: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
    libs   1.5Mb
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 which this enhances but not available for checking: 'asreml'
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
Malformed Description field: should contain one or more complete sentences.
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
  'plot'
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 plot predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "plot")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
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'
NB.plot.likelihood: no visible global function definition for 'plot'
Undefined global functions or variables:
  optimize plot uniroot write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Malformed Description field: should contain one or more complete sentences.
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.
get.split.filename.cmip5: no visible global function definition for
  'tail'
nc.conform.data : <anonymous>: no visible global function definition
  for 'na.omit'
nc.get.subset.recursive: no visible global function definition for
  'head'
nc.get.subset.recursive: no visible global function definition for
  'tail'
nc.put.subset.recursive: no visible global function definition for
  'head'
nc.put.subset.recursive: no visible global function definition for
  'tail'
Undefined global functions or variables:
  head na.omit tail
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
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.
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 significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/nearfar.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/NeatMap.Rcheck/00install.out' for details.
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/i386/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'
File 'NeatMap/libs/x64/NeatMap.dll':
  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.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
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 'plot'
population: no visible global function definition for 'lines'
Undefined global functions or variables:
  coefficients lines lm par plot rpois sd weighted.mean
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "coefficients", "lm", "rpois", "sd",
             "weighted.mean")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
The following files look like leftovers/mistakes:
  'Rplots.pdf', 'Rplots.ps'
Please remove them from your package.
nestedRanksTest.default: no visible global function definition for
  'setNames'
nestedRanksTest.default: no visible global function definition for
  'quantile'
nestedRanksTest.formula: no visible global function definition for
  'terms'
plot.htest_boot: no visible global function definition for 'hist'
plot.htest_boot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline hist quantile setNames terms
Consider adding
  importFrom("graphics", "abline", "hist")
  importFrom("stats", "quantile", "setNames", "terms")
to your NAMESPACE file.
clustConfigurations: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
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.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.2Mb
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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/NetLogoR.Rcheck/00install.out' for details.
simulate.sisnetwork: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
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.
Packages in Depends field not imported from:
  'MASS' 'boot' 'lattice' 'psych'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Package suggested but not available for checking: 'NFPdata'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
compare.CDF: no visible global function definition for 'quantile'
download.single.game: no visible global function definition for
  'download.file'
fit.shot.probs.simple: no visible global function definition for
  'predict'
integrate.old.pieces: no visible global function definition for
  'na.omit'
prob.score.simple.objects: no visible global function definition for
  'binomial'
prob.score.simple.objects: no visible binding for global variable
  'logit'
prob.score.simple.objects: no visible global function definition for
  'predict'
process.pl.new: no visible global function definition for 'na.omit'
read.gif: no visible global function definition for 'download.file'
read.gif: no visible global function definition for 'rgb'
solver.with.nlm: no visible global function definition for 'nlm'
team.table : thisplot: no visible global function definition for 'par'
team.table : thisplot: no visible global function definition for 'plot'
team.table : thisplot: no visible global function definition for 'text'
team.table : thisplot: no visible global function definition for
  'abline'
Undefined global functions or variables:
  abline binomial download.file logit na.omit nlm par plot predict
  quantile rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "par", "plot", "text")
  importFrom("stats", "binomial", "na.omit", "nlm", "predict",
             "quantile")
  importFrom("utils", "download.file")
to your NAMESPACE file.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         6.5Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.3Mb
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/nlcv.Rcheck/00install.out' for details.
nlmeODE: no visible global function definition for 'deriv'
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
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.
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.
Malformed Description field: should contain one or more complete sentences.
Malformed Title field: should not end in a period.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Malformed Description field: should contain one or more complete sentences.
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.
Package suggested but not available for checking: 'hurricaneexposuredata'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
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.
Depends: includes the non-default packages:
  'lpSolve' 'gdata' 'Hmisc' 'rms' 'geometry' 'psych' 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  '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.
'library' or 'require' call to 'colorspace' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.1/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.1/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

LaTeX errors:
! LaTeX Error: File `sfmath.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Execution halted
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.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
Malformed Description field: should contain one or more complete sentences.
mi.inference: no visible binding for global variable 'var'
mi.inference: no visible global function definition for 'qt'
mi.inference: no visible global function definition for 'pt'
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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.
CIPW: no visible global function definition for 'data'
CIPW: no visible binding for global variable 'AtomWeight'
CIPW: no visible binding for global variable 'MinWeight'
CIPW: no visible binding for global variable 'OxiWeight'
CIPW.trace: no visible global function definition for 'data'
CIPW.trace: no visible binding for global variable 'AtomWeight'
CIPW.trace: no visible binding for global variable 'MinWeight'
CIPW.trace: no visible binding for global variable 'OxiWeight'
Undefined global functions or variables:
  AtomWeight MinWeight OxiWeight data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
BoundingRA: no visible global function definition for 'rnorm'
check_y_estimator: no visible global function definition for 'rnorm'
genNORTARA: no visible global function definition for 'rnorm'
genNORTARA: no visible global function definition for 'pnorm'
valid_input_cormat: no visible global function definition for 'rnorm'
valid_input_cormat: no visible global function definition for 'pnorm'
valid_input_cormat: no visible global function definition for 'cor'
y_control_estimator: no visible global function definition for 'pnorm'
y_control_estimator: no visible global function definition for 'cor'
y_control_estimator : <anonymous>: no visible global function
  definition for 'cor'
y_control_estimator: no visible global function definition for 'cov'
y_control_estimator: no visible global function definition for 'var'
y_crude_estimator: no visible global function definition for 'pnorm'
y_crude_estimator: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor cov pnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov", "pnorm", "rnorm", "var")
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.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/npde.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'mclust' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
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 'plot'
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 plot pnorm qnorm smcure
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "integrate", "pnorm", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/npIntFactRep.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
nppbib: no visible global function definition for 'read.table'
nppbib: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq read.table
Consider adding
  importFrom("stats", "pchisq")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
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.
prepare_Rd: lambda.select.Rd:19-20: Dropping empty section \details
prepare_Rd: lambda.select.Rd:21-22: Dropping empty section \value
prepare_Rd: simex.H.density.Rd:28-29: Dropping empty section \details
prepare_Rd: simex.density.Rd:28-29: Dropping empty section \details
prepare_Rd: span.H.select.Rd:28-29: Dropping empty section \details
prepare_Rd: span.H.select.Rd:30-31: Dropping empty section \value
prepare_Rd: span.select.Rd:27-28: Dropping empty section \details
prepare_Rd: span.select.Rd:29-30: Dropping empty section \value
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
Depends: includes the non-default packages:
  'R.methodsS3' 'MASS' 'matrixStats' 'R.oo' 'R.utils' 'aroma.core'
  'aroma.affymetrix' 'DNAcopy'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'DNAcopy' 'MASS' 'R.methodsS3' 'R.oo' 'aroma.affymetrix' 'aroma.core'
  'matrixStats'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
.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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.4Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'nutshell.audioscrobbler' 'nutshell.bbdb'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
'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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'objectSignals'
A package should be listed in only one of these fields.
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.
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.
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.
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/i386/obliclus.dll':
  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/x64/obliclus.dll':
  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.
Malformed Title field: should not end in a period.
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.
Malformed Title field: should not end in a period.
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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.4Mb
    libs   2.0Mb
Running examples in 'OData-Ex.R' failed
The error most likely occurred in:

> ### Name: entitySets
> ### Title: Get a list of EntitySets for a web service base on OData
> ### Aliases: entitySets
> 
> ### ** Examples
> 
> entitySets("http://services.odata.org/TripPinRESTierService/?$format=json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: entitySets -> <Anonymous> -> paste -> readLines -> file
Execution halted
Packages in Depends field not imported from:
  'DBI' 'RJDBC' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to 'XML' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
multifactor: no visible global function definition for 'na.omit'
ruuid: no visible global function definition for 'runif'
Undefined global functions or variables:
  na.omit runif
Consider adding
  importFrom("stats", "na.omit", "runif")
to your NAMESPACE file.
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.
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.
Malformed Description field: should contain one or more complete sentences.
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.
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'
comp.freq: no visible global function definition for 'plot'
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  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.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/onewaytests.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/OpenCL.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'unix'
GNU make is a SystemRequirements.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R        2.4Mb
    libs     6.4Mb
    models   4.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: 'openNLPmodels.en'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.6Mb
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').
prepare_Rd: distance.Rd:21-22: Dropping empty section \details
prepare_Rd: distance.Rd:32-33: Dropping empty section \note
prepare_Rd: filter.Rd:26-27: Dropping empty section \details
prepare_Rd: filter.Rd:28-29: Dropping empty section \value
prepare_Rd: filter.Rd:36-37: Dropping empty section \note
prepare_Rd: findP.Rd:21-22: Dropping empty section \details
prepare_Rd: findP.Rd:34-35: Dropping empty section \note
prepare_Rd: ops-package.Rd:30-31: Dropping empty section \seealso
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.
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.
Malformed Description field: should contain one or more complete sentences.
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.
Malformed Title field: should not end in a period.
calculate.empirical.AUC: no visible global function definition for
  'qnorm'
ci.AgrestiCoull: no visible global function definition for 'qnorm'
ci.GartNam: no visible global function definition for 'qnorm'
ci.NotTransformed: no visible global function definition for 'qnorm'
ci.RubinSchenker: no visible global function definition for 'qnorm'
ci.RubinSchenker: no visible global function definition for 'plogis'
ci.RubinSchenker: no visible global function definition for 'qlogis'
ci.exact: no visible global function definition for 'qf'
ci.quadratic: no visible global function definition for 'qnorm'
ci.transformed: no visible global function definition for 'qnorm'
ci.wald: no visible global function definition for 'qnorm'
function.MinPvalue: no visible global function definition for
  'chisq.test'
function.MinPvalue : PADJMS: no visible global function definition for
  'qnorm'
function.MinPvalue : PADJMS: no visible global function definition for
  'dnorm'
optimal.cutpoints.default: no visible global function definition for
  'na.omit'
optimal.cutpoints.formula: no visible global function definition for
  'terms'
plot.optimal.cutpoints: no visible global function definition for 'par'
plot.optimal.cutpoints: no visible global function definition for
  'plot'
plot.optimal.cutpoints: no visible global function definition for
  'abline'
plot.optimal.cutpoints: no visible global function definition for
  'lines'
plot.optimal.cutpoints: no visible global function definition for
  'points'
Undefined global functions or variables:
  abline chisq.test dnorm lines na.omit par plogis plot points qf
  qlogis qnorm terms
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points")
  importFrom("stats", "chisq.test", "dnorm", "na.omit", "plogis", "qf",
             "qlogis", "qnorm", "terms")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'gurobi'
print.optimbase: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
calc.stress: no visible global function definition for 'sd'
opscale: 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: 'Rmosek'
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.
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
'library' or 'require' calls to packages already attached by Depends:
  'Matrix' 'splines'
  Please remove these calls from your code.
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.
error.bars: no visible global function definition for 'segments'
lambda.interp: no visible global function definition for 'approx'
orderedLasso: no visible binding for global variable 'sd'
orderedLasso.cv: no visible binding for global variable 'var'
plot.orderedLasso.cv: no visible global function definition for 'par'
plot.orderedLasso.cv: no visible global function definition for 'plot'
plot.orderedLasso.cv: no visible global function definition for 'axis'
plot.orderedLasso.cv: no visible global function definition for 'mtext'
plot.orderedLasso.cv: no visible global function definition for
  'points'
plot.orderedLasso.cv: no visible global function definition for
  'abline'
plot.timeLagLasso.cv: no visible global function definition for 'par'
plot.timeLagLasso.cv: no visible global function definition for 'plot'
plot.timeLagLasso.cv: no visible global function definition for 'axis'
plot.timeLagLasso.cv: no visible global function definition for 'mtext'
plot.timeLagLasso.cv: no visible global function definition for
  'points'
plot.timeLagLasso.cv: no visible global function definition for
  'abline'
timeLagLasso: no visible binding for global variable 'sd'
timeLagLasso.cv: no visible binding for global variable 'sd'
timeLagLasso.cv: no visible binding for global variable 'var'
timeLagLasso.path: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline approx axis mtext par plot points sd segments var
Consider adding
  importFrom("graphics", "abline", "axis", "mtext", "par", "plot",
             "points", "segments")
  importFrom("stats", "approx", "sd", "var")
to your NAMESPACE file.
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 'plot'
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 plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  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 'plot'
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 'plot'
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 plot points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
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/i386/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'
File 'OriGen/libs/x64/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (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.
Malformed Description field: should contain one or more complete sentences.
mdr.c: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
dicomTable: no visible global function definition for 'txtProgressBar'
dicomTable: no visible global function definition for
  'setTxtProgressBar'
readDICOM: no visible global function definition for 'txtProgressBar'
readDICOM: no visible global function definition for
  'setTxtProgressBar'
writeHeader: no visible global function definition for 'write.table'
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
Malformed Description field: should contain one or more complete sentences.
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_nodes: no visible global function definition for 'plot'
plot_ways: no visible global function definition for 'plot'
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 plot
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'Rcplex'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.8Mb
Error in re-building vignettes:
  ...
Warning in .local(x, ...) :
  The following sequence IDs are not in the dataset: 311, 222
Warning in .local(x, ...) :
  The following sequence IDs are not in the dataset: 311, 222
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figs/OutbreakTools-out.width==".8\\textwidth"" -> "figs/OutbreakTools-out.width___.8\\textwidth_"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  dots in figure paths replaced with _ ("figs/OutbreakTools-out_width____8//textwidth_")
Warning: The shape palette can deal with a maximum of 6 discrete values because
more than 6 becomes difficult to discriminate; you have 11. Consider
specifying shapes manually if you must have them.
Warning: Removed 58 rows containing missing values (geom_point).
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Quitting from lines 1022-1023 (OutbreakTools.Rnw) 
Error: processing vignette 'OutbreakTools.Rnw' failed with diagnostics:
cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
Execution halted
Malformed Description field: should contain one or more complete sentences.
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.
Electre3_AlphaBetaThresholds: no visible global function definition for
  'plot'
Electre3_SimpleThresholds: no visible global function definition for
  'plot'
Electre_1: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
p3state: no visible global function definition for 'survfit'
p3state: no visible global function definition for 'terms'
p3state: no visible global function definition for 'as.formula'
p3state: no visible global function definition for 'coxph'
p3state: no visible binding for global variable 'na.exclude'
plot.p3state: no visible global function definition for 'matplot'
plot.p3state: no visible global function definition for 'devAskNewPage'
plot.p3state: no visible global function definition for 'persp'
plot.p3state: no visible global function definition for 'colours'
plot.p3state: no visible global function definition for
  'filled.contour'
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
pacbpred : thetaFunc: no visible global function definition for 'lsfit'
pacbpred : thetaFunc: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'var'
pacbpred: no visible global function definition for 'runif'
pacbpred: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
[,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'
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 'plot'
plot.paf: no visible global function definition for 'lines'
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
CalGIF: no visible binding for global variable 'PAGIData'
CalGIF2: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible global function definition for 'p.adjust'
PAGI.Main: no visible global function definition for 'pt'
getclass.labels: no visible binding for global variable 'ExampleData'
getdataset: no visible binding for global variable 'ExampleData'
Undefined global functions or variables:
  ExampleData PAGIData p.adjust pt
Consider adding
  importFrom("stats", "p.adjust", "pt")
to your NAMESPACE file.
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.
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.
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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'lattice' 'vegan'
  Please remove these calls from your code.
EAMM: no visible global function definition for 'anova'
EAMM: no visible global function definition for 'rand'
PAMM: no visible global function definition for 'rand'
PAMM: no visible global function definition for 'anova'
SSF: no visible global function definition for 'rand'
SSF: no visible global function definition for 'anova'
Undefined global functions or variables:
  anova rand
Consider adding
  importFrom("stats", "anova")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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'
ProteinCluster: no visible global function definition for 'plot'
SignificantSubcluster: no visible global function definition for
  'order.dendrogram'
SignificantSubcluster: no visible global function definition for
  'fisher.test'
SignificantSubcluster: no visible global function definition for 'plot'
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
  plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Paneldata.formula: no visible global function definition for
  'model.frame'
Paneldata.formula: no visible global function definition for
  'model.matrix'
Paneldata.formula: no visible global function definition for
  'model.response'
summary.Paneldata: no visible global function definition for 'coef'
summary.Paneldata: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
grow.forest: no visible global function definition for 'model.frame'
grow.tree: no visible global function definition for 'model.frame'
predict.forest: no visible global function definition for 'model.frame'
predict.tree: no visible global function definition for 'model.frame'
predict,forest: no visible global function definition for 'model.frame'
predict,tree: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  model.frame
Consider adding
  importFrom("stats", "model.frame")
to your NAMESPACE file.
File 'ParallelForest/libs/i386/ParallelForest.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'random_utils.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'random_utils.o'
File 'ParallelForest/libs/x64/ParallelForest.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'random_utils.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'random_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.
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.
parallelExport: no visible global function definition for 'setNames'
parallelGetOptions: no visible global function definition for
  'setNames'
parallelStop: no visible global function definition for
  'getFromNamespace'
stopWithJobErrorMessages: no visible global function definition for
  'head'
Undefined global functions or variables:
  getFromNamespace head setNames
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "getFromNamespace", "head")
to your NAMESPACE file.
consensusMCcov: no visible global function definition for 'var'
consensusMCcov: no visible global function definition for 'cov'
consensusMCindep: no visible global function definition for 'var'
semiparamDPE: no visible binding for global variable 'var'
semiparamDPE: no visible global function definition for 'cov'
semiparamDPE: no visible global function definition for 'runif'
Undefined global functions or variables:
  cov runif var
Consider adding
  importFrom("stats", "cov", "runif", "var")
to your NAMESPACE file.
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.
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.formula.make: no visible global function definition for 'formula'
regress: no visible global function definition for 'lm'
regress: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  formula lm model.matrix
Consider adding
  importFrom("stats", "formula", "lm", "model.matrix")
to your NAMESPACE file.
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'
ridge.cv: no visible global function definition for 'plot'
Undefined global functions or variables:
  coef ggm.test.edges plot predict sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "predict", "sd", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
ParentOffspring: no visible global function definition for 'axis'
ParentOffspring: no visible global function definition for 'abline'
ParentOffspring: no visible global function definition for 'title'
ParentOffspring: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "title")
to your NAMESPACE file.
par.nmds : nmdscalc: no visible global function definition for 'runif'
par.nmds : nmdscalc: no visible global function definition for 'dist'
par.nmds: no visible binding for global variable 'j'
par.nmds: no visible global function definition for 'cor'
par.nmds: no visible global function definition for 'dist'
par.spp.est: no visible binding for global variable 'i'
par.spp.est: no visible global function definition for 'sd'
Undefined global functions or variables:
  cor dist i j runif sd
Consider adding
  importFrom("stats", "cor", "dist", "runif", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Calls with DUP:
   .C("aracne", as.double(t(mis)), as.integer(n), as.double(eps), 
       as.double(eta), res = double(n * n), PACKAGE = "parmigene", 
       DUP = FALSE)
   .C("clr", as.double(t(mis)), as.integer(n), res = double(n * 
       n), PACKAGE = "parmigene", DUP = FALSE)
   .C("mrnet", as.double(t(mis)), as.integer(n), res = double(n * 
       n), PACKAGE = "parmigene", DUP = FALSE)
DUP is no longer supported and will be ignored.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'nnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitOR: no visible global function definition for 'multinom'
fitOR: no visible global function definition for 'formula'
fitOR: no visible global function definition for 'coef'
fitOR: no visible global function definition for 'optim'
reportOR: no visible global function definition for 'qnorm'
reportOR: no visible global function definition for 'pchisq'
reportOR: no visible global function definition for 'coef'
simData: no visible global function definition for 'rnorm'
simData: no visible global function definition for 'runif'
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
partitionMap: no visible global function definition for 'predict'
partitionMap: no visible global function definition for 'rnorm'
partitionMap: no visible binding for global variable 'sd'
partitionMap: no visible global function definition for 'sd'
partitionMap: no visible global function definition for 'quantile'
Undefined global functions or variables:
  predict quantile rnorm sd
Consider adding
  importFrom("stats", "predict", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'partsm' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
parviol: no visible global function definition for 'plot.new'
parviol: no visible global function definition for 'plot.window'
parviol: no visible global function definition for 'title'
parviol: no visible global function definition for 'lines'
parviol: no visible global function definition for 'text'
parviol: no visible global function definition for 'rgb'
selecto: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot.new plot.window rgb text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot.new", "plot.window", "text",
             "title")
to your NAMESPACE file.
Packages 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.
'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.
Package in Depends field not imported from: 'datautils'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
animatePatches: no visible global function definition for
  'getTimestamp'
animatePatches: no visible global function definition for 'getElapsed'
colorPlot: no visible global function definition for 'layout'
colorPlot: no visible global function definition for 'par'
colorPlot: no visible global function definition for 'image'
colorPlot: no visible global function definition for 'axis'
drawPatches: no visible global function definition for 'rgb'
getInterRGB: no visible global function definition for 'col2rgb'
getInterRGB: no visible global function definition for 'rgb'
plotGmmOverlay: no visible global function definition for 'rgb'
plotGreyPatches : squarepatch: no visible global function definition
  for 'rgb'
plotGreyPatches : trianglepatch: no visible global function definition
  for 'rgb'
Undefined global functions or variables:
  axis col2rgb getElapsed getTimestamp image layout par rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "axis", "image", "layout", "par")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
Depends: includes the non-default packages:
  'svmpath' 'kernlab' 'affy' 'Biobase' 'ROCR' 'igraph' 'lpSolve'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'ROCR' 'affy' 'igraph' 'kernlab' 'lpSolve' 'svmpath'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
Package in Depends field not imported from: 'shape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
arrow: no visible global function definition for 'arrows'
draw: no visible global function definition for 'rect'
draw: no visible global function definition for 'text'
draw: no visible global function definition for 'plotellipse'
wall: no visible global function definition for 'plot.new'
wall: no visible global function definition for 'plot.window'
Undefined global functions or variables:
  arrows plot.new plot.window plotellipse rect text
Consider adding
  importFrom("graphics", "arrows", "plot.new", "plot.window", "rect",
             "text")
to your NAMESPACE file.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data      2.6Mb
    doc       1.3Mb
    extdata   9.5Mb
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 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > std_getwd <- function() 
  + {
  +   pwd <- getwd()
  +   # Enforce upper case Windows drive letters
  +   substring(pwd, 1, 1) <- toupper(substring(pwd, 1, 1))
  +   pwd
  + }
  > 
  > test_check("pathological")
  Loading required package: pathological
  -- 1. Failure: decompose_path handles paths with a unicode directory name. (@tes
  actual$dirname not equal to expected$dirname.
  1/1 mismatches
  x[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/CRAN"
  y[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/CRAN"
  
  -- 2. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 186 SKIPPED: 18 FAILED: 2
  1. Failure: decompose_path handles paths with a unicode directory name. (@test_decompose_path.R#466) 
  2. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
Checking should be performed on sources prepared by 'R CMD build'.
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
add_noise: no visible global function definition for 'rnorm'
estimate_risk_dream6 : <anonymous>: no visible global function
  definition for 'var'
generate_sample: no visible global function definition for 'rnorm'
generate_sample: no visible global function definition for 'runif'
sample_function: no visible global function definition for 'runif'
sample_function : <anonymous>: no visible global function definition
  for 'var'
sample_function_multi_mod_weight: no visible global function definition
  for 'runif'
sample_function_multi_mod_weight : <anonymous>: no visible global
  function definition for 'var'
sample_function_single_mod: no visible global function definition for
  'runif'
Undefined global functions or variables:
  rnorm runif var
Consider adding
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'PAWL' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
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.
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
S3 methods shown with full name in documentation object 'binds':
  'rbind.ddmatrix' 'cbind.ddmatrix'

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.
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
get.sysenv: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.6Mb
'library' or 'require' call to 'foreach' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dotplot.pbo: no visible global function definition for 'reorder'
pbo: no visible global function definition for '%dopar%'
pbo: no visible global function definition for 'foreach'
pbo: no visible global function definition for 'lm'
xyplot.pbo: no visible global function definition for 'ecdf'
xyplot.pbo: no visible global function definition for 'doubleYScale'
xyplot.pbo: no visible global function definition for 'reorder'
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
a_get_native: no visible global function definition for 'par'
a_get_relative: no visible global function definition for 'par'
brackets: no visible global function definition for 'par'
brackets: no visible global function definition for 'dist'
brackets: no visible global function definition for 'lines'
Undefined global functions or variables:
  dist lines par
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "dist")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
.win.appendLog: no visible binding for global variable 'lines'
plotMC : panel: no visible global function definition for 'points'
plotMC: no visible global function definition for 'pairs'
plotMC: no visible global function definition for 'mtext'
plotMC: no visible global function definition for 'axis'
plotMC: no visible global function definition for 'par'
readADpaths: no visible global function definition for 'read.table'
readRep: no visible global function definition for 'read.table'
saveADpaths: no visible global function definition for 'write.table'
Undefined global functions or variables:
  axis lines mtext pairs par points read.table write.table
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "pairs", "par",
             "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
Malformed Description field: should contain one or more complete sentences.
draw.pcaBootPlot: no visible global function definition for 'plot'
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 plot points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "plot", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   2.7Mb
    libs      1.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   2.3Mb
PCDReg.wf: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
defineTasks: no visible global function definition for 'par'
defineTasks: no visible global function definition for 'abline'
plotCorCoeff: no visible global function definition for 'hist'
plotCorCoeff: no visible global function definition for 'plot.new'
plotCorCoeff: no visible global function definition for 'plot.window'
plotCorCoeff: no visible global function definition for 'rect'
plotCorCoeff: no visible global function definition for 'axis'
plotCorCoeff: no visible global function definition for 'title'
plotCorCoeff: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline axis hist legend par plot.new plot.window rect title
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "par",
             "plot.new", "plot.window", "rect", "title")
to your NAMESPACE file.
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.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs   12.1Mb
    share  11.9Mb
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pdist: no visible global function definition for 'dist'
pdist: no visible global function definition for 'new'
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
band.chol.cv: no visible global function definition for 'cov'
pdsoft.cv: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Package suggested but not available for checking: 'faahKO'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
prepare_Rd: SpectrumBackground.Rd:59: Dropping empty section \keyword
prepare_Rd: SpectrumBackground.Rd:54-55: Dropping empty section \seealso
prepare_Rd: SpectrumBackground.Rd:56-57: Dropping empty section \examples
prepare_Rd: SpectrumDeconvolution.Rd:87: Dropping empty section \keyword
prepare_Rd: SpectrumDeconvolution.Rd:82-83: Dropping empty section \seealso
prepare_Rd: SpectrumDeconvolution.Rd:84-85: Dropping empty section \examples
prepare_Rd: SpectrumSearch.Rd:62: Dropping empty section \keyword
prepare_Rd: SpectrumSearch.Rd:59-60: Dropping empty section \examples
prepare_Rd: SpectrumSmoothMarkov.Rd:55: Dropping empty section \keyword
prepare_Rd: SpectrumSmoothMarkov.Rd:50-51: Dropping empty section \seealso
prepare_Rd: SpectrumSmoothMarkov.Rd:52-53: Dropping empty section \examples
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 'plot'
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 'plot'
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 plot segments title
  ts ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par", "plot",
             "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 'plot'
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 plot rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "plot", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'LinkingTo' for 'ggplot2' is unused as it has no 'include' directory
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo' 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AssoTestProc: no visible global function definition for 'rbinom'
AssoTestProc: no visible global function definition for 'princomp'
AssoTestProc: no visible global function definition for 'loadings'
AssoTestProc: no visible global function definition for 'lm'
CNVtypeAnay: no visible global function definition for 'cov'
ClusProc: no visible global function definition for 'princomp'
ClusProc: no visible global function definition for 'prcomp'
ClusProc0: no visible global function definition for 'kmeans'
ClusProc0: no visible global function definition for 'cov'
Inde: no visible global function definition for 'lm'
Inde: no visible global function definition for 'var'
STE: no visible global function definition for 'pchisq'
STIM: no visible global function definition for 'cor'
STIM: no visible global function definition for 'pchisq'
plot.clust: no visible global function definition for 'princomp'
plot.clust: no visible global function definition for 'loadings'
plot.clust: no visible global function definition for 'qplot'
plot.clust: no visible global function definition for 'geom_histogram'
plot.clust: no visible global function definition for 'aes_string'
plot.clust: no visible global function definition for 'barplot'
plot.clust: no visible global function definition for 'title'
plot.clust: no visible global function definition for 'mtext'
plot.clust: no visible global function definition for 'text'
Undefined global functions or variables:
  aes_string barplot cor cov geom_histogram kmeans lm loadings mtext
  pchisq prcomp princomp qplot rbinom text title var
Consider adding
  importFrom("graphics", "barplot", "mtext", "text", "title")
  importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq",
             "prcomp", "princomp", "rbinom", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
blup: no visible global function definition for 'model.matrix'
blup: no visible global function definition for 'model.frame'
blup: no visible global function definition for 'read.table'
calcG: no visible global function definition for 'as'
gblup: no visible global function definition for 'model.matrix'
gblup: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  as model.frame model.matrix read.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "model.frame", "model.matrix")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
create.data: no visible global function definition for 'rexp'
create.data: no visible global function definition for 'runif'
create.data: no visible global function definition for 'rbinom'
opt.splitval: no visible global function definition for 'na.omit'
opt2D : opt.both: no visible global function definition for 'optim'
Undefined global functions or variables:
  na.omit optim rbinom rexp runif
Consider adding
  importFrom("stats", "na.omit", "optim", "rbinom", "rexp", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
'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.
Malformed Title field: should not end in a period.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/pequod.Rcheck/00install.out' for details.
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').
Malformed Description field: should contain one or more complete sentences.
ksample.pclt: no visible global function definition for 'pchisq'
pCI: no visible global function definition for 'qbeta'
permKS.formula: no visible global function definition for 'terms'
permTREND.default: no visible global function definition for 'cor'
permTREND.formula: no visible global function definition for 'terms'
permTS.formula: no visible global function definition for 'terms'
trend.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor pchisq pnorm qbeta terms
Consider adding
  importFrom("stats", "cor", "pchisq", "pnorm", "qbeta", "terms")
to your NAMESPACE file.
hasMethod: no visible global function definition for 'getS3method'
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Malformed Description field: should contain one or more complete sentences.
colldiag: no visible global function definition for 'na.omit'
perturb : cutsp: no visible global function definition for 'runif'
perturb: no visible global function definition for 'terms'
perturb: no visible global function definition for 'formula'
perturb: no visible global function definition for 'coefficients'
perturb: no visible global function definition for 'as.formula'
print.reclassify: no visible global function definition for
  'addmargins'
reclassify : best.model: no visible global function definition for
  'glm'
reclassify : best.model: no visible global function definition for
  'as.formula'
reclassify : best.model: no visible global function definition for
  'poisson'
reclassify : best.model: no visible global function definition for
  'coef'
reclassify : best.model: no visible global function definition for
  'model.matrix'
reclassify : assocPat: no visible global function definition for
  'model.matrix'
reclassify : assocPat: no visible global function definition for 'glm'
reclassify : assocPat: no visible global function definition for
  'poisson'
summary.perturb: no visible binding for global variable 'sd'
Undefined global functions or variables:
  addmargins as.formula coef coefficients formula glm model.matrix
  na.omit poisson runif sd terms
Consider adding
  importFrom("stats", "addmargins", "as.formula", "coef", "coefficients",
             "formula", "glm", "model.matrix", "na.omit", "poisson",
             "runif", "sd", "terms")
to your NAMESPACE file.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
pGLS: no visible global function definition for 'model.response'
pGLS: no visible global function definition for 'model.matrix'
pGLS: no visible global function definition for 'pt'
Undefined global functions or variables:
  model.matrix model.response pt
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
prepare_Rd: data_fs.Rd:11: Dropping empty section \source
prepare_Rd: var_fs.Rd:12-14: Dropping empty section \references
GNU make is a SystemRequirements.
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.
Packages in Depends field not imported from:
  'ggplot2' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.phtMCMC: no visible global function definition for 'ggplot'
plot.phtMCMC: no visible global function definition for 'melt'
plot.phtMCMC: no visible global function definition for 'geom_line'
plot.phtMCMC: no visible global function definition for 'aes_string'
plot.phtMCMC: no visible global function definition for 'geom_smooth'
plot.phtMCMC: no visible global function definition for 'facet_wrap'
plot.phtMCMC: no visible global function definition for 'ggtitle'
plot.phtMCMC: no visible global function definition for 'xlab'
plot.phtMCMC: no visible global function definition for 'ylab'
plot.phtMCMC: no visible global function definition for 'geom_density'
Undefined global functions or variables:
  aes_string facet_wrap geom_density geom_line geom_smooth ggplot
  ggtitle melt xlab ylab
File 'PhaseType/libs/i386/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'
File 'PhaseType/libs/x64/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.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.
deforestation: no visible global function definition for 'model.frame'
deforestation: no visible global function definition for 'model.matrix'
deforestation: no visible global function definition for
  'model.response'
deforestation: no visible global function definition for 'vcov'
deforestation: no visible global function definition for 'glm'
demography: no visible global function definition for 'model.frame'
demography: no visible global function definition for 'model.matrix'
demography: no visible global function definition for 'model.response'
form.beta.start: no visible global function definition for 'coef'
form.beta.start: no visible global function definition for 'glm'
form.sigma2.start: no visible global function definition for 'var'
form.sigma2.start: no visible global function definition for
  'residuals'
form.sigma2.start: no visible global function definition for 'glm'
rinvgamma: no visible global function definition for 'rgamma'
rwish: no visible global function definition for 'rchisq'
rwish: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  coef glm model.frame model.matrix model.response rchisq residuals
  rgamma rnorm var vcov
Consider adding
  importFrom("stats", "coef", "glm", "model.frame", "model.matrix",
             "model.response", "rchisq", "residuals", "rgamma", "rnorm",
             "var", "vcov")
to your NAMESPACE file.
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
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'
fox: no visible global function definition for 'plot'
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'
kang: no visible global function definition for 'plot'
nahu: no visible global function definition for 'interaction.plot'
nahu: no visible global function definition for 'reorder'
nahu: no visible global function definition for 'plot'
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'
thsu: no visible global function definition for 'plot'
Undefined global functions or variables:
  cor interaction.plot median plot reorder sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
Running examples in 'phenocamapi-Ex.R' failed
The error most likely occurred in:

> ### Name: download_midday_images
> ### Title: Downloading the midday images for PhenoCam sites given a time
> ###   range
> ### Aliases: download_midday_images
> 
> ### ** Examples
> 
> 
> download_dir <- download_midday_images('dukehw',
+  y = 2018,
+  months = 2,
+  days=1,
+  download_dir= tempdir())
Warning in download.file(url, destfile = tmp_dest, quiet = TRUE, mode = "w") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file(url, destfile = tmp_dest, quiet = TRUE, mode = "w") : 
  cannot open URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw-midday.txt'
Warning in get_midday_list(site, direct = FALSE) :
  download from the phenocam server was failed
Error in basename(filepaths) : a character vector argument expected
Calls: download_midday_images -> parse_phenocam_filenames -> gsub -> basename
Execution halted
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  Loading required package: bitops
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Error in download.file(url, destfile = tmp, mode = "w") : 
    cannot open URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  -- 1. Error: (unknown) (@testphenocamapi.R#11)  --------------------------------
  file was not found on the server!
  1: get_pheno_ts(site = "dukehw", vegType = "DB", roiID = 1000, type = "3day") at testthat/testphenocamapi.R:11
  2: stop("file was not found on the server!")
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@testphenocamapi.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Error in download.file(url, destfile = tmp, mode = "w") : 
  cannot open URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Quitting from lines 200-209 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
file was not found on the server!
Execution halted
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').
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
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'
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'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.9Mb
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.
Depends: includes the non-default packages:
  'RGtk2' 'gWidgetsRGtk2' 'cairoDevice' 'lattice' 'rggobi' 'ggplot2'
  'proto'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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.
prepare_Rd: PKgraph.Rd:11-13: Dropping empty section \arguments
prepare_Rd: PKgraph.Rd:17-19: Dropping empty section \examples
prepare_Rd: pkdata.Rd:9-11: Dropping empty section \format
prepare_Rd: pkdata.Rd:14-16: Dropping empty section \examples
prepare_Rd: pkdata2.Rd:9-11: Dropping empty section \format
prepare_Rd: pkdata2.Rd:14-16: Dropping empty section \examples
PKmod: no visible global function definition for 'deriv'
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
PKadjust: no visible binding for global variable 'jpeg'
PKadjust: no visible binding for global variable 'bmp'
PKadjust: no visible binding for global variable 'png'
PKadjust: no visible binding for global variable 'tiff'
PKadjust: no visible binding for global variable 'dev.new'
PKadjust: no visible global function definition for 'dev.off'
PKfigure: no visible global function definition for 'dev.cur'
PKfigure: no visible global function definition for 'dev.off'
PKoutput: no visible global function definition for 'heatmap'
PKoutput: no visible global function definition for
  'packageDescription'
PKshow: no visible global function definition for 'browseURL'
addList1: no visible global function definition for 'formula'
addList1.old: no visible global function definition for 'formula'
addList2: no visible global function definition for 'formula'
generate.plot: no visible global function definition for 'dev.off'
writeHTML: no visible global function definition for
  'packageDescription'
writeLst: no visible global function definition for
  'packageDescription'
writeLst.tab: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for 'quantile'
initialize,nonmem: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
Running examples in 'placement-Ex.R' failed
The error most likely occurred in:

> ### Name: drive_time
> ### Title: Get travel time and distance between two point using the Google
> ###   API.
> ### Aliases: drive_time
> 
> ### ** Examples
> 
> # Bike from the NYC to Google!
> address <- c("350 5th Ave, New York, NY 10118, USA",
+ 			 "1600 Amphitheatre Pkwy, Mountain View, CA 94043, USA")
> 
> coordset <- geocode_url(address, auth="standard_api", privkey="",
+             clean=TRUE, add_date='today', verbose=TRUE)
Sending address vector (n=2) to Google...
Finished. 0 of 2 records successfully geocoded.
> 
> # Save coordinates. Google requires a format of: "lat,lng" (with no spaces)
> start <- paste(coordset$lat[1],coordset$lng[1], sep=",")
> end <- paste(coordset$lat[2],coordset$lng[2], sep=",")
> 
> # Get the travel time by bike (a mere 264 hours!) and distance in miles:
> howfar_miles <- drive_time(address=start, dest=end, auth="standard_api",
+ 						   privkey="", clean=FALSE, add_date='today',
+ 						   verbose=FALSE, travel_mode="bicycling",
+ 						   units="imperial")
Error in vapply(json, function(x) { : values must be length 11,
 but FUN(X[[1]]) result is length 0
Calls: drive_time -> t -> vapply
Execution halted
Package suggested but not available for checking: 'latticist'
'library' or 'require' call to 'lattice' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'latticist' 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:
  'cairoDevice' 'gWidgetsRGtk2' 'grid' 'lattice'
  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:
  'lattice:::lattice.getStatus' 'stats:::biplot.prcomp'
  See the note in ?`:::` about the use of this operator.
S3 methods shown with full name in documentation object 'plotCoords':
  'plotCoords.plot' 'plotCoords.biplot'

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.
Malformed Description field: should contain one or more complete sentences.
bwfw.hmm: no visible global function definition for 'dnorm'
bwfw1.hmm: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
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 examples in 'plotKML-Ex.R' failed
The error most likely occurred in:

> ### Name: plotKML-method
> ### Title: Methods for plotting results of spatial analysis in Google Earth
> ### Aliases: plotKML-method plotKML plotKML,SpatialPointsDataFrame-method
> ###   plotKML,SpatialLinesDataFrame-method
> ###   plotKML,SpatialPolygonsDataFrame-method
> ###   plotKML,SoilProfileCollection-method
> ###   plotKML,SpatialGridDataFrame-method
> ###   plotKML,SpatialPixelsDataFrame-method plotKML,RasterLayer-method
> ###   plotKML,SpatialPhotoOverlay-method plotKML,STIDF-method
> ###   plotKML,STFDF-method plotKML,STSDF-method plotKML,STTDF-method
> ###   plotKML,SpatialPredictions-method
> ###   plotKML,RasterBrickSimulations-method
> ###   plotKML,SpatialVectorsSimulations-method
> ###   plotKML,SpatialMaxEntOutput-method
> ###   plotKML,RasterBrickTimeSeries-method
> ###   plotKML,SpatialSamplingPattern-method plotKML,list-method
> ### Keywords: spatial methods
> 
> ### ** Examples
> 
> plotKML.env(silent = FALSE, kmz = FALSE)
Search for SAGA command line program and modules... 
SAGA command line program not found in the following default paths:
C:/Progra~1/SAGA-GIS
C:/Progra~2/SAGA-GIS
C:/SAGA-GIS
C:/OSGeo4W64/apps/saga
C:/OSGeo4W64/apps/saga-ltr
Search on the entire hard drive...
Error in paths(show.paths = TRUE) : object 'saga.version' not found
Calls: plotKML.env -> paths
Execution halted
Error in re-building vignettes:
  ...
Loading required package: gstat
Loading required package: raster
Loading required package: sp
Loading required package: plotKML
plotKML version 0.5-8 (2017-05-12)
URL: http://plotkml.r-forge.r-project.org/
Loading required package: GSIF
GSIF version 0.5-4 (2017-04-25)
URL: http://gsif.r-forge.r-project.org/

Attaching package: 'XML'

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

    toHTML

Reprojecting to +proj=longlat +datum=WGS84 ...
KML file opened for writing...
Writing to KML...
Closing  eberg.ll__CLYMHT_A__.kml
KML file opened for writing...
Writing to KML...
Closing  eberg.ll.kml
KML file opened for writing...
Reprojecting to +proj=longlat +datum=WGS84 ...

Error: processing vignette 'jss1079.Rnw' failed with diagnostics:
 chunk 12 
Error in paths(show.paths = TRUE) : object 'saga.version' not found
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.0Mb
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 'plot'
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 plot quantile tail title
  var window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "plot", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
generateEnvelope: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
llla.bi: no visible global function definition for 'as.formula'
llla.bi: no visible global function definition for 'glm'
llla.bi: no visible global function definition for 'binomial'
llla.bi: no visible binding for global variable 'logit'
llla.bi: no visible global function definition for 'vcov'
llla.bi: no visible global function definition for 'coef'
llla.mc: no visible global function definition for 'model.matrix'
llla.mc: no visible global function definition for 'as.formula'
llla.mc: no visible global function definition for 'coxph'
llla.mc: no visible global function definition for 'vcov'
llla.mc: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'as.formula'
llla.mle: no visible global function definition for 'glm'
llla.mle: no visible global function definition for 'poisson'
llla.mle: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'vcov'
mclgen: no visible global function definition for 'reshape'
simRasch.1D: no visible global function definition for 'rnorm'
simRasch.1D: no visible global function definition for 'runif'
vcov.sandwich.glm: no visible global function definition for
  'model.matrix'
vcov.sandwich.glm: no visible global function definition for 'weights'
vcov.sandwich.glm: no visible global function definition for
  'residuals'
vcov.sandwich.glm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
print.densityEHpi: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'rbind.fill':
  'rbind.fill'

S3 methods shown with full name in documentation object 'rbind.fill.matrix':
  'rbind.fill.matrix'

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.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
CCA.permute.both: no visible global function definition for
  'winProgressBar'
CCA.permute.both: no visible global function definition for
  'setWinProgressBar'
CCA.permute.justone: no visible global function definition for
  'winProgressBar'
CCA.permute.justone: no visible global function definition for
  'setWinProgressBar'
CCA.permute.xonly: no visible global function definition for
  'winProgressBar'
CCA.permute.xonly: no visible global function definition for
  'setWinProgressBar'
CCA.permute.zonly: no visible global function definition for
  'winProgressBar'
CCA.permute.zonly: no visible global function definition for
  'setWinProgressBar'
cor.xl.error.trace: no visible global function definition for
  'winDialog'
Undefined global functions or variables:
  setWinProgressBar winDialog winProgressBar
Consider adding
  importFrom("utils", "setWinProgressBar", "winDialog", "winProgressBar")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
.MCM: no visible global function definition for 'runif'
.MCM: no visible global function definition for 'rmultinom'
.MCM: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'optimize'
.MCM : f: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'alarm'
.igpark: no visible global function definition for 'kmeans'
.loglik: no visible global function definition for 'mahalanobis'
.plot.gpcm: no visible global function definition for 'plot'
.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 plot rexp rmultinom
  runif
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  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').
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for 'pnorm'
pnmtrem1: no visible global function definition for 'dnorm'
pnmtrem1: no visible global function definition for 'ginv'
pnmtrem1 : fun: no visible global function definition for 'pnorm'
pnmtrem1 : derf: no visible global function definition for 'dnorm'
pnmtrem1 : derf: no visible global function definition for 'pnorm'
pnmtrem1 : fun: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to 'rgenoud' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.sigma: no visible global function definition for 'plot'
smooth: no visible global function definition for 'genoud'
Undefined global functions or variables:
  genoud plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
ColorDendrogram: no visible global function definition for 'plot'
ColorDendrogram: no visible global function definition for 'segments'
CountDataSet: no visible global function definition for 'rexp'
CountDataSet: no visible global function definition for 'runif'
CountDataSet: no visible global function definition for 'rnorm'
CountDataSet: no visible global function definition for 'rnbinom'
NullModel: no visible binding for global variable 'quantile'
NullModel : <anonymous>: no visible global function definition for
  'median'
NullModelTest: no visible binding for global variable 'quantile'
NullModelTest : <anonymous>: no visible global function definition for
  'median'
PoissonDistance: no visible global function definition for 'as.dist'
permute.rows: no visible global function definition for 'runif'
print.poiclacv: no visible global function definition for 'write.table'
se: no visible global function definition for 'sd'
Undefined global functions or variables:
  as.dist median plot quantile rexp rnbinom rnorm runif sd segments
  write.table
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "as.dist", "median", "quantile", "rexp", "rnbinom",
             "rnorm", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
bipoilogMLE: no visible global function definition for 'optim'
bipoilogMLE: no visible global function definition for 'write.table'
poilogMLE: no visible global function definition for 'optim'
rbipoilog : sim: no visible global function definition for 'rnorm'
rbipoilog : sim: no visible global function definition for 'rpois'
rpoilog : sim: no visible global function definition for 'rnorm'
rpoilog : sim: no visible global function definition for 'rpois'
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
approxMargMLE: no visible global function definition for 'optim'
approxMargMLECI : ciFunction: no visible global function definition for
  'qchisq'
approxMargMLECI: no visible global function definition for 'uniroot'
margMLE: no visible global function definition for 'optim'
margMLECI: no visible global function definition for 'optim'
margMLECI : unNormLikeMinusVal: no visible global function definition
  for 'qchisq'
margMLECI: no visible global function definition for 'uniroot'
profMLECI : ciFunction: no visible global function definition for
  'qchisq'
profMLECI: no visible global function definition for 'uniroot'
rtbinom: no visible global function definition for 'rbinom'
rtpois: no visible global function definition for 'rpois'
waldCI: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Packages in Depends field not imported from:
  'combinat' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for 'quantile'
PS.FDR: no visible global function definition for 'quantile'
Permu.Ind: no visible global function definition for 'permn'
Permu.Ind: no visible global function definition for 'hcube'
Trans.Data: no visible global function definition for 'write.table'
Trans.Data: no visible global function definition for 'predict'
Trans.Data: no visible global function definition for 'lm'
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
rpoistweedie: no visible global function definition for 'runif'
testOmegaPT: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: poistweedie.Rd:51: Dropping empty section \references
prepare_Rd: ppoistweedie.Rd:37: Dropping empty section \references
prepare_Rd: qpoistweedie.Rd:40: Dropping empty section \references
prepare_Rd: rpoistweedie.Rd:36: Dropping empty section \references
prepare_Rd: varpt.Rd:31: Dropping empty section \references
Packages in Depends field not imported from:
  'MASS' 'scatterplot3d'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for 'layout'
plot.poLCA: no visible global function definition for 'par'
poLCA: no visible global function definition for 'model.frame'
poLCA: no visible global function definition for 'model.response'
poLCA: no visible global function definition for 'model.matrix'
poLCA: no visible global function definition for 'runif'
poLCA: no visible global function definition for 'ginv'
poLCA: no visible global function definition for 'flush.console'
poLCA.makeplot.dich: no visible global function definition for
  'scatterplot3d'
poLCA.makeplot.poly: no visible global function definition for
  'scatterplot3d'
poLCA.se: no visible global function definition for 'ginv'
poLCA.simdata: no visible global function definition for 'runif'
poLCA.simdata: no visible global function definition for 'rnorm'
poLCA.table: no visible global function definition for 'model.frame'
print.poLCA: no visible global function definition for 'pt'
print.poLCA: no visible global function definition for 'flush.console'
rmulti: no visible global function definition for 'runif'
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Package suggested but not available for checking: 'pollimetrydata'
Running examples in 'PoloniexR-Ex.R' failed
The error most likely occurred in:

> ### Name: ReturnOrderBook,PoloniexPublicAPI-method
> ### Title: Returns the order book for a given market, as well as a sequence
> ###   number for use with the Push API and an indicator specifying whether
> ###   the market is frozen.
> ### Aliases: ReturnOrderBook,PoloniexPublicAPI-method
> 
> ### ** Examples
> 
> poloniex.public <- PoloniexPublicAPI()
> 
> pair <- "BTC_NXT"
> depth <- 2
> order.book <- ReturnOrderBook(poloniex.public,
+                               pair  = pair,
+                               depth = depth)
> order.book$bid
         bid       amount
1 0.00000792 442.13258977
2 0.00000788  38.02918782
> order.book$ask
         ask        amount
1 0.00000793  228.64927901
2 0.00000794 4997.32956804
> order.book$frozen
[1] FALSE
> order.book$seq
[1] 85447486
> 
> pair <- "all"
> depth <- 2
> order.book <- ReturnOrderBook(poloniex.public,
+                               pair  = pair,
+                               depth = depth)
Error in matrix(unlist(pair.book$bids), ncol = 2, byrow = TRUE) : 
  'data' must be of a vector type, was 'NULL'
Calls: ReturnOrderBook ... ReturnOrderBook -> lapply -> FUN -> as.data.frame -> matrix
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.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   2.5Mb
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'matrixcalc' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'matrixcalc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for 'pnorm'
print.pom: no visible global function definition for 'pnorm'
siteocc : get.mod.matrix: no visible binding for global variable
  'na.pass'
siteocc : get.mod.matrix: no visible global function definition for
  'formula'
siteocc : get.mod.matrix: no visible global function definition for
  'model.matrix'
siteocc: no visible global function definition for 'nlminb'
siteocc: no visible global function definition for
  'is.positive.definite'
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Error in .requirePackage(package) : 
    unable to find required package 'raster'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
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.
Malformed Description field: should contain one or more complete sentences.
popRangeSim: no visible global function definition for 'write.table'
Undefined global functions or variables:
  write.table
Consider adding
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in 'popRange-Ex.R' failed
The error most likely occurred in:

> ### Name: popRangeSim
> ### Title: popRangeSim
> ### Aliases: popRangeSim
> 
> ### ** Examples
>  
> ## Example: In this scenario, we are simulating a 3x3 grid of populations for 50 
> ## generations. Each population starts with 100 diploid individuals. Each individual 
> ## has a 0.01 probability of migrating away from their populations. There are 100 
> ## SNPs that all have a starting frequency of 0.5, and the program outputs the standard 
> ## "results" file, as well as a PLINK file. 
> 
> ## Commands
> 
> mat = matrix(1,nrow=3,ncol=3) 
> popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,
+               mig = 0.01, SNP_model = 0, nSNPs = 100, SNPs_starting_freq = 0.5, 
+               outfile= "outFile1", PLINK=TRUE)
Error in loadNamespace(name) : there is no package called 'reticulate'
[1] "Could not find an acceptable version of python with numpy installed. This should be able to locate python \n      anywhere on your computer, but perhaps try adding python to your PATH if you think this message is an error."
Error in popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,  : 
  
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'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.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

powell: no visible global function definition for 'Quote'
Undefined global functions or variables:
  Quote
Consider adding
  importFrom("methods", "Quote")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File 'powell/libs/i386/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'
File 'powell/libs/x64/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
fnfam: no visible global function definition for 'qnorm'
fx: no visible global function definition for 'qnorm'
normplot : <local> : replot: no visible global function definition for
  'qnorm'
normplot : <local> : replot: no visible global function definition for
  'pnorm'
normplot : <local> : replot: no visible global function definition for
  'plot'
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'
plotDom: no visible global function definition for 'plot'
plotNsibs: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'plot'
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 plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
pps1: no visible global function definition for 'runif'
ppss: no visible global function definition for 'runif'
ppswr: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: calif.Rd:5-6: Dropping empty section \arguments
prepare_Rd: calif.Rd:8-9: Dropping empty section \examples
prepare_Rd: califcty.Rd:5-6: Dropping empty section \arguments
prepare_Rd: califcty.Rd:8-9: Dropping empty section \examples
prepare_Rd: sizesok.Rd:12-13: Dropping empty section \examples
prepare_Rd: stratumsizes.Rd:11-12: Dropping empty section \examples
Malformed Description field: should contain one or more complete sentences.
LDA.Tree : Find.proj: no visible binding for global variable 'var'
LDA.Tree : Find.proj: no visible binding for global variable 'IQR'
LDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'var'
PDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.Tree : Find.proj: no visible binding for global variable 'var'
PP.Tree : Find.proj: no visible binding for global variable 'median'
PP.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.optimize.Huber: no visible binding for global variable 'sd'
PP.optimize.anneal: no visible binding for global variable 'sd'
PP.optimize.plot: no visible binding for global variable 'sd'
PP.optimize.plot: no visible global function definition for 'hist'
PP.optimize.plot: no visible global function definition for 'text'
PP.optimize.plot: no visible global function definition for 'par'
PP.optimize.plot: no visible global function definition for 'plot'
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 plot sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "plot", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Malformed Description field: should contain one or more complete sentences.
TT.test : <anonymous>: no visible global function definition for
  't.test'
TT.test: no visible binding for global variable 'sd'
TT.test: no visible global function definition for 'setNames'
kirjelda : combo: no visible binding for global variable 'sd'
kor.tabel: no visible binding for global variable 'cor.test'
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
Package suggested but not available for checking: 'Rmosek'
Malformed Description field: should contain one or more complete sentences.
gausspred: no visible global function definition for 'qt'
mvapred: no visible global function definition for 'qt'
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'predmixcor/R/firstlib.r':
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for 'dbinom'
abs_cor: no visible global function definition for 'cor'
gen.alpha.IGamma: no visible global function definition for 'qgamma'
gendata.mix: no visible global function definition for 'runif'
gendata.mix: no visible global function definition for 'rbeta'
mh1.unif: no visible global function definition for 'runif'
train_predict_mix: no visible global function definition for 'dbinom'
training: no visible global function definition for 'runif'
training: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Title field: should not end in a period.
Found the following hidden files and directories:
  data/.Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'deSolve' which was already attached by Depends.
  Please remove these calls from your code.
LVCompGames: no visible global function definition for 'runif'
LVCompGames: no visible global function definition for 'plot'
LVCompGames: no visible global function definition for 'axis'
LVCompGames: no visible global function definition for 'box'
LVCompGames: no visible global function definition for 'lines'
LVCompGames: no visible global function definition for 'points'
MetaSim: no visible global function definition for 'runif'
chesson: no visible global function definition for 'rbeta'
chesson: no visible global function definition for 'dbeta'
chesson : rhof: no visible global function definition for 'dbeta'
chesson: no visible global function definition for 'integrate'
pimmlawton: no visible global function definition for 'runif'
Undefined global functions or variables:
  axis box dbeta integrate lines plot points rbeta runif
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot", "points")
  importFrom("stats", "dbeta", "integrate", "rbeta", "runif")
to your NAMESPACE file.
basisplot: no visible global function definition for 'plot'
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 'plot'
varperc: no visible global function definition for 'lines'
varperc: no visible global function definition for 'text'
varsimp: no visible global function definition for 'plot'
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 plot points screeplot strwidth terms
  text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "strwidth", "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: 'gurobi'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.6Mb
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.main: no visible global function definition for 'plot'
.pfda.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov dist plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
prepare_Rd: ProbForecastGOP-package.Rd:42-43: Dropping empty section \seealso
Malformed Description field: should contain one or more complete sentences.
GPois: no visible global function definition for 'dnorm'
GPois: no visible binding for global variable 'poisson'
GPois: no visible global function definition for 'predict'
GPois: no visible global function definition for 'fitted'
GPois: no visible global function definition for 'residuals'
GPois: no visible global function definition for 'smooth.spline'
ProDenICA: no visible global function definition for 'rnorm'
d.gaussmix: no visible global function definition for 'dnorm'
djordan: no visible global function definition for 'dt'
djordan: no visible global function definition for 'dunif'
mixmat: no visible global function definition for 'rnorm'
mixmat: no visible global function definition for 'runif'
plot.ProDenICA: no visible global function definition for 'plot'
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 plot poisson predict residuals rmultinom rnorm
  rt runif smooth.spline
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
profBinary: no visible global function definition for 'model.frame'
profBinary: no visible global function definition for 'model.matrix'
profLinear: no visible global function definition for 'model.frame'
profLinear: no visible global function definition for 'model.matrix'
profLinear: no visible global function definition for 'model.response'
profLinear: no visible global function definition for 'model.extract'
summary.profBinary: no visible global function definition for 'terms'
summary.profBinary: no visible global function definition for 'qbeta'
summary.profLinear: no visible global function definition for 'terms'
Undefined global functions or variables:
  model.extract model.frame model.matrix model.response qbeta terms
Consider adding
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "model.response", "qbeta", "terms")
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.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      1.6Mb
'library' or 'require' call to 'ggplot2' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.simplify : <anonymous>: no visible binding for global variable 'hist'
.simplify : <anonymous>: no visible binding for global variable 'start'
.simplify: no visible binding for global variable 'start'
.simplify: no visible binding for global variable 'end'
ggplot.profr: no visible global function definition for 'ggplot'
ggplot.profr: no visible global function definition for 'geom_rect'
ggplot.profr: no visible global function definition for 'aes'
ggplot.profr: no visible binding for global variable 'start'
ggplot.profr: no visible binding for global variable 'end'
ggplot.profr: no visible global function definition for 'geom_text'
ggplot.profr: no visible binding for global variable 'time'
ggplot.profr: no visible global function definition for
  'scale_y_continuous'
ggplot.profr: no visible global function definition for
  'scale_x_continuous'
plot.profr: no visible global function definition for 'plot'
plot.profr: no visible global function definition for 'rect'
plot.profr: no visible binding for global variable 'time'
plot.profr: no visible global function definition for 'text'
profr: no visible global function definition for 'Rprof'
Undefined global functions or variables:
  Rprof aes end geom_rect geom_text ggplot hist plot rect
  scale_x_continuous scale_y_continuous start text time
Consider adding
  importFrom("graphics", "hist", "plot", "rect", "text")
  importFrom("stats", "end", "start", "time")
  importFrom("utils", "Rprof")
to your NAMESPACE file.
Package suggested but not available for checking: 'qtbase'
Malformed Description field: should contain one or more complete sentences.
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.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
Found the following significant warnings:
  WARNING: Rtools is required to build R packages, but is not currently installed.
See 'd:/Rcompile/CRANpkg/local/3.5/prophet.Rcheck/00install.out' for details.
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 'plot'
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 plot predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "plot")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Cul: no visible global function definition for 'qf'
blockScale: no visible binding for global variable 'sd'
cochranTest: no visible global function definition for 'prcomp'
cochranTest: no visible binding for global variable 'var'
cochranTest: no visible global function definition for 'matplot'
cochranTest: no visible global function definition for 'legend'
continuumRemoval : crfun: no visible global function definition for
  'chull'
continuumRemoval : crfun: no visible global function definition for
  'approx'
continuumRemoval : crfun: no visible global function definition for
  'splinefun'
detrend: no visible binding for global variable 'sd'
duplex: no visible global function definition for 'prcomp'
e2m: no visible global function definition for 'cov'
kenStone: no visible global function definition for 'prcomp'
naes: no visible global function definition for 'prcomp'
naes: no visible global function definition for 'kmeans'
puchwein: no visible global function definition for 'prcomp'
readASD: no visible global function definition for 'read.table'
resample : resfun: no visible global function definition for 'approx'
resample : resfun: no visible global function definition for
  'splinefun'
shenkWest: no visible global function definition for 'prcomp'
spliceCorrection : extrapfun: no visible global function definition for
  'lm'
standardNormalVariate: no visible binding for global variable 'sd'
Undefined global functions or variables:
  approx chull cov kmeans legend lm matplot prcomp qf read.table sd
  splinefun var
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cov", "kmeans", "lm", "prcomp", "qf",
             "sd", "splinefun", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
estimateLSEparam: no visible global function definition for 'lm'
estimateMLEparam: no visible global function definition for 'optim'
getCCnlL: no visible global function definition for 'dnorm'
iterateScampi: no visible global function definition for 'quantile'
plot.scampi: no visible global function definition for 'hist'
plot.scampiVal: no visible global function definition for 'par'
plot.scampiVal: no visible global function definition for 'hist'
plot.scampiVal: no visible global function definition for 'abline'
plot.scampiVal: no visible global function definition for 'qqnorm'
plot.scampiVal: no visible global function definition for 'qqline'
sampleInitialVector: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline dnorm hist lm optim par qqline qqnorm quantile runif
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "dnorm", "lm", "optim", "qqline", "qqnorm",
             "quantile", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'class' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'class'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addcircle: no visible global function definition for 'lines'
addclassifierboundary: no visible global function definition for 'par'
addclassifierboundary: no visible global function definition for
  'contour'
plot.protoclass: no visible global function definition for 'plot'
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 plot points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "plot",
             "points")
to your NAMESPACE file.
plotwithprototypes: no visible global function definition for 'plot'
plotwithprototypes: no visible global function definition for
  'strwidth'
plotwithprototypes: no visible global function definition for
  'strheight'
plotwithprototypes: no visible global function definition for 'rect'
plotwithprototypes: no visible global function definition for 'text'
protoclust: no visible global function definition for 'as.dist'
protocut: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cutree plot rect strheight strwidth text
Consider adding
  importFrom("graphics", "plot", "rect", "strheight", "strwidth", "text")
  importFrom("stats", "as.dist", "cutree")
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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
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.
Malformed Description field: should contain one or more complete sentences.
candidate.overlap: no visible global function definition for
  'write.table'
fisher: no visible global function definition for 'fisher.test'
fisher.iteration: no visible global function definition for
  'download.file'
fisher.iteration: no visible global function definition for
  'read.table'
pSI.list: no visible global function definition for 'write.table'
specificity.index: no visible global function definition for 'png'
specificity.index: no visible global function definition for 'par'
specificity.index: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off download.file fisher.test par png read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par")
  importFrom("stats", "fisher.test")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
'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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/PST.Rcheck/00install.out' for details.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'EffectsRelBaseline' 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable 'sumSqCat'
compExclusionFraction: no visible global function definition for
  'rpois'
compExclusionFraction: no visible global function definition for
  't.test'
compExclusionFraction: no visible global function definition for 'glm'
compExclusionFraction: no visible global function definition for
  'anova'
compPowerCatSelectivity: no visible binding for global variable
  'fRatioStat'
compPowerGeneralRespDetection: no visible binding for global variable
  'sumSqCat'
compPowerRespDetection: no visible binding for global variable
  'sumSqCat'
compRejectionFraction: no visible global function definition for
  'rpois'
compRejectionFraction: no visible global function definition for
  't.test'
compRejectionFraction: no visible global function definition for 'glm'
compRejectionFraction: no visible global function definition for
  'anova'
simCatResp: no visible global function definition for 'rpois'
simNormCatResp: no visible global function definition for 'rnorm'
testCatEffectBoot: no visible global function definition for 'boot'
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'multilevel' 'nlme'
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  'multilevel' 'nlme'
  Please remove these calls from your code.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   2.4Mb
Running examples in 'psychReport-Ex.R' failed
The error most likely occurred in:

> ### Name: aovDispMeans
> ### Title: aovDispMeans
> ### Aliases: aovDispMeans
> 
> ### ** Examples
> 
> library(psychReport)
> requiredPackages(c("ez"))
Warning: unable to access index for repository http://cran.us.r-project.org/src/contrib:
  cannot open URL 'http://cran.us.r-project.org/src/contrib/PACKAGES'
Error in requiredPackages(c("ez")) : Package ez not available!
Execution halted
Malformed Description field: should contain one or more complete sentences.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.2Mb
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'R.utils' 'rmeta'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChisqTest_expect: no visible global function definition for 'pchisq'
plot_chase_observed_expected: no visible global function definition for
  'meta.MH'
plot_chase_observed_expected: no visible global function definition for
  'txtProgressBar'
plot_chase_observed_expected: no visible global function definition for
  'setTxtProgressBar'
test.one.treated: no visible global function definition for
  'fisher.test'
test_one: no visible global function definition for 'rbinom'
test_one: no visible global function definition for 'fisher.test'
Undefined global functions or variables:
  fisher.test meta.MH pchisq rbinom setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "fisher.test", "pchisq", "rbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
PurBayes: no visible global function definition for 'update'
PurBayes: no visible global function definition for 'sd'
plot.PurBayes: no visible global function definition for 'plot'
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 plot quantile sd update
Consider adding
  importFrom("graphics", "lines", "plot")
  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.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
.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').
pyramid: no visible global function definition for 'plot'
pyramid: no visible global function definition for 'segments'
pyramid: no visible global function definition for 'lines'
pyramid: no visible global function definition for 'text'
pyramid: no visible global function definition for 'rect'
pyramidf: no visible global function definition for 'segments'
pyramidf: no visible global function definition for 'lines'
pyramidf: no visible global function definition for 'text'
pyramidf: no visible global function definition for 'rect'
Undefined global functions or variables:
  lines plot rect segments text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "segments", "text")
to your NAMESPACE file.
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 'plot'
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 plot points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "plot", "points",
             "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
dmm_fn: no visible global function definition for 'dnorm'
dmm_noweights_fn: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'biom'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/qlcVisualize.Rcheck/00install.out' for details.
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.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

Calc.Expr: no visible global function definition for 'read.csv'
Calc.Expr: no visible binding for global variable 'Type'
Calc.Expr: no visible binding for global variable 'Identifier'
Calc.Expr: no visible binding for global variable 'Fluor'
GroupPlot: no visible global function definition for 'read.csv'
GroupPlot: no visible binding for global variable 'Type'
GroupPlot: no visible global function definition for
  'aggregate.data.frame'
plot.CT: no visible global function definition for 'sd'
plot.CT: no visible global function definition for 'barplot'
plot.CT: no visible binding for global variable 'tr_gene_name'
plot.CT : errorbars: no visible global function definition for 'arrows'
plot.CT: no visible global function definition for 'box'
Undefined global functions or variables:
  Fluor Identifier Type aggregate.data.frame arrows barplot box
  read.csv sd tr_gene_name
Consider adding
  importFrom("graphics", "arrows", "barplot", "box")
  importFrom("stats", "aggregate.data.frame", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
prepare_Rd: Calc.Expr.Rd:38-40: Dropping empty section \details
prepare_Rd: Calc.Expr.Rd:41-47: Dropping empty section \value
prepare_Rd: Calc.Expr.Rd:54-56: Dropping empty section \note
prepare_Rd: Calc.Expr.Rd:48-50: Dropping empty section \references
prepare_Rd: Calc.Expr.Rd:60-62: Dropping empty section \seealso
prepare_Rd: GroupPlot.Rd:34-36: Dropping empty section \details
prepare_Rd: GroupPlot.Rd:37-43: Dropping empty section \value
prepare_Rd: GroupPlot.Rd:50-52: Dropping empty section \note
prepare_Rd: GroupPlot.Rd:44-46: Dropping empty section \references
prepare_Rd: GroupPlot.Rd:56-58: Dropping empty section \seealso
prepare_Rd: cal.CT.Rd:18-20: Dropping empty section \details
prepare_Rd: cal.CT.Rd:21-23: Dropping empty section \source
prepare_Rd: cal_ct.Rd:48-50: Dropping empty section \note
prepare_Rd: cal_ct.Rd:42-44: Dropping empty section \references
prepare_Rd: cal_ct.Rd:54-56: Dropping empty section \seealso
prepare_Rd: filename.Rd:16-18: Dropping empty section \references
prepare_Rd: plot.CT.Rd:25-27: Dropping empty section \details
prepare_Rd: plot.CT.Rd:28-34: Dropping empty section \value
prepare_Rd: plot.CT.Rd:41-43: Dropping empty section \note
prepare_Rd: plot.CT.Rd:35-37: Dropping empty section \references
prepare_Rd: plot.CT.Rd:47-49: Dropping empty section \seealso
prepare_Rd: repeatnum.Rd:15-17: Dropping empty section \details
prepare_Rd: repeatnum.Rd:18-20: Dropping empty section \source
prepare_Rd: repeatnum.Rd:21-23: Dropping empty section \references
prepare_Rd: tr_gene_name.Rd:15-17: Dropping empty section \details
prepare_Rd: tr_gene_name.Rd:18-20: Dropping empty section \source
prepare_Rd: tr_gene_name.Rd:21-23: Dropping empty section \references
prepare_Rd: tr_group_name.Rd:15-17: Dropping empty section \details
prepare_Rd: tr_group_name.Rd:18-20: Dropping empty section \source
prepare_Rd: tr_group_name.Rd:21-23: Dropping empty section \references
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
ci.length: no visible global function definition for 'qexp'
detectable.bc: no visible global function definition for 'uniroot'
detectable.f2: no visible global function definition for 'uniroot'
detectable.ri: no visible global function definition for 'uniroot'
nu: no visible global function definition for 'pnorm'
nullinfo: no visible global function definition for 'qnorm'
nullinfo: no visible global function definition for 'dnorm'
optselection.bc: no visible global function definition for 'optimize'
optselection.f2: no visible global function definition for 'optimize'
optspacing.bc: no visible global function definition for 'optim'
optspacing.bc: no visible global function definition for 'optimize'
optspacing.f2: no visible global function definition for 'optim'
optspacing.f2: no visible global function definition for 'optimize'
powercalc.bc: no visible global function definition for 'pchisq'
powercalc.f2: no visible global function definition for 'pchisq'
samplesize.bc: no visible global function definition for 'uniroot'
samplesize.f2: no visible global function definition for 'uniroot'
samplesize.ri: no visible global function definition for 'uniroot'
tailprob: no visible global function definition for 'pchisq'
thresh: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dnorm optim optimize pchisq pnorm qexp qnorm uniroot
Consider adding
  importFrom("stats", "dnorm", "optim", "optimize", "pchisq", "pnorm",
             "qexp", "qnorm", "uniroot")
to your NAMESPACE file.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
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').
Malformed Title field: should not end in a period.
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'
qualint: no visible global function definition for 'plot'
qualval: no visible global function definition for 'qnorm'
qualval: no visible global function definition for 'plot'
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 plot pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.3Mb
    libs   3.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
Package suggested but not available for checking: 'fastshp'
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  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/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  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.
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.
'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.
Packages suggested but not available for checking: 'rcom' 'RDCOMClient'
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
r2stl: no visible global function definition for 'persp'
Undefined global functions or variables:
  persp
Consider adding
  importFrom("graphics", "persp")
to your NAMESPACE file.
Packages suggested but not available for checking: 'rcom' 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'rgl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'leaps' 'rgl' 's20x'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.6Mb
Package suggested but not available for checking: 'rpvm'
'library' or 'require' call to 'rpvm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
race : killSlaves.exit: no visible global function definition for
  '.PVM.initsend'
race : killSlaves.exit: no visible global function definition for
  '.PVM.send'
race : killSlaves.exit: no visible global function definition for
  '.PVM.exit'
race: no visible global function definition for '.PVM.mytid'
race: no visible global function definition for '.PVM.spawn'
race: no visible global function definition for '.PVM.initsend'
race: no visible global function definition for '.PVM.pkstrvec'
race: no visible global function definition for '.PVM.send'
race: no visible global function definition for '.PVM.recv'
race: no visible global function definition for '.PVM.bufinfo'
race: no visible global function definition for '.PVM.upkstrvec'
race : job.start: no visible global function definition for
  '.PVM.initsend'
race : job.start: no visible global function definition for
  '.PVM.pkint'
race : job.start: no visible global function definition for '.PVM.send'
race : job.wait: no visible global function definition for '.PVM.recv'
race : job.wait: no visible global function definition for
  '.PVM.bufinfo'
race : job.wait: no visible global function definition for
  '.PVM.upkint'
race : job.wait: no visible global function definition for
  '.PVM.upkdblvec'
race : aux2.friedman: no visible global function definition for
  'pchisq'
race : aux2.friedman: no visible global function definition for 'qt'
race : aux.friedman: no visible global function definition for
  'wilcox.test'
race : aux.ttest: no visible global function definition for 't.test'
race : aux.ttest: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  .PVM.bufinfo .PVM.exit .PVM.initsend .PVM.mytid .PVM.pkint
  .PVM.pkstrvec .PVM.recv .PVM.send .PVM.spawn .PVM.upkdblvec
  .PVM.upkint .PVM.upkstrvec p.adjust pchisq qt t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "qt", "t.test",
             "wilcox.test")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
getsonde: no visible global function definition for 'read.table'
plotsonde: no visible global function definition for 'par'
plotwind: no visible global function definition for 'plot'
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 'plot'
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 plot points polygon read.table sd
  segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "plot", "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Malformed Description field: should contain one or more complete sentences.
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.
cpc_get_rawdata: 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.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   8.9Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   2.8Mb
Malformed Description field: should contain one or more complete sentences.
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
.forwardSelection: no visible binding for global variable 'var'
.forwardSelection: no visible global function definition for 'glm'
.forwardSelection: no visible global function definition for 'formula'
.forwardSelection: no visible global function definition for 'binomial'
.forwardSelection: no visible global function definition for 'lm'
.forwardSelection: no visible global function definition for 'predict'
.predict.internal: no visible global function definition for 'predict'
randomGLM: no visible binding for global variable 'cor'
randomGLM: no visible binding for global variable 'sd'
randomGLM: no visible global function definition for 'var'
thinRandomGLM: no visible global function definition for 'glm'
thinRandomGLM: no visible global function definition for 'binomial'
thinRandomGLM: no visible global function definition for 'lm'
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
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.
Malformed Description field: should contain one or more complete sentences.
bartels.rank.test: no visible global function definition for 'na.omit'
bartels.rank.test: no visible global function definition for 'pbeta'
bartels.rank.test: no visible global function definition for 'pnorm'
cox.stuart.test: no visible global function definition for 'pbinom'
difference.sign.test: no visible global function definition for
  'na.omit'
difference.sign.test: no visible global function definition for 'pnorm'
rank.test: no visible global function definition for 'na.omit'
rank.test: no visible global function definition for 'pnorm'
rruns: no visible global function definition for 'runif'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'na.omit'
runs.test: no visible global function definition for 'points'
runs.test: no visible global function definition for 'abline'
runs.test: no visible global function definition for 'gray'
runs.test: no visible global function definition for 'pnorm'
turning.point.test: no visible global function definition for 'embed'
turning.point.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
rank.L2R: no visible global function definition for 'kmeans'
rank.L2R: no visible global function definition for 'pnorm'
rank.LN: no visible global function definition for 'kmeans'
rank.LN: no visible global function definition for 'pnorm'
rank.gs: no visible global function definition for 'qnorm'
rank.wald: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  kmeans pnorm qnorm
Consider adding
  importFrom("stats", "kmeans", "pnorm", "qnorm")
to your NAMESPACE file.
CropSpatialPolygonsDataFrame: no visible global function definition for
  'bbox'
CropSpatialPolygonsDataFrame: no visible global function definition for
  'clipPolys'
DiagnoseFailure: no visible global function definition for 'points'
Undefined global functions or variables:
  bbox clipPolys points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: RANN
Loading required package: PBSmapping

-----------------------------------------------------------
PBS Mapping 2.70.5 -- Copyright (C) 2003-2018 Fisheries and Oceans Canada

PBS Mapping comes with ABSOLUTELY NO WARRANTY;
for details see the file COPYING.
This is free software, and you are welcome to redistribute
it under certain conditions, as outlined in the above file.

A complete user guide 'PBSmapping-UG.pdf' is located at 
D:/temp/Rtmp6toSed/RLIBS_2fcc259520a7/PBSmapping/doc/PBSmapping-UG.pdf

Packaged on 2018-06-05
Pacific Biological Station, Nanaimo

All available PBS packages can be found at
https://github.com/pbs-software

To see demos, type '.PBSfigs()'.
-----------------------------------------------------------


Warning in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) :
  cannot open URL 'https://maps.googleapis.com/maps/api/staticmap?center=37.77173,-122.4306&zoom=13&size=550x550&maptype=mobile&format=png32&sensor=true&key=': HTTP status was '403 Forbidden'

Error: processing vignette 'RapidPolygonLookup.Rnw' failed with diagnostics:
 chunk 1 
Error in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) : 
  cannot open URL 'https://maps.googleapis.com/maps/api/staticmap?center=37.77173,-122.4306&zoom=13&size=550x550&maptype=mobile&format=png32&sensor=true&key='
Execution halted
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'BSgenome.Hsapiens.UCSC.hg19' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
freq: no visible global function definition for 'xtabs'
freq: no visible binding for global variable 'na.pass'
freq: no visible global function definition for 'melt'
freq: no visible global function definition for 'complete.cases'
freq: no visible global function definition for 'tail'
kurtosis: no visible global function definition for 'na.omit'
label: no visible global function definition for 'tail'
name: no visible global function definition for 'tail'
nvalid : <anonymous>: no visible global function definition for
  'na.omit'
rp.desc: no visible global function definition for 'melt.data.frame'
rp.desc: no visible global function definition for 'cast'
rp.desc: no visible global function definition for 'na.omit'
rp.desc : <anonymous>: no visible global function definition for 'tail'
rp.desc : <anonymous>: no visible global function definition for 'head'
rp.freq: no visible global function definition for 'xtabs'
rp.freq: no visible binding for global variable 'na.pass'
rp.freq: no visible global function definition for 'melt'
rp.freq: no visible global function definition for 'complete.cases'
rp.freq: no visible global function definition for 'tail'
rp.label: no visible global function definition for 'tail'
rp.name: no visible global function definition for 'tail'
rp.outlier : lundcrit: no visible global function definition for 'qf'
rp.outlier: no visible global function definition for 'lm'
rp.outlier: no visible global function definition for 'rstandard'
rp.valid : <anonymous>: no visible global function definition for
  'na.omit'
skewness: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  cast complete.cases head lm melt melt.data.frame na.omit na.pass qf
  rstandard tail xtabs
Consider adding
  importFrom("stats", "complete.cases", "lm", "na.omit", "na.pass", "qf",
             "rstandard", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
fnRAP: no visible global function definition for 'chisq.test'
fnRAP: no visible global function definition for 'combn'
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: 'gurobi'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   2.3Mb
plotarc: no visible global function definition for 'par'
plotarc: no visible global function definition for 'plot'
plotarc: no visible global function definition for 'lines'
plotpoly: no visible global function definition for 'par'
plotpoly: no visible global function definition for 'plot'
plotpoly: no visible global function definition for 'polygon'
Undefined global functions or variables:
  lines par plot polygon
Consider adding
  importFrom("graphics", "lines", "par", "plot", "polygon")
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.
Malformed Description field: should contain one or more complete sentences.
BiogTest.individual: no visible global function definition for 'combn'
BiogTest.individual: no visible global function definition for 'runif'
BiogTest.individual: no visible global function definition for 'rlnorm'
BiogTest.individual: no visible global function definition for
  'rnbinom'
BiogTest.sample: no visible global function definition for 'combn'
BiogTest.sample: no visible global function definition for 'runif'
BiogTest.sample: no visible global function definition for 'rlnorm'
BiogTest.sample: no visible global function definition for 'rnbinom'
BiogTest.sample: no visible global function definition for 'aggregate'
EcoTest.individual: no visible global function definition for 'xtabs'
plot.BiogTest: no visible global function definition for 'quantile'
plot.BiogTest: no visible global function definition for 'combn'
plot.EcoTest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate combn quantile rlnorm rnbinom runif xtabs
Consider adding
  importFrom("stats", "aggregate", "quantile", "rlnorm", "rnbinom",
             "runif", "xtabs")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.3Mb
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.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    etc    1.9Mb
    po     1.2Mb
.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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.7Mb
GNU make is a SystemRequirements.
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.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
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.
bn2nbn: no visible binding for global variable 'bn.fit'
chain4chain: no visible binding for global variable 'head'
chain4chain: no visible binding for global variable 'tail'
estimate8arcs: no visible global function definition for 'lm'
estimate8arcs: no visible global function definition for 'coefficients'
estimate8nbn: no visible global function definition for 'lm'
estimate8nbn: no visible global function definition for 'as.formula'
estimate8nbn: no visible global function definition for 'anova'
estimate8nbn: no visible global function definition for 'coefficients'
generate8chain: no visible global function definition for 'runif'
generate8chain: no visible global function definition for 'rbinom'
generate8nbn: no visible global function definition for 'runif'
generate8nbn: no visible global function definition for 'rbinom'
nbn2bnfit: no visible global function definition for 'model2network'
nbn2bnfit: no visible global function definition for 'custom.fit'
simulate8gema: no visible global function definition for 'rnorm'
simulate8mn: no visible global function definition for 'mvrnorm'
simulate8nbn: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  anova as.formula bn.fit coefficients custom.fit head lm model2network
  mvrnorm rbinom rnorm runif tail
Consider adding
  importFrom("stats", "anova", "as.formula", "coefficients", "lm",
             "rbinom", "rnorm", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
SumTestSens: no visible global function definition for 'pnorm'
binarysens: no visible global function definition for 'dbinom'
hlsens: no visible global function definition for 'wilcox.test'
iv_sens: no visible global function definition for 'pnorm'
mcontrol: no visible global function definition for 'pnorm'
psens: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dbinom pnorm wilcox.test
Consider adding
  importFrom("stats", "dbinom", "pnorm", "wilcox.test")
to your NAMESPACE file.
':::' call which should be '::': 'tools:::file_path_as_absolute'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'tools:::file_test'
  See the note in ?`:::` about the use of this operator.
genBugsScript: no visible global function definition for 'runif'
getBugsOutput: no visible global function definition for 'read.table'
rbugs2coda: no visible global function definition for 'as.mcmc'
rbugs2coda: no visible global function definition for 'mcmc'
rbugs2coda: no visible global function definition for 'as.mcmc.list'
Undefined global functions or variables:
  as.mcmc as.mcmc.list mcmc read.table runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
find_available_versions: no visible global function definition for
  'contrib.url'
find_available_versions: no visible global function definition for
  'available.packages'
install_version: no visible global function definition for
  'contrib.url'
install_version: no visible global function definition for
  'available.packages'
install_version: no visible global function definition for
  'install_url'
load_available_packages: no visible global function definition for
  'contrib.url'
validate_installed_package: no visible global function definition for
  'installed.packages'
Undefined global functions or variables:
  available.packages contrib.url install_url installed.packages
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "installed.packages")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' calls to packages already attached by Depends:
  'RColorBrewer' 'classInt' 'maptools'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RColorBrewer' 'classInt' 'maptools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
Malformed Description field: should contain one or more complete sentences.
.onAttach: no visible global function definition for
  'packageDescription'
rselect.list: no visible global function definition for 'select.list'
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
climdex.data.frame: no visible global function definition for
  'as.PCICt'
Undefined global functions or variables:
  as.PCICt
Malformed Description field: should contain one or more complete sentences.
get_ClinicalCodes: no visible global function definition for 'read.csv'
get_ClinicalCodes : <anonymous>: no visible global function definition
  for 'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
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 significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/RcmdrMisc.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'biclust' 'fabia' 'iBBiG' 'superbiclust' 'BcDiag' 'rqubic' 'BicARE'
  's4vd' 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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.
'library' or 'require' calls in package code:
  'abind' 'e1071' 'qcc'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
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
Malformed Description field: should contain one or more complete sentences.
BOXWP: no visible binding for global variable 'top'
BOXWP: no visible binding for global variable 'buttonsFrame'
HIST: no visible binding for global variable 'top'
HIST: no visible binding for global variable 'buttonsFrame'
QQN: no visible binding for global variable 'top'
QQN: no visible binding for global variable 'buttonsFrame'
Undefined global functions or variables:
  buttonsFrame top
Namespaces with empty importFrom:
  'stats' 'tcltk'
Malformed Description field: should contain one or more complete sentences.
fncLRpROC: no visible global function definition for 'palette'
fncLRpROC : onOK : convert: no visible global function definition for
  'col2rgb'
fncLRpROC : onOK : convert: no visible global function definition for
  'rgb'
fncPairedpROC: no visible global function definition for 'palette'
fncPairedpROC : onOK : convert: no visible global function definition
  for 'col2rgb'
fncPairedpROC : onOK : convert: no visible global function definition
  for 'rgb'
fncUnpairedpROC: no visible global function definition for 'palette'
fncUnpairedpROC : onOK : convert: no visible global function definition
  for 'col2rgb'
fncUnpairedpROC : onOK : convert: no visible global function definition
  for 'rgb'
fncvpROC: no visible global function definition for 'palette'
fncvpROC : onOK : convert: no visible global function definition for
  'col2rgb'
fncvpROC : onOK : convert: no visible global function definition for
  'rgb'
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
SampleSizes: no visible global function definition for 'xtabs'
SampleSizes: no visible global function definition for 'weighted.mean'
SampleSizes: no visible global function definition for 'reshape'
stage1Sample.fn: no visible global function definition for 'runif'
stage2Sample.fn: no visible global function definition for 'runif'
strata.options : onOK: no visible global function definition for
  'packageDescription'
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'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'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.1Mb
Malformed Description field: should contain one or more complete sentences.
brewer.pal: no visible global function definition for 'rgb'
display.brewer.all: no visible global function definition for 'par'
display.brewer.all: no visible global function definition for 'plot'
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 plot rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "plot", "rect", "text")
to your NAMESPACE file.
Running 'testthat.R' [263s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Error: Quantidade de itens por requisição (@test_proposicoes.R#83)  ------
  API did not return json
  1: expect_equal(dim(fetch_proposicao(dataInicio = "2007-01-01", dataFim = "2017-01-01", 
         itens = 386)), TAM_DF_386REQ) at testthat/test_proposicoes.R:83
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: fetch_proposicao(dataInicio = "2007-01-01", dataFim = "2017-01-01", itens = 386)
  5: .fetch_using_queries(parametros, .PROPOSICOES_PATH) %>% .assert_dataframe_completo(.COLNAMES_PROPOSICAO) %>% 
         .coerce_types(.COLNAMES_PROPOSICAO)
  6: eval(lhs, parent, parent)
  7: eval(lhs, parent, parent)
  8: .fetch_using_queries(parametros, .PROPOSICOES_PATH)
  9: .fetch_itens(.verifica_parametros_entrada(parametros), API_path)
  10: query %>% tibble::as.tibble() %>% dplyr::rowwise() %>% dplyr::do(.congresso_api(API_path, 
         .)) %>% dplyr::bind_rows(req_ultima_pagina %>% tibble::as.tibble() %>% dplyr::rowwise() %>% 
         dplyr::do(.congresso_api(API_path, .)))
  ...
  15: freduce(value, `_function_list`)
  16: function_list[[i]](value)
  17: dplyr::do(., .congresso_api(API_path, .))
  18: do.rowwise_df(., .congresso_api(API_path, .))
  19: eval_tidy(args[[j]], mask)
  20: .congresso_api(API_path, .)
  21: .get_from_api(path, query)
  22: .use_backoff_exponencial(path, query, timeout, tentativa + 1)
  23: .get_from_api(path, query, final_timeout, tentativa)
  24: stop(.ERRO_RETORNO_JSON, call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 73 SKIPPED: 0 FAILED: 1
  1. Error: Quantidade de itens por requisição (@test_proposicoes.R#83) 
  
  Error: testthat unit tests failed
  Execution halted
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.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rcplex.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
    libs      1.6Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.8Mb
File which contains pragma(s) suppressing diagnostics:
  'inst/include/RcppBlazeConfig.h'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
Gauss: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.8Mb
    libs      2.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.7Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       8.9Mb
    libs      1.0Mb
GNU make is a SystemRequirements.
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    libs     26.1Mb
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/ql/math/distributions/normaldistribution.hpp'
  'inst/include/ql/math/matrix.hpp'
  'inst/include/ql/math/optimization/levenbergmarquardt.hpp'
  'inst/include/ql/math/statistics/incrementalstatistics.hpp'
  'inst/include/ql/time/date.hpp' 'inst/include/ql/time/imm.hpp'
  'inst/include/ql/utilities/dataparsers.hpp'
  'inst/include/ql/utilities/null.hpp'
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    include   6.3Mb
    libs      2.0Mb
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'Rcompression'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
GNU make is a SystemRequirements.
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 'plot'
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 plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "new")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in 'rcv-Ex.R' failed
The error most likely occurred in:

> ### Name: import_data
> ### Title: Imports election data
> ### Aliases: import_data
> 
> ### ** Examples
> 
> import_data("http://www.sfelections.org/results/20161108/data/20161206/20161206_masterlookup.txt",
+  header = FALSE)
`curl` package not installed, falling back to using `url()`
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: import_data ... read_delimited -> read_connection -> open -> open.connection
Execution halted
get.datamarket.csv: no visible global function definition for
  'read.csv'
getUserAgent: no visible global function definition for 'sessionInfo'
Undefined global functions or variables:
  read.csv sessionInfo
Consider adding
  importFrom("utils", "read.csv", "sessionInfo")
to your NAMESPACE file.
Running 'testthat.R' [37s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("rdefra")
  > 
  > test_check("rdefra")
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  -- 1. Failure: Metadata should be in the right format (@test-data.R#44)  -------
  `x` not equal to `expected`.
  1 element mismatch
  
  Error in file(file, "rt") : cannot open the connection
  -- 2. Failure: Data should be in the right format (@test-data.R#55)  -----------
  `x` not equal to `expected`.
  'is.NA' value mismatch: 0 in current 1 in target
  
  == testthat results  ===========================================================
  OK: 39 SKIPPED: 1 FAILED: 2
  1. Failure: Metadata should be in the right format (@test-data.R#44) 
  2. Failure: Data should be in the right format (@test-data.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine sichere in eine nicht sichere Verbindung.'
Error in file(file, "rt") : cannot open the connection
No data available for station MY1
Warning: Unknown or uninitialised column: 'unit'.
Warning: Unknown or uninitialised column: 'unit'.

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Warning: Unknown or uninitialised column: 'datetime'.
Quitting from lines 117-123 (rdefra_vignette.Rmd) 
Error: processing vignette 'rdefra_vignette.Rmd' failed with diagnostics:
do not know how to convert 'df$datetime' to class "POSIXlt"
Execution halted
distimage: no visible binding for global variable 'terrain.colors'
distimage: no visible global function definition for 'filled.contour'
distimage: no visible global function definition for 'title'
distimage: no visible global function definition for 'axis'
distimage: no visible global function definition for 'lines'
drawkpc: no visible global function definition for 'plot'
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 plot rnorm runif segments terrain.colors
  title topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "plot",
             "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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/re2/prog.h' 'inst/include/re2/re2.h'
  'inst/include/re2/regexp.h' 'src/dfa.cc' 'src/onepass.cc'
File 'readr/libs/i386/readr.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'readr/libs/x64/readr.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'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.
prepare_Rd: bestmods.Rd:47-49: Dropping empty section \note
prepare_Rd: bestmods.Rd:43-44: Dropping empty section \references
prepare_Rd: cic.Rd:24-26: Dropping empty section \details
prepare_Rd: cic.Rd:40-42: Dropping empty section \note
prepare_Rd: cvic.Rd:49-51: Dropping empty section \note
prepare_Rd: eic.Rd:31-33: Dropping empty section \details
prepare_Rd: eic.Rd:50-52: Dropping empty section \note
prepare_Rd: eic.Rd:56-58: Dropping empty section \seealso
prepare_Rd: ic.min.Rd:22-24: Dropping empty section \details
prepare_Rd: ic.min.Rd:47-49: Dropping empty section \note
prepare_Rd: ic.min.Rd:53-55: Dropping empty section \seealso
prepare_Rd: reams-package.Rd:16-17: Dropping empty section \references
prepare_Rd: reams-package.Rd:19-20: Dropping empty section \seealso
prepare_Rd: reams-package.Rd:21-22: Dropping empty section \examples
prepare_Rd: scoremods.Rd:26-28: Dropping empty section \details
prepare_Rd: scoremods.Rd:43-45: Dropping empty section \note
prepare_Rd: xy.Rd:46-48: Dropping empty section \note
prepare_Rd: xy.Rd:52: Dropping empty section \seealso
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ReCiPa: no visible global function definition for 'count.fields'
ReCiPa: no visible global function definition for 'read.table'
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Malformed Description field: should contain one or more complete sentences.
Running examples in 'REDCapR-Ex.R' failed
The error most likely occurred in:

> ### Name: redcap_version
> ### Title: Determine version of REDCap instance
> ### Aliases: redcap_version
> 
> ### ** Examples
> 
> library(REDCapR) #Load the package into the current R session.
> uri      <- "https://bbmc.ouhsc.edu/redcap/api/"
> token    <- "9A81268476645C4E5F03428B8AC3AA7B"
> redcap_version(redcap_uri=uri, token=token)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 10054
Calls: redcap_version ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 70-73 (BasicREDCapROperations.Rmd) 
Error: processing vignette 'BasicREDCapROperations.Rmd' failed with diagnostics:
OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 10054
Execution halted
Running examples in 'RedditExtractoR-Ex.R' failed
The error most likely occurred in:

> ### Name: user_network
> ### Title: User relationship network
> ### Aliases: user_network
> 
> ### ** Examples
> 
> # load libraries
> 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(RedditExtractoR)
> target_urls <- reddit_urls(search_terms="cats", subreddit="Art", cn_threshold=50)
> target_df <- target_urls %>% 
+ filter(num_comments==min(target_urls$num_comments)) %$% 
+ URL %>% reddit_content # get the contents of a small thread

  |                                                                            
  |                                                                      |   0%Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'

  |                                                                            
  |======================================================================| 100%
> network_list <- target_df %>% user_network(include_author=FALSE, agg=TRUE) # extract the network
Error in left_join_impl(x, y, by_x, by_y, aux_x, aux_y, na_matches) : 
  Can't join on 'response_to' x 'response_to' because of incompatible types (factor / logical)
Calls: %>% ... as.data.frame -> left_join -> left_join.tbl_df -> left_join_impl
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
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'
plot.REEMtree: no visible global function definition for 'plot'
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 plot predict residuals terms
Consider adding
  importFrom("graphics", "plot")
  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.
Running 'testthat.R' [315s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(refuge)
  > 
  > test_check("refuge")
  -- 1. Error: all restrooms works (@test-all-restrooms.R#4)  --------------------
  HTTP error 503.
  1: rfg_all_restrooms(accessible = TRUE, unisex = TRUE) at testthat/test-all-restrooms.R:4
  2: query_looper(query, verbose, tidy)
  3: jsonlite::fromJSON(paste0(query, "00&page=", seq_list[[i]]), flatten = TRUE)
  4: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  5: parseJSON(txt, bigint_as_char)
  6: parse_con(txt, bigint_as_char)
  7: open(con, "rb")
  8: open.connection(con, "rb")
  
  -- 2. Error: location works (@test-location.R#4)  ------------------------------
  
  1: rfg_location(lat = 39, lng = -75, accessible = TRUE, tidy = TRUE) at testthat/test-location.R:4
  2: query_looper(query, verbose, tidy)
  3: stop(sprintf("Refuge API request failed [%s]\n%s\n<%s>", httr::status_code(got), 
         got$message, got$documentation_url), call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 2 FAILED: 2
  1. Error: all restrooms works (@test-all-restrooms.R#4) 
  2. Error: location works (@test-location.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 27-67 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Execution halted
Data2wd: no visible binding for global variable 'var'
getRsq: no visible global function definition for 'var'
plot.wcr: no visible global function definition for 'plot'
plot.wcr: no visible global function definition for 'image'
plot.wcr: no visible global function definition for 'par'
plot.wnet: no visible global function definition for 'plot'
plot.wnet: no visible global function definition for 'image'
plot.wnet: no visible global function definition for 'par'
waveletGetCV: no visible binding for global variable 'median'
waveletGetCV: no visible binding for global variable 'sd'
wcr: no visible binding for global variable 'var'
wcr: no visible global function definition for 'cov'
wcr: no visible global function definition for 'lm'
wcr: no visible global function definition for 'ginv'
wcr: no visible global function definition for 'glm'
wnet: no visible binding for global variable 'var'
wnet: no visible global function definition for 'predict'
Undefined global functions or variables:
  cov ginv glm image lm median par plot predict sd var
Consider adding
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov", "glm", "lm", "median", "predict", "sd",
             "var")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
cluster.reg: no visible global function definition for 'rnorm'
cluster.reg: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
.area.my: no visible global function definition for 'density'
optimalGT : <anonymous>: no visible global function definition for
  'median'
optimalGT: no visible global function definition for 'png'
optimalGT: no visible global function definition for 'dev.off'
permutation: no visible global function definition for 'flush.console'
plot.wls: no visible global function definition for 'par'
plot.wls: no visible global function definition for 'plot'
plot.wls: no visible global function definition for 'text'
plot.wls: no visible global function definition for 'abline'
reGenotyper: no visible global function definition for 'flush.console'
reGenotyper: no visible binding for global variable 'var'
reGenotyper: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline density dev.off flush.console median par plot png text var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "par", "plot", "text")
  importFrom("stats", "density", "median", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Warning in fun(libname, pkgname) :
  package regtest is under development and still may change considerably

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

Probably some imports need to be declared in the NAMESPACE file.
binregtest: no visible global function definition for 'str'
binregtest: no visible binding for global variable 'str'
binregtest: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif str
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'Rcplex'
'library' or 'require' call to 'parallel' 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
  'packageDescription'
.relax.cv.elnet: no visible global function definition for 'predict'
.relax.cv.elnet: no visible binding for global variable 'weighted.mean'
.relax.cv.lognet: no visible global function definition for 'predict'
.relax.cv.lognet: no visible binding for global variable
  'weighted.mean'
.relax.cvcompute: no visible binding for global variable
  'weighted.mean'
.single.column: no visible global function definition for 'glm'
.single.column: no visible global function definition for 'coef'
cv.alpha.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.alpha.relaxnet: no visible global function definition for 'mclapply'
cv.relaxnet: no visible global function definition for 'predict'
cv.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.relaxnet: no visible global function definition for 'mclapply'
predict.cv.alpha.relaxnet: no visible global function definition for
  'predict'
predict.cv.relaxnet: no visible global function definition for
  'predict'
predict.relaxnet: no visible global function definition for 'predict'
Undefined global functions or variables:
  coef glm mc.reset.stream mclapply packageDescription predict
  weighted.mean
Consider adding
  importFrom("stats", "coef", "glm", "predict", "weighted.mean")
  importFrom("utils", "packageDescription")
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.
Malformed Title field: should not end in a period.
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 'plot'
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 'plot'
plot.toymkt: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline coef legend lm par plot rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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'
colorDendClass: no visible global function definition for 'plot'
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 plot rainbow runif
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend", "plot")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'MASS' 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GlobTestMissing: no visible global function definition for 'lme'
GlobTestMissing: no visible global function definition for 'anova'
TestStatSP: no visible global function definition for 'pf'
TestStatSimple: no visible global function definition for 'ginv'
TestStatSimple: no visible global function definition for 'pf'
Undefined global functions or variables:
  anova ginv lme pf
Consider adding
  importFrom("stats", "anova", "pf")
to your NAMESPACE file.
CA: no visible global function definition for 'readClipboard'
LL: no visible global function definition for 'readClipboard'
US: no visible global function definition for 'readClipboard'
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'
latexlist: no visible global function definition for 'readClipboard'
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'
strWrap: no visible global function definition for 'readClipboard'
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 readClipboard tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "readClipboard",
             "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.
.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').
Malformed Title field: should not end in a period.
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<-
S3 methods shown with full name in documentation object 'all.vars.character':
  'all.vars.character'

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.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
GUI_template : onHelp: no visible global function definition for 'help'
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Warning: no function found corresponding to methods exports from 'retimes' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Warning: no function found corresponding to methods exports from 'retimes' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dexgauss: no visible global function definition for 'pnorm'
loglik: no visible global function definition for 'pnorm'
mexgauss: no visible global function definition for 'sd'
rexgauss: no visible global function definition for 'rnorm'
rexgauss: no visible global function definition for 'rexp'
timefit: no visible global function definition for 'optim'
timefit: no visible global function definition for 'sd'
timefit: no visible global function definition for 'par'
timefit: no visible global function definition for 'hist'
timefit: no visible global function definition for 'density'
timefit: no visible global function definition for 'curve'
timefit: no visible global function definition for 'new'
plot,timefit: no visible global function definition for 'density'
plot,timefit: no visible global function definition for 'par'
plot,timefit: no visible global function definition for 'curve'
Undefined global functions or variables:
  curve density hist new optim par pnorm rexp rnorm sd
Consider adding
  importFrom("graphics", "curve", "hist", "par")
  importFrom("methods", "new")
  importFrom("stats", "density", "optim", "pnorm", "rexp", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.reweight: no visible global function definition for 'par'
plot.reweight: no visible global function definition for 'plot'
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 plot quantile rug
Consider adding
  importFrom("graphics", "par", "plot", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
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.
Malformed Description field: should contain one or more complete sentences.
fs_author_ids : <anonymous>: no visible global function definition for
  'select.list'
fs_download : <anonymous>: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
.testLTS: no visible binding for global variable 'stackloss'
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
NeedsCompilation field should likely be 'yes'
gabriel.plot: no visible global function definition for 'barplot'
gabriel.plot: no visible global function definition for 'arrows'
rgabriel: no visible binding for global variable 'sd'
rgabriel : psmm_x: no visible global function definition for 'pnorm'
rgabriel : psmm: no visible global function definition for 'integrate'
rgabriel : qsmm: no visible global function definition for 'qnorm'
rgabriel : qsmm: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  arrows barplot integrate pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "arrows", "barplot")
  importFrom("stats", "integrate", "pnorm", "qnorm", "sd", "uniroot")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: 'gsl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gammaIntegral: no visible global function definition for 'integrate'
gammaIntegral : <anonymous>: no visible global function definition for
  'hyperg_1F1'
gammaMLE: no visible global function definition for 'weighted.mean'
gammaMME: no visible binding for global variable 'sd'
gammaMME: no visible binding for global variable 'var'
Undefined global functions or variables:
  hyperg_1F1 integrate sd var weighted.mean
Consider adding
  importFrom("stats", "integrate", "sd", "var", "weighted.mean")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
installed size is 80.3Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
Malformed Description field: should contain one or more complete sentences.
genoud: multiple local function definitions for 'fn1.bfgs' with
  different formal arguments
genoud: multiple local function definitions for 'gr1' with different
  formal arguments
genoud: multiple local function definitions for 'hess.fn' with
  different formal arguments
genoud_transform: multiple local function definitions for 'fn1.bfgs'
  with different formal arguments
genoud_transform: multiple local function definitions for 'gr1' with
  different formal arguments
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.8Mb
gexf.to.igraph: no visible global function definition for 'rgb'
igraph.to.gexf: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  col2rgb rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.0Mb
Packages suggested but not available for checking: 'pmg' 'SVGAnnotation'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'gWidgetsRGtk2' 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:
  'RGtk2' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.6Mb
    libs   5.1Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.2Mb
.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
GNU make is a SystemRequirements.
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.
Missing or unexported object: 'estimatr::tidy.lm_robust'
Running examples in 'ri2-Ex.R' failed
The error most likely occurred in:

> ### Name: conduct_ri
> ### Title: Conduct Randomization Inference
> ### Aliases: conduct_ri
> 
> ### ** Examples
> 
> 
> # Data from Gerber and Green Table 2.2
> 
> 
> # Randomization Inference for the Average Treatment Effect
> 
> table_2.2 <-
+     data.frame(d = c(1, 0, 0, 0, 0, 0, 1),
+                y = c(15, 15, 20, 20, 10, 15, 30))
> 
> ## Declare randomization procedure
> declaration <- declare_ra(N = 7, m = 2)
> 
> ## Conduct Randomization Inference
> out <- conduct_ri(y ~ d,
+                       declaration = declaration,
+                       assignment = "d",
+                       sharp_hypothesis = 0,
+                       data = table_2.2)
Error: 'tidy.lm_robust' is not an exported object from 'namespace:estimatr'
Execution halted